Patient-derived liver organoids recapitulate liver epithelial heterogeneity and enable precision modeling of alcohol-related liver disease

Abstract

Background & aims: Alcohol-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.

Methods: b-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.

Results: Phenotypic 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 captures the epithelial complexity and specific patient features. This approach helps 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 capture 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.

Keywords: ALD; alcohol-associated liver disease; cell plasticity; chronic liver disease; ductular reaction; epithelial cells; liver; organoid; precision medicine; steatotic liver disease.