"The LungMap" RFA tasks Research Centers to work in a consortium to build an open access molecular resource for the study of human and mouse lung during later stages of development. Our research plan will focus to the generation and analysis of detailed NexGen gene expression data for both human and mouse lung from the late canalicular-saccular through the alveolar periods of development. The lung is comprised of diverse parenchymal- and hematopoietic derived cells, whose abundance, differentiation, and functions vary developmentally, regionally, and among species. Temporal and spatial interactions among diverse cell types orchestrate formation and function of the lung. While many of the genes and networks regulating lung formation are shared among vertebrate species, the physiology, structure and regional specific cell types, and gene expression patterns vary between murine and human lung. To effectively translate data from mouse models to humans, it is critical to understand their molecular similarities and differences at the cellular level. We will generate a detailed cell specific RNA database for human and mouse lung parenchyma. Single cell RNA-seq will be interpreted with data derived from laser capture microdissection (LCM), FACS, RNA analyses, and molecular imaging to create an expression map of human and mouse lung. Computational and "systems biology" approaches will integrate these data to create readily accessible databases that will synergize research related to pulmonary development, disease, and function. This application will focus to the analysis of cells from normal lung parenchyma (e.g., conducing airway and alveolar epithelial cells;vascular endothelial cells, including venous, arterial, lymphatic, and capillary cells;stromal and adventitial cells, including fibroblasts, pericytes, myofibroblasts, and cartilage;and neuroepithelial and neuronal cells).
Aim 1 : Cell Specific NexGen RNA Analyses to Create an "Atlas" of Gene Expression In the Murine Lung. Single cell isolation, FACS purification, and LCM of lung parenchymal cells, and RNA-Seq will create a temporal-spatial map of gene expression in the mouse from E15.5 to postnatal day 28.
Aim 2 : Cell Specific NexGen RNA Analysis to Create an Atlas of Gene Expression In Human Fetal Lung. Single cell isolation, LCM, and FACS analysis followed by RNA-Seq will create a map of the temporal-spatial patterns of the gene expression during human lung formation from 22 weeks of gestation through the postnatal-alveolar period.
Aim 3 : Bioinformatics Analysis of NexGen RNAs to Define Gene Expression During Murine and Human Lung Formation. Bioinformatics and computational biology of RNA sequence data from the murine and human lung studies will be analyzed, curated using defined anatomic ontologies, and integrated to provide a sensitive and quantitative measure of gene expression patterns of the precise RNA splice forms, microRNAs and other noncoding RNAs expressed during lung formation.
Lung function is entirely dependent upon the formation and maintenance of pulmonary alveoli where oxygen and carbon dioxide are exchanged;defects in alveolar formation and repair are a common cause of morbidity and mortality in preterm infants, children, and adults that have life-long consequences. The LungMap project seeks to provide a detailed cell and molecular Atlas regarding lung alveolar formation that will provide a framework to understand the pathogenesis of lung disease in the future. Data will be integrated with available anatomic ontologies, genomic, proteomic, and other omics databases, and made readily accessible to the research community.