bioRxiv. 2026 Jan 19. pii: 2026.01.17.700056. [Epub ahead of print]
Delong Li,
Wenxin Zhang,
Michaela Medina,
Jan F M Stuke,
Andre Schwarz,
Jonas Brill,
Johann Brenner,
Felix Kraus,
Simon Ohlerich,
Javier Lizarrondo,
Jeremy Pflaum,
Julia H Grass,
Lena-Marie Soltow,
Dietmar Hammerschmid,
Natalie Weber,
Sonja Welsch,
Julian D Langer,
Maike Windbergs,
J Wade Harper,
Erin Schuman,
Gerhard Hummer,
Danielle A Grotjahn,
Florian Wilfling.
Lysosomal membrane integrity is essential for cellular homeostasis, and its failure drives lysosomal storage disorders (LSD) and neurodegeneration. The dipeptide L-leucyl-L-leucine methyl ester (LLOMe) is widely used to model lysosomal damage, yet its mechanism remains poorly understood. The prevailing view holds that LLOMe polymerizes into membrane-permeabilizing peptide chains within the lysosomal lumen. Using cryo-electron tomography in cultured cells and primary neurons, we visualized the structural basis of LLOMe-induced lysosomal damage. We reveal that LLOMe forms amyloid structures within lysosomes that directly interact with and rupture the limiting membrane through mechanical stress. In vitro reconstitution confirms this amyloid-mediated mechanism. These findings establish a structural paradigm for lysosomal membrane disruption and provide insights into how disease-relevant protein aggregates, implicated in neurodegeneration and LSD, may compromise lysosomal integrity.