Single cell RNAseq of co-cultured mouse iPSC-derived lung mesenchyme and mouse iPSC-derived lung epithelial progenitors in distal and proximal differentiation media

Co-cultures of lung epithelium and mesenchyme are useful tools to study epithelial-mesenchymal crosstalk in lung development and disease. However, many previous attempts to generate such co-cultures have yielded poor juxtaposition between the epithelial and the mesenchymal lineage. In addition, induced pluripotent stem cell (iPSC)-derived co-cultures often contain generic mesenchyme that is not necessarily lung-specific. We sought to establish co-cultures of purified mouse iPSC-derived lung-specific mesenchyme and iPSC-derived lung epithelial progenitors. We used a mouse iPSC line carrying a lung mesenchyme-specific reporter/tracer (Tbx4-LERGFP) to generate lung mesenchymal progenitors by directed differentiation via a lateral plate mesodermal progenitor state (induced lung mesenchyme, iLM). In parallel we differentiated a mouse embryonic stem (ES) cell line carrying a Nkx2-1mCherry reporter into lung epithelial progenitor cells using our established directed differentiation protocol. We then combined the purified lung epithelial and mesenchymal progenitor cells and co-cultured them in distal or proximal differentiation media for 1 week on Matrigel. We find that cells self-organize into complex 3-dimensional organoids with closely juxtaposed epithelial and mesenchymal cells. Furthermore, co-culture affects the molecular phenotype of both lineages. Our iPSC-derived co-culture model can 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 ESC-derived lung epithelial progenitors cultured alone or with iPSC-derived lung mesenchyme (iLM) in distal or proximal differentiation media: 1) “e pre”: ESC-derived lung epithelium before co-culture carrying a Nkx2-1mCherry reporter, sorted based on Epcam+/Nkx2-1mCherry+, 2) “iLM pre” iPSC-derived lung mesenchyme before co-culture carrying a Tbx4-LERGFP reporter, sorted based on Tbx4-LERGFP+, 3) e-dist: ESC-derived lung epithelium carrying a Nkx2-1mCherry reporter cultured in distal differentiation medium for 7 days, sorted based on Epcam+/Nkx2-1mCherry+. 4) e-prox: ESC-derived lung epithelium carrying a Nkx2-1mCherry reporter cultured in proximal differentiation medium for 7 days, sorted based on Epcam+/Nkx2-1mCherry+. 5) me-dist: iPSC-derived lung epithelium carrying a Nkx2-1mCherry reporter and iPSC-derived lung mesenchyme carrying a Tbx4-LERGFP reporter co-cultured in distal differentiation medium for 7 days, sorted based on Epcam+/Nkx2-1mCherry+ and Tbx4-LERGFP+ and recombined at a 1/1 epithelial/mesenchymal ratio. 6) me-prox: iPSC-derived lung epithelium carrying a Nkx2-1mCherry reporter and iPSC-derived lung mesenchyme carrying a Tbx4-LERGFP reporter co-cultured in proximal differentiation medium for 7 days, sorted based on Epcam+/Nkx2-1mCherry+ and Tbx4-LERGFP+ and recombined at a 1/1 epithelial/mesenchymal ratio.