Cellular crosstalk mediated by TGF-β drives epithelial-mesenchymal transition in patient-derived multilineage biliary organoids [bulk RNA-seq]

The developmental integrity of bile duct epithelium and peribiliary glands (PBGs) plays a key role in maintaining bile flow and preventing liver diseases. We emplpoyed multilineage biliary organoids (MBOs) engineered from co-cultures of human liver epithelial cells, umbilical vein endothelial cells (HUVECs), and mesenchymal stem cells (MSCs) to model biliary development and pathogenesis of biliary atresia (BA). Self organization of these cells into MBOs recapitulated the dual compartmentalization of bile ducts with the epithelial layer and PBGs. Notably, BA patient-derived MBOs exhibited markers of epithelial-mesenchymal transition (EMT) and activated TGF-β/Activin-SMAD2/3 signaling pathways, suggesting a link to the delayed maturation of bile duct epithelium. Inhibition of TGF-β signaling suppressed EMT, promoted epithelial maturation, and improved organoid structure. In in vivo, TGF-β inhibitor treatment in a neonatal mouse model of BA reduced biliary injury and liver fibrosis. These data support the critical role of epithelial and mesenchymal cell interactions in bile duct development, give insight into molecular mechanisms of BA, and point to the therapeutic potential of targeting TGF-β signaling. MBOs generated by co-culturing HUVECs and human MSCs with dissociated epithelial organoid cells derived from liver biopsies of controls (n=3) and BA patients (n=3) were subjected to bulk RNA-seq after 14 days of culturing.