Accumulation of extracellular matrix (ECM) in liver fibrosis is associated with changes in protein abundance and composition depending upon etiology of the underlying liver disease. Current efforts to unravel etiology-specific mechanisms and pharmacological targets rely on several models of experimental fibrosis. Here, we characterize and compare dynamics of hepatic proteome remodeling during fibrosis development and spontaneous healing in experimental mouse models of hepatotoxic (carbon tetrachloride [CCl4] intoxication) and cholestatic (3,5-diethoxycarbonyl-1,4-dihydrocollidine [DDC] feeding) injury. Using detergent-based tissue extraction and mass spectrometry, we identified compartment-specific changes in the liver proteome with detailed attention to ECM composition and changes in protein solubility. Our analysis revealed distinct time-resolved CCl4 and DDC signatures, with identified signaling pathways suggesting limited healing and a potential for carcinogenesis associated with cholestasis. Correlation of protein abundance profiles with fibrous deposits revealed extracellular chaperone clusterin with implicated role in fibrosis resolution. Dynamics of clusterin expression was validated in the context of human liver fibrosis. Atomic force microscopy of fibrotic livers complemented proteomics with profiles of disease-associated changes in local liver tissue mechanics. This study determined compartment-specific proteomic landscapes of liver fibrosis and delineated etiology-specific ECM components, providing thus a foundation for future antifibrotic therapies.

Alcoholism or chronic conditions like hepatitis damage the liver. Over time, scar tissue builds up in the liver, causing cirrhosis. The scaring results from the liver’s repeated attempts to repair itself by creating more structural proteins called extracellular matrix proteins. A buildup of these scaffolding proteins leads to tissue stiffening or fibrosis. Fibrosis may heal in some cases but in others, it may progress to cirrhosis, liver cancer or liver failure. Learning more about these processes may help scientists and clinicians understand why fibrosis is reversible in some cases but not others. It may also allow them to develop treatments that can treat or reverse fibrosis and prevent cirrhosis, liver cancer, or liver failure. The first step is studying how fibrosis occurs in mouse models that mimic different types of liver disease. For example, repetitive ingestion of a toxic substance, such as alcohol, can cause one type of liver disease. However, slowing or stalling bile flow through the biliary system (the liver, gallbladder, and bile ducts), leads to a different type of chronic liver injury. Jirouskova et al. identify an extracellular protein called clusterin that may help heal fibrosis. The experiments used mouse models of two different types of liver disease. One mimicked liver disease caused by repetitive toxin injury, and the other modelled liver disease caused by chronic stalling of the bile flow in the liver (cholestasis). In the experiments, Jirouskova et al. looked at all the proteins made in each type of liver disease as the animals developed fibrosis or their fibrosis resolved. They also studied extracellular matrix proteins and how they affected molecular signaling in the liver tissue. The experiments revealed different patterns of protein production and healing in the different types of liver disease. The animals with liver diseases caused by chronic cholestatic injury were less likely to heal their livers and showed potential to progress to liver cancer. Production of the clusterin protein was connected with better liver recovery from toxic injuries. Jirouskova et al. provide a comprehensive map of all the proteins produced over the course of liver fibrosis progression and healing in two different animal models of liver disease. Scientists and clinicians may use this information to study liver disease types. It may also one day help them personalize patient's therapies. The experiments show that extracellular matrix proteins are essential contributors to fibrosis and key signaling agents in liver disease. This may make them good targets for new therapies. Boosting clusterin production may be one approach to promoting liver recovery. More studies are needed to confirm this before such therapies can be developed and tested in humans.

Clinical and Transplant Pathology Centre Institute for Clinical and Experimental Medicine Prague Czech Republic

Department of Animal Physiology Faculty of Science Charles University Prague Czech Republic

Department of Mathematics Informatics and Cybernetics University of Chemistry and Technology Prague Czech Republic

Department of Pathology The 3rd Faculty of Medicine Charles University and University Hospital Kralovske Vinohrady Prague Czech Republic

Helmholtz Munich Research Unit Precision Regenerative Medicine; Comprehensive Pneumology Center Member of the German Center for Lung Research Munich Germany

Institute of Experimental Pneumology LMU University Hospital Ludwig Maximilians University Munich Germany

Laboratory of Integrative Biology Institute of Molecular Genetics of the Czech Academy of Sciences Prague Czech Republic

Laboratory of Mass Spectrometry BIOCEV Faculty of Science Charles University Prague Czech Republic

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doi: 10.1101/2024.03.26.586230 PubMed

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doi: 10.7554/eLife.98023.1 PubMed

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doi: 10.7554/eLife.98023.2 PubMed

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