Journal Club: LYVAC/PDZD8 is a lysosomal vacuolator

Science 21 Aug 2025 Vol 389, Issue 6762 DOI: 10.1126/science.adz0972

Editor’s summary

Enlarged lysosomal vacuoles are observed in many conditions, including aging, infection, and prion and other neurodegenerative diseases. However, little is known about how these vacuoles are formed, precluding understanding of their pathophysiological functions. Through unbiased proteomics, Yang et al. identified lysosomal vacuolator (LYVAC, also known as PDZD8) as a key driver of lysosomal vacuolation (see the Perspective by Lippincott-Schwartz). Lysosomal osmotic stress remodeled lysosomal lipid composition and increased membrane tension, thereby coordinating LYVAC recruitment and lipid transfer from the endoplasmic reticulum to support lysosomal vacuolation. The general requirement of LYVAC for lysosomal osmotic vacuolation across diverse conditions suggests broad pathophysiological relevance of this lipid-transfer pathway. —Stella M. Hurtley

Structured Abstract

INTRODUCTION

Lysosomes degrade a wide range of macromolecules, supporting cellular growth, metabolism, and stress resilience. Under various pathophysiological conditions, including lysosomal storage disorders, aging, infection, and neurodegeneration, lysosomes can form large vacuoles associated with lysosomal dysfunction. Although lysosomal vacuolation has been observed for decades and is presumed to be an adaptive stress response, its underlying mechanisms and physiological functions remain poorly understood.

RATIONALE

Lysosomal vacuolation could potentially result from lysosomal osmotic stress owing to increased luminal solute load, which would drive water influx and membrane swelling. Lysosomal osmotic stress can be induced by diverse stimuli, including lysosomotropic weak bases, storage substrates such as sucrose, or a hypotonic extracellular environment. In several disease models, including prion diseases and cadmium toxicity, lysosomal vacuolation is linked to loss of function of the lipid kinase PIKfyve, which in turn causes lysosomal osmotic stress by triggering ion storage. We used PIKfyve inhibition in human cell lines as a model of lysosomal vacuolation to explore the molecular mechanisms underlying vacuole formation.

RESULTS

Our proteomics analysis identified PDZD8 (PDZ domain–containing 8), which we propose to be renamed as LYVAC (lysosomal vacuolator), as the top hit selectively enriched on vacuolating lysosomes after PIKfyve inhibition. LYVAC is an endoplasmic reticulum (ER)–anchored lipid transfer protein, suggesting its potential role in mediating vacuole formation by transferring lipids from the ER to lysosomes.

Genetic deletion of LYVAC strongly suppressed lysosomal vacuolation caused by either inhibition or genetic deletion of PIKfyve. LYVAC was also essential for lysosomal vacuolation triggered by a variety of unrelated stressors, including weak base compounds, sucrose storage, and hypotonic stress. These findings establish LYVAC as a general mediator of lysosomal vacuole formation.

LYVAC was recruited to lysosomes under all tested vacuolating conditions, each of which induced lysosomal osmotic stress. LYVAC and another lipid transfer protein, ATG2, selectively responded to lysosomal osmotic stress and membrane damage, respectively.

Domain analysis revealed that LYVAC was recruited through multivalent weak interactions mediated by two distinct domains: one that binds to RAB7, a marker of late endosomes and lysosomes, and another that binds to negatively charged lipids, particularly phosphatidylserine (PS). Lysosomal osmotic stress triggered phosphoinositide signaling that drove the ER-to-lysosome transfer of PS and cholesterol, both of which were required for lysosomal vacuolation.

PS and cholesterol not only promoted LYVAC recruitment but also activated its lipid transfer function. The lipid transfer domain of LYVAC directly binds to PS- and cholesterol-enriched membranes through conserved motifs recognizing the presence of both PS and cholesterol. In cells, label-free chemical imaging revealed LYVAC-dependent large-scale, ER-to-lysosome lipid movement after vacuole induction. In vitro reconstitution assays and molecular dynamics simulations supported the idea that this directional lipid movement was driven by lysosomal osmotic membrane tension and lipid composition differences between the ER and lysosomes.

CONCLUSION

Our study identifies LYVAC-mediated, directional ER-to-lysosome lipid transfer as an essential mechanism for lysosomal vacuolation. Diverse vacuolating stimuli converged on a common pathway involving lysosomal osmotic stress, lipid signaling, and regulation of LYVAC recruitment and lipid transfer. By linking lysosomal osmotic imbalance to vacuole formation, LYVAC underlies a robust cellular response with broad implications for lysosomal adaptation, osmoresilience, lysosomal storage pathology, and neurodegeneration.