Scientists Discover LYVAC Protein That Drives Lysosomal Swelling in Disease

Lysosomal vacuolation — the dramatic ballooning of lysosomes — is observed across a wide range of diseases including neurodegeneration, lysosomal storage disorders, prion disease, viral infection, and chemotherapy exposure, yet its molecular machinery was poorly understood. This landmark study in Science identifies LYVAC (lysosomal vacuolator, previously called PDZD8) as the central executor of this process.

The researchers began by using Lyso-TurboID, a proximity biotinylation system anchored to the lysosomal surface, to capture proteins recruited during vacuolation induced by apilimod — a pharmacological inhibitor of PIKfyve, the kinase that generates the critical lysosomal lipid PI(3,5)P2. The top proteomic hit was PDZD8/LYVAC, an ER-resident lipid transfer protein previously linked to ER-endolysosome membrane contact sites but lacking a defined functional role in vacuolation. Knockout of LYVAC in multiple cell lines completely abolished apilimod-induced vacuolation, as well as vacuolation triggered by genetic loss of PIKfyve or FIG4 — mutations linked to Charcot-Marie-Tooth disease.

Critically, LYVAC was required not just in one model but across a broad spectrum of lysosomal osmotic stressors: weak-base drugs (metoclopramide, doxorubicin, topotecan, sunitinib), the ionophore monensin, sucrose loading mimicking lysosomal storage disease, and even hypotonic media. In each case, LYVAC was recruited to stressed lysosomes before vacuole formation, consistent with a causal rather than reactive role. Water channel blockade with phloretin abolished both LYVAC recruitment and vacuolation, confirming the osmotic mechanism. LYVAC did not respond to ER stress-induced vacuolation or lysosomal membrane damage, distinguishing it clearly from the lipid transfer protein ATG2, which repairs damaged lysosomes.

Domain-deletion experiments and AlphaFold structural modeling revealed that LYVAC functions as a homodimer. Its recruitment to stressed lysosomes requires three loosely coupled domains — the transmembrane anchor (TM), a C1 lipid-binding domain, and a coiled-coil (CC) domain that binds the lysosomal GTPase RAB7. These three domains act cooperatively in a multivalent interaction system, with stress-induced changes in lysosomal phosphatidylserine (PS) and cholesterol enhancing C1 and SMP domain engagement. The SMP lipid transfer domain itself, which forms a hydrophobic tunnel for lipid passage, was absolutely required for vacuolation, confirming that directional ER-to-lysosome bulk lipid transfer is the mechanism of membrane expansion. Stimulated Raman scattering (SRS) lipid imaging directly demonstrated lipid flow from ER to lysosomes during vacuolation in a LYVAC-dependent manner.

The physiological and pathological implications are substantial. LYVAC loss sensitized cancer cells to lysosome-sequestered chemotherapeutics and to monensin-induced cell death, suggesting that lysosomal vacuolation serves a cytoprotective buffering role. In hepatitis A virus infection, LYVAC deletion reduced both vacuolation and viral protease-induced cell death. These findings reframe lysosomal vacuolation not merely as a pathological bystander but as an active, regulated stress response with survival consequences — and place LYVAC at its center.