Transcriptional characterisation of human lung cells identifies novel mesenchymal lineage markers

Rationale: The lung mesenchyme gives rise to multiple distinct lineages of cells in the mature respiratory system, including smooth muscle cells of the airway and vasculature. However, a thorough understanding of the specification and mesenchymal cell diversity in the human lung is lacking. Methods: We completed single-cell RNA sequencing analysis of fetal human lung tissues. Canonical correlation analysis, clustering, cluster marker gene identification and t-distributed stochastic neighbour embedding representation was performed in Seurat. Cell populations were annotated using ToppFun. Immunohistochemistry and in situ hybridisation were used to validate spatiotemporal gene expression patterns for key marker genes. Results: We identified molecularly distinct populations representing committed fetal human lung endothelial cells, pericytes and smooth muscle cells. Early endothelial lineages expressed classic endothelial cell markers (platelet endothelial cell adhesion molecule/CD31 and claudin 5), while pericytes expressed platelet-derived growth factor receptor-beta, Thy-1 membrane glycoprotein and basement membrane molecules (collagen IV, laminin and proteoglycans). We observed a large population of nonspecific human lung mesenchymal progenitor cells characterised by expression of collagen 1 and multiple elastin fibre genes (ELN, NIFAP2 and FBN1). We closely characterised the diversity of mesenchymal lineages defined by alpha(2)-smooth muscle actin (AC2A2) expression. Two cell populations, with the highest levels of ACTA2 transcriptional activity, expressed unique sets of markers associated with airway or vascular smooth muscle cells. Spatiotemporal analysis of these marker genes confirmed early and persistent spatial specification of airway (HHIP MYLK and IGFI) and vascular (NTRK3 and MEF2C) smooth muscle cells in the developing human lung. Conclusion: Our data suggest that specification of distinct airway and vascular smooth muscle cell phenotypes is established early in development and can be identified using the markers we provide.