Patient-derived liver biopsy organoids enable precision alcohol-associated liver disease modeling

Arino, S.; Zannatto, L.; Martinez-Garcia de la Torre, R. A.; Ferrer-Lorente, R.; Cratacos-Gines, J.; Belen Rubio, A.; Perez, M.; Aguilar-Bravo, B.; Serrano, G.; Atkinson, S.; Xu, Z.; Cantallops-Vila, P.; Sererols-Vinas, L.; Ruiz-Blazquez, P.; Rill, A.; Lozano, J. J.; Coll, M.; Ochoa, I.; Affo, S.; Moles, A.; Mereu, E.; Bataller, R.; Pose, E.; Sancho-Bru, P.

doi:10.1101/2025.03.22.644563

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bioRxiv · 10.1101/2025.03.22.644563

Patient-derived liver biopsy organoids enable precision alcohol-associated liver disease modeling

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Abstract

Background & AimsAlcohol-associated liver disease (ALD) is a major cause of liver disease worldwide with scarce therapeutic options. Animal models poorly recapitulate advanced ALD precluding the development of new treatments. Organoids have emerged as a powerful human-based preclinical tool. However, current patient-derived liver organoids fail to recapitulate the epithelial heterogeneity and its generation requires liver surgical resections, thus limiting personalized disease modeling. Here, we report the development of organoids from liver needle biopsies (b-Orgs) from patients with ALD. Methodsb-Orgs were generated from tru-cut biopsies from patients at early (n=28) and advanced (n=34) stages of ALD. b-Orgs were characterized by immunofluorescence, bulk and single cell RNA-sequencing and compared to parental tissues. b-Orgs were used to model ALD progression, identify pathogenic drivers, induce alcohol-associated hepatitis (AH) and evaluate response to prednisolone. ResultsPhenotypic and functional analysis of b-Orgs showed hepatocyte- enriched features. Single-cell RNA-sequencing revealed a heterogeneous cell composition comprising hepatocyte, biliary and progenitor populations, mirroring the epithelial landscape found in patients with advanced ALD. Moreover, b-Orgs preserved disease-stage features and allowed to identify the association of ELF3 with cell plasticity and disease progression. Finally, stimulation of b-Orgs with drivers of ALD induced pathophysiological features of alcohol-associated hepatitis, including ROS production, lipid accumulation, inflammation and decreased cell proliferation, which were mitigated in response to prednisolone. Conclusions Overall, we provide a human-based model that recapitulates epithelial complexity and patient specific features, allowing to identify drivers of cell plasticity and expanding organoid-based liver disease modeling for personalized medicine. Impact and implications Here, we describe the generation of biopsy-derived organoids (b-Orgs) from patients with liver disease. b-Orgs reproduce the liver epithelial cell composition found in patients liver tissue and are efficiently generated from different stages of the disease, providing a platform for patient- tailored disease modeling and drug testing.

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Arino, S., Zannatto, L., Martinez-Garcia de la Torre, R. A., Ferrer-Lorente, R., Cratacos-Gines, J., Belen Rubio, A., Perez, M., Aguilar-Bravo, B., Serrano, G., Atkinson, S., Xu, Z., Cantallops-Vila, P., Sererols-Vinas, L., Ruiz-Blazquez, P., Rill, A., Lozano, J. J., Coll, M., Ochoa, I., Affo, S., Moles, A., Mereu, E., Bataller, R., Pose, E., Sancho-Bru, P.. 2025-03-25. Patient-derived liver biopsy organoids enable precision alcohol-associated liver disease modeling. https://doi.org/10.1101/2025.03.22.644563

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