Building a Multidimensional Map of Developing Human Lung ? Jeffrey A. Whitsett, M.D. PI Our LungMAP2 project seeks to work in a collaborative consortium to develop operational pipelines to study human lung development from the saccular, alveolar stages of morphogenesis at single cell level of resolution. The project will integrate single cell transcriptomic, chromatin accessibility, 2D and 3D high-resolution confocal microscopy, immunofluorescence, multiprobe RNA in situ hybridization studies to create a detailed molecular map of the cells, cell-cell and cell scaffold interactions in their precise anatomic positions in the developing human lung. Our LungMAP2 Center will work in close concert with the Data Coordinating Center (DCC), other LungMAP2 Centers and the Human Tissue Procurement Core (HTPC) to obtain, annotate, preserve and store human tissues using optimal conditions for imaging and omics analyses. Our LungMAP2 project will produce a detailed structural expression atlas of multiple regions, niches in the human lung. We will develop and validate new technologies for tissue clearing, 3D reconstructions of high-resolution images, multi-probe RNA and IF analysis. We will develop new tissue digestion single cell and single nuclear RNA analyses for precise regional niches of the normal developing human lung, tissue from and in infants with rare congenital lung disorders. We will work in a Consortium to develop useful bioinformatic programs, modeling cell-cell, cell matrix interactions to define the signaling and transcriptional programs building and maintaining organ structure and function. Working with the DCC and other LungMAP2 Centers, our bioinformatics pipelines will enable data visualization, interrogation in user friendly web portals for sharing with members of the LungMAP2 Consortium, the DCC and for the research community in general.
Building a Multidimensional Map of Developing Human Lung Our LungMAP2 Center is committed to working with other members of the Consortium to generate, analyze and present complex transcriptomic, genomic, epigenomic, proteomic, lipidomic and imaging data human lung for research community. Our Center prioritized lung imaging and generation of single cell, sorted cell, nuclear and bulk RNA Seq data linked to lipidomic and proteomic data from collaborating Centers. We developed interactive websites to host data, developed the algorithms for data analysis, integration and presentation in open access portals: Lung Gene Expression Analytic Web Portal (LGEA) (https://research.cchmc.org/pbge/lunggens/mainportal.html), LungGENS (https://research.cchmc.org/pbge/lunggens/default.html), Lung Image (https://research.cchmc.org/lungimage/) and LungOntology (https://research.cchmc.org/pbge/LGEAOntologyBrowser/#/index.html). These tools are designed to integrate data from the LungMAP research sites in an interactive web based format, providing data and code (JavaScript) to the Data Coordinating Center (DCC) for hosting on the ?LungMAP website ?Breath? (www.Lungmap.net). Data are available on our websites in LGEA and ToppCell. Our LungMAP2 Center will collaborate and produce ?multiomic? and structural analyses of the developing human lung. Since lung function is entirely dependent upon the delivery of gases to the alveoli where oxygen and carbon dioxide are exchanged; defects in airway and alveolar structure and function underlie the pathogenesis of lung diseases in preterm infants and children that have life-long consequences. We are prioritizing study of the normal human lung morphogenesis; our project will include multiomic studies of tissue from normal infants, children and infants with carefully selected congenital and genetic disorders affecting lung formation and function. LungMAP2 will provide a detailed cellular and molecular atlas of human lung morphogenesis presented in an intuitive web-based format. Genomic, proteomic, lipidomic and epigenetic data will be integrated with anatomic and cellular ontologies, working with the DCC to build centralized database and web service for the research community.
