Idiopathic pulmonary fibrosis (IPF) is a fatal disease of unknown etiology characterized by progressive lung fibrosis. It leads to death within 5 years unless patients undergo a lung transplant. Up to 34,000 cases of IPF are diagnosed in the United States each year. IPF lungs are characterized by increased accumulation of (myo)fibroblasts, activated fibroblasts with a contractile phenotype that are believed to be key effector cells leading to matrix deposition. Although the source of (myo)fibroblasts has not been definitively established, recent studies suggest that a significant portion of these cells arise from alveolar epithelial cells (AEC), through the process of epithelial-to-mesenchymal transition (EMT). Numerous observations point to a key role for AEC in the initiation and development of IPF. Alveolar epithelium consists of cuboidal type 2 (AEC2) cells and long thin type 1 (AEC1) cells, each with distinct morphologies, functions, and patterns of gene expression. AEC2 are a major source of pulmonary surfactants. They are believed to both self-renew and serve as progenitors for AEC1 for restoration of epithelial integrity following injury. In contrast, AEC1 mediate gas exchange and are believed to be terminally differentiated and unable to proliferate. AEC have been shown to undergo EMT in vivo in response to transforming growth factor beta (TGF-?), giving rise to (myo)fibroblasts. AEC differentiation can be recapitulated in vitro;in the absence of added growth factors, purified AEC2 differentiate into AEC1-like cells. In contrast, when treated with TGF-?, AEC2 undergo EMT, producing (myo)fibroblasts. This unique model system allows the temporal dissection of events that drive differentiation in the peripheral lung under conditions of health and disease. This proposal aims to identify genome-wide transcriptional and epigenetic changes of human AEC2 at distinct time points as the cells transition to AEC1- like cells or to (myo)fibroblasts. For comparison, primary AEC2 and AEC1 cells from normal lungs, and AEC2 and (myo)fibroblasts from the lungs of IPF patients will be examined.
The Specific Aims are: 1) Transcriptome profiling of human AEC2 during the transition to AEC1-like cells or (myo)fibroblasts. Primary cells from healthy lung (AEC2 and AEC1) and IPF lung (AEC2 and (myo)fibroblasts) will be similarly analyzed. 2) Epigenomic profiling of the cells from Aim 1, using genome-wide approaches to assess DNA methylation patterns, histone modifications, polycomb group complex occupancy, chromosome remodeling complex occupancy, and selected transcription factor occupancy. 3) Integration of the data from Aims 1 and 2 to model the temporal and spatial relationships between the various epigenetic modifications and transcription of mRNAs and small non- coding RNAs. 4) Validation of a subset of newly identified expression patterns, epigenetic control networks and regulatory pathways using independent cultures of AEC and (myo)fibroblasts. Knowledge of the transcriptional and epigenetic programs driving AEC (mis)differentiation will provide insights into potential new avenues for lung restoration and will help develop strategies to treat and ultimately prevent diseases such as IPF.
Nobody knows why each year up to 34,000 Americans develop idiopathic pulmonary fibrosis, IPF, a lethal disease in which the lungs are slowly destroyed by scar tissue, ultimately resulting in suffocation. Evidence suggests that in patients with IPF, certain lung cells differentiate into scar tissue instead of growing normally. Using a unique system of cultured human lung cells, we will examine how the information that is layered on top of the genes (epigenetic information) makes lung cells grow in normal as well as abnormal ways, with the objective to develop new treatment and prevention strategies for IPF and other lung diseases.
|Zhou, Beiyun; Flodby, Per; Luo, Jiao et al. (2018) Claudin-18-mediated YAP activity regulates lung stem and progenitor cell homeostasis and tumorigenesis. J Clin Invest 128:970-984|
|Luo, Jiao; Chimge, Nyam-Osor; Zhou, Beiyun et al. (2018) CLDN18.1 attenuates malignancy and related signaling pathways of lung adenocarcinoma in vivo and in vitro. Int J Cancer 143:3169-3180|
|Flodby, Per; Li, Changgong; Liu, Yixin et al. (2017) Cell-specific expression of aquaporin-5 (Aqp5) in alveolar epithelium is directed by GATA6/Sp1 via histone acetylation. Sci Rep 7:3473|
|Stueve, Theresa Ryan; Li, Wen-Qing; Shi, Jianxin et al. (2017) Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers. Hum Mol Genet 26:3014-3027|
|Vannini, Ivan; Wise, Petra M; Challagundla, Kishore B et al. (2017) Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs. Nat Commun 8:1801|
|Marconett, Crystal N; Zhou, Beiyun; Sunohara, Mitsuhiro et al. (2017) Cross-Species Transcriptome Profiling Identifies New Alveolar Epithelial Type I Cell-Specific Genes. Am J Respir Cell Mol Biol 56:310-321|
|Zuber, Verena; Marconett, Crystal N; Shi, Jianxin et al. (2016) Pleiotropic Analysis of Lung Cancer and Blood Triglycerides. J Natl Cancer Inst 108:|
|Stueve, Theresa Ryan; Marconett, Crystal N; Zhou, Beiyun et al. (2016) The importance of detailed epigenomic profiling of different cell types within organs. Epigenomics 8:817-29|
|Liebler, Janice M; Marconett, Crystal N; Juul, Nicholas et al. (2016) Combinations of differentiation markers distinguish subpopulations of alveolar epithelial cells in adult lung. Am J Physiol Lung Cell Mol Physiol 310:L114-20|
|Borok, Zea (2014) Alveolar epithelium: beyond the barrier. Am J Respir Cell Mol Biol 50:853-6|
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