Freshly isolated rat liver sinusoidal endothelial cells and Kupffer cells - Ion Torrent mRNA sequencing

Liver sinusoidal endothelial cells (LSECs) and Kupffer cells (KCs) have important roles in liver homeostasis and host defense. Sharing the same microenvironment in the liver sinusoid, they form an effective scavenger cell system for removal of potentially harmful blood-borne substances. Unlike most other endothelia, LSECs are highly efficient in endocytosis of nanoparticles, including virus. Though controversial, LSECs have been reported to act as antigen presenting cells, thus contributing importantly to induction of immune tolerance in liver. There are also controversies about LSEC and KC specific markers, which may be due to overlapping cell functions, species differences, and/or problems with cell purification. We therefore aimed to characterize and quantitatively compare expressed gene products of freshly isolated, highly pure rat LSECs (SE-1/CD32b positive) and KCs (CD11b/c positive) using high throughput RNA-sequencing, and label-free proteomics. Additional validation was done by immunohistochemistry, and flow cytometry. We found that most immune genes expressed in KCs were also expressed in LSECs, albeit at a lower density, and they also have overlap in cell surface marker expression. Both cell types express high levels of scavenger receptors and immune lectins.