Lipid-manager autophagy proteins ATG2 and ATG9 regulate extracellular vesicle secretion via amphisome biogenesis and cell lipidome modulation

Abstract Autophagy intersects with endocytic trafficking to regulate extracellular vesicle (EV) biogenesis, but how upstream lipid-handling autophagy proteins influence this crosstalk is unclear. Here we show that the autophagy lipid-supply proteins ATG9A and ATG2A/B restrain small EV (sEV) secretion by promoting amphisome formation and controlling cellular lipid composition. Deletion of ATG9A or ATG2A/B in cells, which abolishes autophagosome biogenesis, causes a RAB27A-dependent increase in secretion of CD63-enriched, smaller sEVs, and accumulation of intraluminal vesicles within multivesicular endosomes. Under lysosomal inhibition, wild-type cells release LC3- and autophagy cargo receptor-positive sEVs, whereas ATG9A- and ATG2A/B-deficient cells, despite hypersecretion of sEVs, fail to load LC3 or canonical cargo receptors, indicating a block in amphisome-mediated export. Proteomics reveals selective depletion of autophagy receptors and ferritinophagy factors and enrichment of RNA-binding proteins and endosomal trafficking regulators in sEVs from ATG9A- and ATG2A/B-deficient cells. Whole-cell lipidomics uncovers extensive rewiring of the lipidome, with accumulation of ceramides and neutral lipids, altered phospholipid balance, and transcriptional remodeling of lipid metabolic enzymes, while neutral sphingomyelinase inhibition normalizes sEV output. These findings identify ATG9A and ATG2A/B as lipid-dependent gatekeepers that couple autophagosome and amphisome formation, regulating membrane partition between degradative autophagy and exosome-mediated secretion.