Mapping embryonic mouse lung development using enhanced spatial transcriptomics

Summary The mature mammalian lung contains ∼50 different cell types that are located in precise positions along and around the airway epithelial tree. Here, we investigated how these spatial patterns are progressively established during development. Specifically, we optimized a microfluidics-enabled, deterministic barcoding-based sequencing (DBiT-seq) workflow to achieve highly sensitive spatial mapping of tissue sections from early embryonic mouse lungs. 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. Spatial mapping of mesenchymal populations revealed a previously unrecognized mesenchymal cluster that 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. Competing Interest Statement The authors have declared no competing interest. Footnotes Abbreviations: CARD, conditional autoregressive-based deconvolution; DBiT-seq, deterministic barcoding in tissue for spatial omics sequencing; ECM, extracellular matrix; NGS, next-generation sequencing; Ptn, Pleiotrophin; scRNA-seq, single-cell RNA sequencing; UMI, unique molecular identifier.