Discovering the Developmental Basis of Trachea‐Esophageal Birth Defects: Evidence for Endosome‐opathies

Abstract

The trachea and esophagus (TE) arise from a common foregut tube during embryonic development. Disruptions in TE morphogenesis cause congenital trachea‐esophageal defects (TEDs) such as esophageal atresia, tracheoesophageal fistula and tracheoesophageal clefts. TEDs occur in approximately 1 in 3500 births, but their etiology is poorly understood. We have established the www.CLEARconsortium.org; a multidisciplinary team of clinicians, geneticists, bioinformaticians, stem cell and developmental biologists using patient genome sequencing, animal models and iPSC‐derived human organoids to discover the genetic and developmental basis of trachea‐esophageal birth defects. Using the complementary advantages of Xenopus and mouse models we have defined the conserved molecular and cellular mechanisms that regulate normal TE morphogenesis. We show that downstream of Hedgehog/Gli signaling endosome‐mediated epithelial remodeling regulates TE morphogenesis which when disrupted results in tracheoesophageal clefts similar to human Pallister Hall syndrome patients. Proband‐parent trio genome sequencing identified an enrichment of potential damaging de novo variants in genes encoding membrane/vesicular‐trafficking proteins, suggesting a common “endosome‐opathy” pathway. Ongoing CRISPR mutagenesis screens in Xenopus tropicalis assessing candidate causative variants from patients confirms that the endosome protein Itsn1 is essential for TE morphogenesis, suggesting that the ITSN1 variant is likely pathogenic in the patient. Finally, leveraging results from animal models we have generated multi‐lineage human esophageal organoids from iPSCs with patient mutations to identify how mutations impact human esophageal differentiation. Together these results significantly advance our understanding of TEDs with the goal of revealing phenotype‐genotype associations that will inform prognosis and clinical treatment.