Unlocking liver physiology: comprehensive pathway maps for mechanistic understanding

Luiz Ladeira^1*Anouk Verhoeven^2*Jonas van Ertvelde²Jian Jiang²Alessio Gamba¹Julen Sanz Serrano²Tamara Vanhaecke²Harm Heusinkveld³Ramiro Jover⁴Mathieu Vinken²Liesbet Geris^1,5,6*Bernard Staumont^1*

• ¹Biomechanics Research Unit, GIGA Institute, University of Liège, Belgium, Liège, Belgium
• ²Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit, Brussels, Belgium
• ³Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
• ⁴Department of Biochemistry & Molecular Biology, University of Valencia; Exp. Hepatology Joint Unit, IIS Hospital La Fe; CIBERehd, Valencia, Spain
• ⁵Skeletal Biology and Engineering Research Center, KU Leuven, Leuven, Belgium
• ⁶Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium

In silico methods provide a resourceful toolbox for new approach methodologies (NAMs). They can revolutionize chemical safety assessment by offering more efficient and human-relevant alternatives to traditional animal testing. In this study, we introduce two Liver Physiological Maps (PMs); comprehensive and machine-readable graphical representations of the intricate mechanisms governing two major liver functions. Methods: Two PMs were developed through manual literature curation, integrating data from established pathway resources and domain expert knowledge. An interactive version is available online for exploration. Cross-comparison analysis with existing Adverse Outcome Pathway (AOP) networks was performed to benchmark physiological coverage and identify knowledge gaps. Results: The LiverLipidPM focuses on liver lipid metabolism, detailing pathways involved in fatty acid synthesis, triglycerides, cholesterol metabolism, and lipid catabolism in hepatocytes. The LiverBilePM represents bile acid biosynthesis and secretion processes, detailing biosynthesis, transport, and secretion processes between hepatocytes and cholangiocytes. Both maps integrate metabolism with signaling pathways and regulatory networks. The interactive interface enable visualization of molecular pathways, linkage to ontologies, and overlay of experimental data. Comparative analysis revealed unique mechanisms and overlaps with AOP networks. Chemical-target queries identified new potential targets, which might represent new molecular initiating events for the AOPs. Conclusion: The developed liver PMs serve as valuable resources for hepatology research, with focus on hepatotoxicity, supporting the refinement of AOP networks and the development of human-oriented NAMs for chemical toxicity assessment. They provide a foundation for creating computational models and mode-of-action ontologies while potentially extending their utility to systems biology and drug discovery applications.