Mapping Embryonic Mouse Lung Development Using Enhanced Spatial Transcriptomics

The mature mammalian lung contains ∼50 different cell types that are located in precise positions along and around the airway epithelial tree. Here, we apply spatial transcriptomics to early embryonic mouse lungs to investigate how these spatial patterns are progressively established during development. Specifically, we optimized a microfluidics-enabled, deterministic barcoding-based sequencing (DBiT-seq) workflow to achieve sensitive spatial mapping of tissue sections, resulting in up to a twofold increase in average transcript recovery compared with previous implementations. Spatial mapping of epithelial populations revealed that Sox9⁺ epithelial progenitors are located throughout the epithelial tree at early stages before becoming confined to the distal ends. Moreover, we describe a previously unrecognized mesenchymal cluster that exhibits consistent spatial position, expresses high levels of extracellular matrix proteins, and appears to promote embryonic lung innervation. These findings provide new insights into the spatial organization and cellular dynamics underlying early lung development, and demonstrate the power of spatial transcriptomics to uncover hidden patterns and populations of cells.