Single-cell RNA sequencing reveals transcriptome alterations of liver sinusoidal endothelial cells in different zonal microenvironments of cirrhotic livers

Dysfunction of liver endothelial cells (ECs), especially sinusoid endothelial cells (LSECs), play a key role in progression of liver fibrosis/cirrhosis. Here, we reported a map which reveals heterogeneity and spatial distribution of liver ECs in normal versus cirrhotic mouse liver and determined liver zonal specific transcriptomic changes of LSECs associated with liver cirrhosis using single-cell RNA sequencing technology. We identified 6 clusters of liver EC populations including 3 clusters of LSECs, 2 clusters of vascular ECs (arterial and central venous ECs) and 1 cluster of lymphatic ECs. Particularly, we mapped the 3 clusters of LSECs in Zone1-3. We found that liver EC identities are conserved even in liver cirrhosis and that Zone3 LSECs are most susceptible to damages associated with liver cirrhosis with increased capillarization and decreased abilities to regulate endocytosis and vascular tone. Altogether, this study deepens our knowledge for the pathophysiology of cirrhosis at a spatial and cell-specific level, which are indispensable for the development of novel therapeutic strategies to target liver ECs. We performed 10x scRNA sequencing analysis on liver EC enriched populations isolated from control and cirrhotic mice. All mice used were EC-specific enhanced green fluorescent protein (eGFP) expressing mice (Cdh5-Cre+, mTmG mice).GFP-positive and non-apoptotic liver ECs were selected from non-parenchymal cell fractions pooled from 3 mice per group by FACS.