High-definition Spatial Transcriptomic Atlas Reveals New Principles Of Liver Homeostasis,Regeneration And Fibrosis

The liver is one of the largest mammalian organs and performs fundamental body functions.Microscopically,the liver lobes contain repetitive units,or lobules,comprising concentric layers of parenchymal hepatocytes radially organized around a central vein and several peripheral portal nodes.Behind this apparent simplicity hides a tremendous functional complexity,arising from the presence of environmental gradients and the participation of non-parenchymal cells（NPCs）.This creates a physiological phenomenon termed zonation consisting in the tightly organized and intertwined division of labor for all cell types along the porto-central axis.Another major characteristic is that hepatocytes have a relatively high turnover in homeostasis and a remarkable capacity to regenerate after acute injury.While chronic liver injury leads to progressive liver fibrosis and ultimately cirrhosis,which subsequently causes liver fibrosis and ultimately cirrhosis,a major cause of morbidity and mortality worldwide.Understanding the intricacies of the mammalian liver microenvironment in homeostatic or pathological condition is critical to develop new preventive or therapeutic approaches for highly prevalent diseases such as fatty liver,fibrosis,or cancer.In addition,revealing the mechanisms controlling the sparking and closing of hepatocyte proliferation holds clues for regenerative medicine and for clarifying the roadmap to malignant transformation.Liver disease is a highly orchestrated process dependent on intercellular communication.Despite its striking histological structure,how the responses of individual liver cells are coordinated in homeostasis and perturbation is poorly understood.This is due to the difficulty of studying multiple cell types in different states and locations,particularly when these are transient.Here,we used Stereo-seq（Spatio-Temporal Enhanced REsolution Omics-sequencing）combined with single-cell transcriptomic analysis to investigate mouse liver homeostasis and regeneration upon partial（2/3）hepatectomy（PHx）at whole lobe scale.Our integrative analysis dissects in unprecedented detail and at whole lobe scale the transcriptomic gradients controlling liver cell function in homeostasis.And exploring the dynamic changes of liver cell types and cell-cell interactions across the liver lobule,including aspects such as hepatocyte and immune zonation,signaling and gene regulatory networks,hepatocyte proliferation and division of labor during regeneration.Among other important regulators,we identified the transcriptional cofactor TBL1XR1 as an inflammation-induced regeneration rheostat that derepresses genes necessary for hepatocyte proliferation.Our work lays the foundation for future high-definition tissue scale atlases of organ physiology and malfunction.To reveal the multicellular networks regulating mammalian liver fibrosis from mild to severe phenotypes,we generated a single-nucleus transcriptomic atlas encompassing 49,919nuclei corresponding to all main liver cell types at different stages of murine carbon tetrachloride（CCl₄）-induced progressive liver fibrosis.Integrative analysis distinguished the sequential responses in hepatocytes,hepatic stellate cells and endothelial cells.Moreover,we have reconstructed the cell–cell interactions and gene regulatory networks implicating in these processes.These integrative analyses uncovered previously overlooked aspects of hepatocyte proliferation exhaustion and disrupted pericentral metabolic functions,dysfunction for clearance by apoptosis of activated hepatic stellate cells,accumulation of pro-fibrotic signals,and the switch from an anti-angiogenic to a pro-angiogenic program during CCl4-induced progressive liver fibrosis.Our dataset thus constitutes a useful resource for understanding the molecular basis of progressive liver fibrosis using a relevant animal model.Overall,our dataset and the analytical pipelines lay the foundation for future high-definition spatio-temporal atlases of mammalian（human and domestic animal）liver physiology and malfunction.