The recent discovery of induced pluripotent stem cells (iPSCs) has provided unprecedented opportunities to model human disease in vitro and better understand human development. The clinical translation of the iPSC in vitro model system is the goal of this project, whose aim is to learn about the earliest stages of human development, focused on the role in development and human disease of the earliest known marker of lung fate, the key transcriptional regulator NKX2.1. For these studies we will utilize reprogramming technology we have developed that has allowed us to establish a comprehensive bank of iPSCs generated from children with lung diseases caused by mutations in genes (such as NKX2.1) that are active from the earliest moments of lung lineage specification. These disease-specific cell lines provide naturally occurring human models of the effects of hypomorphic, mutant, or dominant negative gene expression in human beings, providing exciting opportunities to understand mechanisms that control normal vs. aberrant early lung development. Ultimately a detailed understanding of lung developmental biology should result in better treatments for patients with lung disease, exemplified by the children to be studied in this project, namely 4 individuals with divergent clinical phenotypes resulting from mutations in the coding region of NKX2.1. We will correlate our in vitro studies and models with microarrays established from the lung tissue of these children and we will test our hypothesis: the in vitro iPSC system can be applied to model and understand genetic lung diseases, exemplified by patients with divergent lung-thyroid-brain clinical phenotypes arising from reduced or augmented activity of NKX2.1. Aim 1 proposes to define the normal vs. disease-specific genetic signatures of differentiating human lung epithelial progenitors and to assess how these in vitro model systems compare to the clinical phenotypes observed in the patients from whom these cells are derived. Aim 2 evaluates the molecular mechanism, such as binding or inactivating alterations of NKX2.1 responsible for disease pathogenesis in these patients, and Aim 3 tests mechanistically-driven potential therapies for ameliorating the NKX2.1-related human disease phenotypes.