Single cell RNA sequencing of mouse indced pluripotent stem cell (iPSC)-derived and mouse primary embryonic lung mesenchyme

The lung mesenchyme plays important roles in lung development and is affected in many respiratory diseases, yet relatively little is known about the biology of lung mesenchymal progenitors. We sought to establish an induced pluripotent stem cell (iPSC)-based model to study lung mesenchyme development and epithelial-mesenchymal interactions. We generated a mouse iPSC line carrying a lung mesenchyme-specific reporter/tracer to establish a protocol for differentiation into lung mesenchymal progenitors. We derived lung mesenchyme from iPSCs both by directed differentiation via a lateral plate mesodermal progenitor state (induced lung mesenchyme, iLM), and by co-development during lung epithelial differentiation (co-developed lung mesenchyme, cLM). We found that directed differentiation via a lateral plate mesoderm progenitor was not only more efficient, but also yielded engineered lung mesenchymal cells that were more similar to primary lung mesenchyme from day 12.5 mouse embryos, as determined by single cell RNAseq. Our iPSC-derived population will provide an inexhaustible source of cells for studying lung development, modeling diseases, and developing therapeutics. Overall design: Global transcriptomic profiling at single cell resolution of iPSC-derived cells and primary embryonic lung cells. 3 samples contain iPSC-derived cells : 1) "iLM": Tbx4-LERGFP+ cells (i.e. lung mesenchyme) generated using directed lung mesenchymal differentiation; 2) "iLMneg": Tbx4-LERGFP- cells (i.e. non-lung mesenchyme) generated using directed lung mesenchymal differentiation; 3) "cLM": Tbx4-LERGFP+ cells (i.e. lung mesenchyme) and Epcam+/Tbx4-LERGFP- (i.e. epithelial) cells "co-developed" by directed lung epithelial differentiation to simultaneously produce both endoderm/epithelia and mesenchyme. A 4th sample contains primary E12.5 lung mesenchyme and epithelium.