Summary (Overall) The overarching goal of this Program Project is to better understand the Developmental Mechanisms of Trachea-Esophageal Birth Defects (TEDs) in order to advance our knowledge of their etiology, enhance diagnosis, improve treatment, and inform strategies to generate TE tissue from human pluripotent stem cells (PSCs) that might ultimately be used for transplantation The trachea and esophagus (TE) arise from the separation of a common foregut tube during early fetal development. Defects in TE morphogenesis cause a spectrum of life-threatening TEDs that prevent proper breathing and feeding in newborns. TEDs including esophageal atresia (EA) and trachea-esophageal fistula (TEF) are corrected by invasive neonatal surgery and are often associated with long-term co-morbidity. The etiology of TEDs, which occur in ~1:3500 births, is poorly understood. Although there is compelling evidence for a major genetic component, causative mutation are. only known in ~12% of TED cases worldwide. Moreover, even for the few cases where the genes involved have been identified, such as the HEDGEHOG (HH) and BMP signaling pathway genes, how these regulate fetal TE morphogenesis, and hence the structural basis of TEDs, is unknown. The long-term goal of this project is to determine the genetic and developmental mechanisms underlying TEDs in order to improve our understanding of their etiology, enhance diagnosis, improve treatment, and inform strategies to generate human tissue from pluripotent stem cells (PSCs) that might ultimately be used for transplantation. We have assembled an experienced and highly collaborative multi-disciplinary team of clinicians, geneticists, bioinformaticians, data scientists, imaging experts, developmental biologists and human stem cell biologists to tackle this problem using an innovative combination of human genetics, neonatal MRI, animal modeling in Xenopus and mouse, quantitative cell biology, genome editing and human PSCs derived esophageal organoids. This will be a Multi-PI project centered at Cincinnati Children’s Hospital Medical Center (CCHMC) in collaboration with Columbia University Medical Center. The Multi-PIs will be: Aaron Zorn PhD (contact PI;; CCHMC), Paul Kingma MD PhD (CCHMC), James Wells PhD (CCHMC) and Wendy Chung MD PhD (Columbia). These combined expertise and resources creates a synergistic program not found at any single institution. We propose 3 innovative and highly synergistic projects and a Genomics Core to reveal the genetic, molecular and cellular basis of TED · Project-1: Comprehensive phenotypic and genetic assessment of TED patients. · Project-2: Modeling the molecular and cellular mechanisms of TEDs in animals. · Proj...