PROJECT SUMMARY Lung diseases are one of the leading causes of morbidity and mortality worldwide. Chronic Obstructive Pulmonary Disease (COPD) and other Chronic Lung Diseases (CLDs) are among the most prevalent of these lung diseases worldwide and their prevalence is increasing emphasizing the dire need to develop novel therapies to alleviate the heavy burden of these diseases on the medical care system and to provide better quality of life for this increasing patient population. The Molecular Atlas of Lung Development Program (LungMap3) proposes research teams to expand our growing knowledge of the human lung with specific interest in better defining the spatial, molecular, and cellular changes that occur in human respiratory diseases. For Phase 3 funding, we propose to focus on three emerging concepts and challenges: 1) catalogue the phenotypes of adult human lung diseases at the spatial and single cell level with a focus on COPD, CLDs and more rare diseases that we have access to via our Human Lung Tissue Bank including alpha-1 anti-trypsin deficiency (A1AT), 2) identify molecular defects present in the progenitor cell populations of human CLDs through dynamic integration of single cell analytics with spatial resolution technologies to elucidate disease progression signatures, and 3) develop and implement new ex vivo and in vivo platforms to mechanistically define the molecular and cellular defects that occur during the progression of CLDs. This will require the use of advanced transcriptomic, epigenomic, and bioinformatic approaches to phenotyping cell-cell communication and cell-niche interactions. The Penn LungMAP Research Center Team has an existing pipeline to acquire normal and diseased lung tissue, and we have developed extensive bioinformatic software to interrogate changes in cell fates and states in disease from deep spatial and single cell analysis. The Penn LungMAP Research Center has been extremely productive during LungMAP Phase 2 support, defining novel cell lineages present in the human lung, characterizing aspects of emphysematous disease pathology including COPD, and we have begun to define rare CLDs such as A1AT at a single cell level in addition to providing high quality single cell data from pediatric and adult healthy lung samples for the LungMap DCC web based platform and the lung research community at large. The strategy of the Penn LungMAP 3 Research Center is to phenotype the cellular and molecular changes that occur in CLDs at the single cell level and identify the mechanisms that drive disease progression using novel approaches to integrate progenitor cell niche regulation using carefully validated ex vivo model systems.