Molecular Characterization Core

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PROJECT SUMMARY Emphysema and pulmonary fibrosis are two responses of the lung to chronic cigarette smoke exposure, both of which may be affected by mitochondrial dysfunction and chitinase pathways. Gene expression profiling has successfully identified numerous genes involved in idiopathic pulmonary fibrosis (IPF); gene expression studies in chronic obstructive pulmonary disease (COPD) have had more variable results. The spectrum of cellular heterogeneity in the lung can now be assayed by single cell RNA sequencing, which has been performed in human IPF and recently in human COPD lung tissue, serving as a comparison in an IPF study. To support all three projects, the Molecular Characterization core will use single cell and standard RNA sequencing to test for differences in cell types, cell subpopulations, and cell-type specific gene expression changes in COPD and IPF in human samples collected in this PPG and in the mouse models which will be used in Projects 1 and 2. We will address the following Specific Aims: (1) We will perform single cell RNA-sequencing in lung tissues from murine models of bleomycin and cigarette smoke exposure to identify cellular changes associated with lung fibrosis and airspace enlargement, respectively. We will localize cellular expression of relevant genes from all three projects. (2) We will perform single cell RNA-sequencing in mouse lungs from the cigarette smoke-poly I:C model to identify cellular changes associated with the combined airspace enlargement and airway fibrosis in this model. We will localize cellular expression of relevant genes from all three projects. (3) We will perform bulk and single cell RNA-sequencing on airway epithelial cells and alveolar macrophages collected at bronchoscopy in the Clinical Biorepository Core. We will identify cell subpopulations and gene expression differences between COPD, IPF, and control smokers. This new core will interact closely with Projects 1 and 2 regarding the murine models and with Project 3 and Core C (Clinical Biorepository) for the human studies. Analysis of the large-scale data generated in this core will require collaboration with Core B (Respiratory Computational Discovery).