Single Cell RNA Sequencing Reveals Gene Expression Continuums Along the Spatial Hierarchy of the Pulmonary Circulation

Abstract

BackgroundThe lung vasculature is comprised of a series of branching vessels extending from the main pulmonary artery to the alveolar capillaries, then back to the pulmonary veins. Lung endothelial cells (EC) exist along this continuum, exposed to gradients of shear stress, oxygen tension and pressure. Single cell RNA sequencing (scRNA-seq) has identified lung EC subsets, but many aspects of the vascular continuum, including vessel size and capillary polarity remain undefined from transcriptomic data. MethodsWe created an endothelial-enriched scRNA-seq dataset from the P3 mouse lung. Using diffusion pseudotime across all lung EC, we developed an analytical framework to delineate transcriptomic gradients and assign vessel-size scores to categorize individual endothelial cells (EC) along the vascular continuum. We confirmed size-related gene expression patterns with fluorescence in situ hybridization. ResultsWe categorized capillary 1, arterial and venous EC along two gradients: arterio-venous zonation and vessel size. This approach distinguished large arteries from arterioles, large veins from venules, and revealed arterio-venous polarity within the capillaries. Our data recapitulated previously established zonally defined cell signaling axes, such as high Cxcl12-Cxcr4 signaling in arterioles. We also identified unique cellular communication occurring in large versus small arteries and veins, and localized injury-induced venous EC proliferation to vessels of specific size. This analytical framework was successfully applied to several published mouse and human datasets across different stages of lung development. ConclusionsThese findings provide a comprehensive transcriptional map of EC across the pulmonary vascular tree, enabling assignment of each individual cell to vessels with defined size and position. This framework offers spatial inferences and novel mechanistic insights from scRNA-seq data sets that may elucidate therapeutic targets to treat pulmonary vascular diseases affecting specific vascular segments. We speculate that similar frameworks could be applied to tissues outside the lung.