The human liver is an essential multifunctional organ, and liver diseases are rising with limited treatment options. However, the cellular complexity and heterogeneity of the liver remain poorly understood. Here, we performed single-cell RNA-sequencing of ~5,000 cells from normal liver tissue of 6 human donors to construct the first human liver cell atlas. Our analysis revealed previously unknown sub-types among endothelial cells, Kupffer cells, and hepatocytes with transcriptome-wide zonation of these populations.We show that the EPCAM + population is highly heterogeneous and consists of hepatocyte progenitors, cholangiocytes and a MUC6 + stem cell population with a specific potential to form liver organoids. As proof-of-principle, we applied our atlas to unravel phenotypic changes in cells from hepatocellular carcinoma tissue and to investigate cellular phenotypes of human hepatocytes and liver endothelial cells engrafted into a humanized 2 FAH -/-mouse liver. Our human liver cell atlas provides a powerful and innovative resource enabling the discovery of previously unknown cell types in the normal and diseased liver. 4 cell populations on the basis of cell surface markers (Extended Data Fig. 1, Methods).Since fresh liver tissue material is scarce and difficult to preserve, and biobanks with cryopreserved liver tissue derived from patients represent rich resources, we attempted to generate single-cell transcriptome data from cryopreserved cells in addition to single cell suspensions from freshly prepared liver resection specimens (Methods). We then used RaceID3 for the identification of cell types (Methods) 5 .Cells from different patients, isolated from freshly prepared (P301, P304) or cryopreserved (P301, P304, P308, P309, P310, P311) single-cell suspensions generally co-clustered (Extended Data Fig. 1), showing that our pipeline is robust and can be used for sequencing cells from cryopreserved samples.Based on the expression of marker genes, our atlas reveals all the main liver cell types, including hepatocytes, EPCAM + bile duct epithelial cells (cholangiocytes) and liver stem cells, CLEC4G + liver sinusoidal endothelial cells (LSECs), CD34 + PECAM high macro-vascular endothelial cells (MaVECs), hepatic stellate cells and myofibroblasts, Kupffer cells, NKT cells, NK cells, T cells and B cells ( Fig. 1b-d). Several clusters corresponding to distinct sub-types were identified within these major populations (Fig. 1c), indicating previously unknown heterogeneity across liver cell types.
Heterogeneity and zonation of endothelial cells, Kupffer cells, and hepatocytesHepatocytes are spatially heterogeneous and sub-specialized, or zonated, along the portal-central axis of the liver lobule [11][12][13][14][15] . Based on the metabolic sub-specialization of hepatocytes, the liver lobule has been divided into three zones; the periportal zone nearest to the portal vein, hepatic artery and bile duct, the central zone nearest to the central vein, and the mid zone located between the central and periportal zones 11,13,15 ...