Single-cell transcriptome unveils unique transcriptomic signatures of human organ-specific endothelial cells

The heterogeneity of endothelial cells (ECs) across human tissues remains incompletely inventoried. We constructed an atlas of > 210,000 ECs derived from 38 regions across 24 human tissues. Our analysis reveals significant differences in transcriptome, phenotype, metabolism and transcriptional regulation among ECs from various tissues. Notably, arterial, venous, and lymphatic ECs shared more common markers in multiple tissues than capillary ECs, which exhibited higher heterogeneity. This diversity in capillary ECs suggests their greater potential as targets for drug development. ECs from different tissues and vascular beds were found to be associated with specific diseases. Importantly, tissue specificity of EC senescence is more determined by somatic site than by tissue type (e.g. subcutaneus adipose tissue and visceral adipose tissue). Additionally, sex-specific differences in brain EC senescence were observed. Our EC atlas offers valuble resoursce for identifying EC subclusters in single-cell datasets from body tissues or organoids, facilitating the screen of tissue-specific targeted therapies, and serving as a powerful tool for future discoveries.