Idiopathic pulmonary fibrosis (IPF) is a chronic progressive disease that kills 40,000 Americans annually. The disease is characterized by a derangement of the lung stroma, ultimately resulting in respiratory failure due to proliferation of lung fibroblasts and accumulation of their extracellular matrix (ECM) products. This leads to obliteration of alveolar air spaces. The IPF lung fibroblast has lost key negative control mechanisms of its trophic signaling axis. This leads to genome-wide changes in ribosome recruitment to genes governing proliferation and other key cell functions. What is not known is how much of this aberrant genome-wide translation is due to abnormalities that are inherent to the fibroblasts, how much is due to the pathological ECM on which they reside and how much requires both. Here we propose to answer this question by utilizing an experimental system that closely simulates that in vivo environment: decellularized human lung tissue. We will adopt a genome-wide, systems biology approach to examining the pathobiology of the IPF fibroblast in a fibrotic microenvironment at a level that is known to be altered in IPF-ribosome recruitment. By comparing genome-wide expression patterns in primary lung fibroblasts derived from IPF and control patients on decellularized IPF and control lung slices, we are positioned to determine the relative importance of the cell-origin and the ECM-origin to the disease phenotype. Data will be generated using a combined polyribosome/RNA-Seq procedure. This translational data set will be used to generate a mathematical model of RNA regulatory element activity that can be used to understand the post-transcriptional processes that underlie the disease. Our central hypothesis is that IPF ECM can reprogram fibroblasts. We further posit that this reprogramming will manifest as highly organized changes in ribosome recruitment and that a mathematical model of these changes will pinpoint disease-defining pathology in the ECM-driven IPF signaling circuitry.
Our specific aim i s to use a genome-wide approach to characterize lung fibroblast gene expression (IPF and control) on decellularized lung ECM (IPF and control) and identify genes whose ribosome recruitment differs based on cell type, ECM type, cell and ECM type;and genes that are invariant across all conditions.
Idiopathic Pulmonary Fibrosis (IPF) is an incurable lung disease that kills 40,000 Americans annually. Efforts to find treatments for the disease have been severely hampered by the lack of knowledge of the causes of the disease. As the disease progresses the lung fills with scar tissue. We have discovered that the cells responsible for producing this scar tissue (fibroblasts) have lost control of mechanisms that prevent it from proliferating. We have found that certain proteins normally associated with cancer are activated in the IPF fibroblast, but only when it resides in the diseased lung. This abnormality affects the multi-step process that controls gene expression, and we have identified the abnormal step. Here we propose to answer the following questions 1) How much of the disease process is caused by diseased fibroblasts, 2) How much is caused by the diseased tissue;and 3) How much requires both. This knowledge would greatly aid researchers in the search for treatments of this disease.
|Parker, Matthew W; Rossi, Daniel; Peterson, Mark et al. (2014) Fibrotic extracellular matrix activates a profibrotic positive feedback loop. J Clin Invest 124:1622-35|