Supporting Data For 'Disease-Associated Amyloid-β Filaments in Biliary Atresia, an Incurable Liver Disease in Infants'

Biliary atresia (BA) is an obstructive bile duct disease in newborns with a complex and diverse etiology, with most cases lacking a clear genetic basis. Infants with BA show altered regulation of genes involved in amyloid-β (Aβ) biology and exhibit abnormal intracellular inclusions within hepatic bile ducts that are immunoreactive to amyloid-β precursor protein (APP). However, the identity, structure, and pathogenic role of these inclusions remain unclear. In this study, we employed cryogenic electron microscopy (cryo-EM) to resolve the structures of protein aggregates isolated from the livers of four infants diagnosed with BA. Our analysis revealed that these aggregates are composed of amyloid-β 42 (Aβ42) peptides. Specifically, we identified two structurally related M-shaped Aβ42 protofilament folds, which form two distinct filament types: left-handed twisted type BA I dimeric filaments (residues V12–A42) with extensive protofilament interfaces, and right-handed twisted type BA II trimeric filaments, consisting of the type BA I dimeric core (residues V12–A42 and G9–A42) along with a third distinctively folded protofilament representing the C-terminal portion of Aβ42 (residues G29–A42). The Aβ42 filaments found in BA livers are structurally identical across all cases but differ from those in extracellular neural plaques characteristic of Alzheimer’s disease or Down syndrome. Furthermore, Aβ42 filaments derived from BA livers induce morphological and transcriptional changes associated with BA in healthy liver organoids. This study provides evidence of amyloid-β aggregation outside the brain and offers new insights into the pathobiology of BA. Understanding the structural properties of Aβ42 filaments in BA could aid in developing improved model systems, structure-based inhibitors targeting amyloid-β deposition, and diagnostic tools for this currently incurable condition.