SMAD6 is required for normal foregut development in humans and frogs

Esophageal atresia/tracheoesophageal fistula (EA/TEF) are congenital malformations of the foregut, and we identified two EA/TEF patients with two variants in the BMP/TGFβ repressor SMAD6. We investigated the function of SMAD6 in tracheoesophageal development using two orthogonal approaches in Xenopus embryos, both resulting in foregut malformations including EA/TEF. We then used human Pluripotent Stem Cell-derived foregut epithelium and mesenchyme to explore the separate roles of SMAD6 in these germ layers. CRISPR-mediated disruption of human SMAD6 caused an increase in BMP signaling in foregut epithelium and mesenchyme consistent with its role as a BMP repressor. Loss of SMAD6 caused patterning defects in both tissue types; SMAD6−/- endoderm shows increased expression of distal gut tube markers and SMAD6−/- mesenchyme shows increased expression of ventral and posterior markers including markers of cardiac and liver mesenchyme lineages. Furthermore, SMAD6−/- mesenchyme had decreased ability to form CD31-positive endothelial cells. Our results demonstrate that SMAD6 is required for foregut development and that rare variants in this gene are likely causative for foregut malformations in EA/TEF patients.