Currently there are no effective antifibrotic therapies for liver cirrhosis, a major killer worldwide. To obtain a cellular resolution of directly-relevant pathogenesis and to inform therapeutic design, we profile the transcriptomes of over 100,000 primary human single cells, yielding molecular definitions for the major non-parenchymal cell types present in healthy and cirrhotic human liver. We uncover a novel scar-associated TREM2 + CD9 + macrophage subpopulation with a fibrogenic phenotype, that has a distinct differentiation trajectory from circulating monocytes. In the endothelial compartment, we show that newly-defined ACKR1 + and PLVAP + endothelial cells expand in cirrhosis and are topographically located in the fibrotic septae. Multi-lineage ligand-receptor modelling of specific interactions between the novel scar-associated macrophages, endothelial cells and collagen-producing myofibroblasts in the fibrotic niche, reveals intra-scar activity of several major pathways which promote hepatic fibrosis. Our work dissects unanticipated aspects of the cellular and molecular basis of human organ fibrosis at a single-cell level, and provides the conceptual framework required to discover rational therapeutic targets in liver cirrhosis.
MainLiver cirrhosis is a major global healthcare burden. Recent estimates suggest that 844 million people worldwide have chronic liver disease, with a mortality rate of two million deaths per year and a rising incidence 1 . In health, the liver serves a myriad of functions including detoxification, metabolism, bile production and immune surveillance. Chronic liver disease, the result of iterative liver injury secondary to any cause, results in progressive fibrosis, disrupted hepatic architecture, vascular changes and aberrant regeneration, defining characteristics of liver cirrhosis 2 . Importantly, the degree of liver fibrosis predicts adverse patient outcomes, including the development of cirrhosis-related complications, hepatocellular carcinoma and death 3 . Hence, there is a clear therapeutic imperative to develop effective anti-fibrotic approaches for patients with chronic liver disease 4-7 .Liver fibrosis involves a complex, orchestrated interplay between multiple nonparenchymal cell (NPC) lineages including immune, endothelial and mesenchymal cells spatially located within areas of scarring, termed the fibrotic niche. Despite rapid progress in our understanding of the cellular interactions underlying liver fibrogenesis accrued using rodent models, there remains a significant 'translational gap' between putative targets and effective patient therapies 4,5 . This is in part due to the very limited definition of the functional heterogeneity and interactome of cell lineages that contribute to the fibrotic niche of human liver cirrhosis, which is imperfectly recapitulated by rodent models 4,6 .Single-cell RNA sequencing (scRNA-seq) has the potential to deliver a step change in both our understanding of healthy tissue homeostasis as well as disease pathogenesis, allowing the interr...