Endolysosomal damage promotes intraluminal protein condensate formation that limits cytosolic leakage

Abstract

Endolysosomal membrane damage is a detrimental process in mammalian cells that results in leakage of the luminal contents into the cytosol. However, the nature and extent of the leakage during membrane damage is unknown. Here, we show that endomembrane damage induces the rapid formation of intraluminal condensates in endolysosomes. A subset of resident luminal proteins undergo spatially coordinated condensation upon endomembrane damage. Electron microscopy reveals distinct luminal morphology, and cryo-electron tomography confirms the condensed ultrastructure in their native state. Condensate formation occurs across mechanistically distinct modes of membrane injury and is reversibly dissociated upon lysosomal recovery. Remarkably, these condensates impose a previously unrecognised barrier to endolysosomal escape of therapeutic oligonucleotides. Despite endomembrane damage, luminal oligonucleotide therapeutics are sequestered in damaged endolysosomes through condensate-mediated biophysical immobilisation. Targeting condensate sequestration could represent a novel strategy to improve oligonucleotide-based therapeutics.