Landscape of intercellular crosstalk in fatty liver disease revealed by single-cell secretome analysis

Cell-cell communications via ligand-receptor signaling are a fundamental feature of complex organs. In addition to hepatocytes, the mammalian liver harbors several distinct cell types, including endothelial cells, hepatic stellate cells (HSC), cholangiocytes, the resident macrophage Kupffer cells, and other immune cells, collectively known as non-parenchymal cells (NPC) 1-5. Paracrine signaling among NPC is important for tissue homeostasis and has been implicated in the pathogenesis of nonalcoholic steatohepatitis (NASH), an emerging epidemic linked to metabolic syndrome 6-8. Despite this, the global landscape of intercellular signaling in the liver has not been comprehensively elucidated. Here we perform single-cell RNA sequencing and secretome analysis on liver NPC isolated from healthy and diet-induced NASH mice. Our analysis revealed highly specific patterns of the cellular sources of secreted ligands and membrane receptors and a network of paracrine and autocrine signaling at the single-cell level. Comparative analysis of secretome gene expression uncovered a global disruption of the liver endothelial signaling network during NASH pathogenesis. The HSC secretome encompasses extracellular matrix proteins, signaling ligands (stellakines) and three distinct functional classes of membrane receptors. Liver macrophage undergoes a marked expansion in NASH with the emergence of a new population marked by expression of Triggering receptor expressed on myeloid cells 2 (Trem2) and activation of a transcriptional program underlying phagocytosis, lysosomal degradation and antigen presentation. These results provide a high-resolution blueprint of intercellular crosstalk in mammalian liver and illustrate the complexity and richness of cell-cell signaling in liver physiology and disease. Single cell RNA-seq on non-parenchymal cells of healthy vs NASH mouse liver.