Amyloid-like aggregates cause lysosomal defects in neurons via gain-of-function toxicity

The autophagy-lysosomal pathway is impaired in many neurodegenerative diseases characterized by protein aggregation, but the link between aggregation and lysosomal dysfunction remains poorly understood. Here, we use artificial amyloid-like β-sheet proteins (β proteins) to investigate the gain-of-function effects of protein aggregation in primary neurons. We show that β proteins form fibrillar aggregates and cause neurotoxicity. Cryo-electron tomography reveals lysosomal alterations reminiscent of lysosomal storage disorders. Mass spectrometry-based analysis of the β protein interactome shows that β proteins sequester AP-3μ1, a subunit of the AP-3 adaptor complex involved in protein trafficking to lysosomal organelles. Importantly, restoring AP-3μ1 expression ameliorates neurotoxicity caused by β proteins. Our results point to lysosomes as particularly vulnerable organelles in neurodegenerative diseases, and emphasize the role of toxic gain-of-function of protein aggregates in lysosomal defects.