Generation of E9.0 mouse embryonic progenitors

Multipotent Nkx2-1-positive lung epithelial primordial progenitors of the foregut endoderm are thought to be the developmental precursors to all adult lung epithelial lineages. However, little is known about the global transcriptomic programs or gene networks that regulate these gateway progenitors in vivo due to their rarity and transient presence during a narrow developmental window, embryonic day E9.0 in mice. Here we describe the unique genetic program of in vivo lung primordial progenitors and computationally identify the signaling pathways that are involved in their cell-fate determination from pre-specified embryonic foregut. We integrate this information in computational models to generate in vitro engineered lung primordial progenitors from mouse pluripotent stem cells, improving the fidelity of the resulting cells through unbiased, easy-to-interpret similarity scores and modulation of cell culture conditions, including biomechanical cues. As the genetic characterization of early in vivo embryonic progenitors is rapidly expanding, the methodology proposed here can have wide applicability to the in vitro derivation of bona fide tissue progenitors of all germ layers. Overall design: For E9.0 single cell RNA-Seq data, Nkx2-1GFP-expressing domains (forebrain, thyroid, and lung) were isolated from E9.0 embryos and monodispersed using the collagenase-dispase method with the purpose of assessing the resemblance of our PSC-derived lung progenitors to in vivo lung primordial progenitors