Cathepsin-dependent amyloid formation drives mechanical rupture of lysosomal membranes

Li, D.; Zhang, W.; Medina, M.; Stuke, J. F. M.; Schwarz, A.; Brill, J.; Brenner, J.; Kraus, F.; Ohlerich, S.; Lizarrondo, J.; Pflaum, J.; Grass, J. H.; Soltow, L.-M.; Hammerschmid, D.; Weber, N.; Welsch, S.; Langer, J.; Windbergs, M.; Harper, W. J.; Schuman, E.; Hummer, G.; Grotjahn, D. A.; Wilfling, F.

doi:10.64898/2026.01.17.700056

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bioRxiv · 10.64898/2026.01.17.700056

Cathepsin-dependent amyloid formation drives mechanical rupture of lysosomal membranes

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Abstract

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.

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Li, D., Zhang, W., Medina, M., Stuke, J. F. M., Schwarz, A., Brill, J., Brenner, J., Kraus, F., Ohlerich, S., Lizarrondo, J., Pflaum, J., Grass, J. H., Soltow, L.-M., Hammerschmid, D., Weber, N., Welsch, S., Langer, J., Windbergs, M., Harper, W. J., Schuman, E., Hummer, G., Grotjahn, D. A., Wilfling, F.. 2026-01-19. Cathepsin-dependent amyloid formation drives mechanical rupture of lysosomal membranes. https://doi.org/10.64898/2026.01.17.700056

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