Generation of esophageal organoids from human pluripotent stem cells and their use to study human development

Tracheoesophageal disorders and diseases are prevalent in humans such that an organoid model of human esophagus could be greatly beneficial. We therefore established a three-dimensional esophageal organoid culture system through the directed differentiation of human pluripotent stem cells (hPSCs). We identified that sequential manipulation of several signaling pathways resulted in patterning of definitive endoderm to dorsal anterior foregut spheroids (dAFGs). Outgrowth of dAFGs for 1-2 months resulted in human esophageal organoids (HEOs) with a stratified squamous epithelium comparable to a late gestation mouse embryonic esophagus. These 1 and 2 month old HEOs were harvested for RNA to transcriptionally profile and compare them to profiles of esophageal tissue biopsies and keratinocytes. We then used HEOs and mouse embryos to identify how SOX2 mediates separation of the esophageal and respiratory lineages and found that loss of endodermal Sox2 results in complete esophageal agenesis. Using a SOX2 CRISPR interference iPS line, we generated dorsal and ventral anterior foregut progenitors (by manipulating BMP signaling) with or without SOX2-knockdown. At the transcriptional level, SOX2 acts to promote esophageal specification in both mice and humans in part by inhibiting Wnt signaling in the dorsal AFG and promoting survival of esophageal epithelium. In addition to this use of hPSC-derived esophageal organoids to study development, HEOs can be used for future studies of esophageal pathologies, such as Barrett's metaplasia and carcinoma. Overall design: Human pluripotent stem cells (H1 line) were differentiated into human esophageal organoids (HEOs) and harvested at 1 and 2 months. Induced pluripotent stem cells (iPS CRISPRi-SOX2 line) were differentiated to dorsal or ventral anterior foregut cultures by manipulating BMP signaling (Noggin or BMP4) and treated with or without doxycycline (1ug/mL) to induce expression of CRISPR interference construct. For all experiments, total RNA was extracted, and polyA-selected libraries was generated and sequenced.