Foxe1 deficiency impairs thyroid fate while supporting lung differentiation.

Patterning of mammalian endoderm into lung and thyroid lineages depends upon a correct early expression of a homeobox domain-containing transcription factor, Nkx2-1. However, the gene networks distinguishing the differentiation of those lineages remain largely unknown. In this work, by using mouse stem cell lines, scRNA-seq, and transcriptomic and chromatin accessibility profiling, we show that Foxe1 knockout impairs Nkx2-1+ cell differentiation and maturation into thyroid follicular-like cells. Concomitantly, a subset of Foxe1 null/Nkx2-1+ cells follows a lung epithelial differentiation program and form lung-like organoids harboring cells transcriptionally similar to mouse fetal lung types. Chromatin analyses reveal that, while accessibility at the Pax8 locus is reduced, loci associated with lung programs are in an open configuration, indicating that lung fate can be adopted without additional chromatin remodeling. These findings demonstrate that Foxe1 loss destabilizes thyroid commitment but also creates a permissive state in which Nkx2-1+ foregut progenitors can adopt an alternative lung fate. Our study illustrates how the interplay between transcription factors and chromatin context governs lineage decisions in vitro and provides a platform to investigate mechanisms underlying organ specification and plasticity.