A human liver cell atlas reveals heterogeneity and epithelial progenitors

Abstract

The human liver is an essential multifunctional organ, and liver diseases are rising with limited treatment options. However, the cellular composition of the liver remains poorly understood. Here, we performed single-cell RNA-sequencing of ~10,000 cells from normal liver tissue of 9 human donors to construct a human liver cell atlas. Our analysis revealed previously unknown sub-types among endothelial cells, Kupffer cells, and hepatocytes with transcriptome-wide zonation of some of these populations. We reveal heterogeneity of the EPCAM + population, which comprises hepatocyte-biased and cholangiocyte populations as well as a TROP2 int progenitor population with strong potential to form bipotent liver organoids. As proof-of-principle, we utilized our atlas to unravel phenotypic changes in hepatocellular carcinoma cells and in human hepatocytes and liver endothelial cells engrafted into a mouse liver. Our human liver cell atlas provides a powerful resource enabling the discovery of previously unknown cell types in the normal and diseased liver.

A Single‐Cell Perspective of the Mammalian Liver in Health and Disease

“…By taking advantage of the knowledge on zonated hepatocyte transcriptomes, Halpern et al developed a paired‐cell sequencing approach to probe heterogeneity of liver endothelial cells and bioinformatically inferred their spatial information . Similar molecular signatures of LSEC zonation were observed in independent scRNA‐seq studies on NPCs isolated from healthy and NASH mouse liver and in human liver . Comparative analysis of LSEC transcriptomes obtained from healthy and NASH livers revealed profound defects in endothelial gene expression and vascular signaling that may contribute to disease pathogenesis .…”

“…RNA sequencing and proteomic analyses of these pooled hepatocytes revealed greater details of spatial gene expression in the liver at mRNA, micro RNA and protein levels. In a separate study, scRNA‐seq of human liver cells revealed remarkably conserved features of liver zonation between mouse and human …”

“…Similar to mouse BECs, EpCAM+ cells isolated from fetal and adult human livers also contained heterogeneous cell populations. Single‐cell analysis of EpCAM+ human BECs revealed the existence of three transcriptionally heterogeneous populations that correspond to hepatocytes, bipotent progenitor cells, and cholangiocytes with low‐to‐high gradient expression of TROP2 . The putative progenitor cells with intermediate levels of TROP2 expression exhibited the highest organoid forming capacity in culture.…”

Liver gene regulatory networks: Contributing factors to nonalcoholic fatty liver disease

“…In the first study, scRNA‐seq was performed in approximately 10,000 cells obtained from nine human donors to build a reference mRNA expression atlas for this organ, which is freely available for browsing and further exploration at http://human-liver-cell-atlas.ie-freiburg.mpg.de/. In depth analysis of this dataset reinforced again the notion that the liver is a highly heterogeneous organ, with identification of multiple subtypes of endothelial cells, Kupffer cells and hepatocytes, along with detection of a subpopulation of bile duct cells with liver progenitor features (Aizarani et al, ). These results expand on previously made observations by MacParland et al (), who identified multiple macrophage populations in the human liver.…”

Transcriptomic Traces of Adult Human Liver Progenitor Cells

“…For instance, the ability to unambiguously identify adult human liver stem cells or progenitor cells—their more restricted progeny—would profoundly affect the direction of translational research, yet the existence and characteristics of such cells remain hotly contested. In a recent study published in Nature , Aizarani and colleagues addressed this problem by interrogating the adult human liver environment on a single‐cell scale . In the second such study of its kind, Aizarani and colleagues used fresh and frozen cell preparations from 9 donors to map the gene expression of all major cell types in the human liver onto an interactive cell atlas.…”