The V-ATPase/ATG16L1 axis drives membrane remodeling during epithelial morphogenesis

Epithelial tubulogenesis shapes organs by transforming unpolarized epithelial cords into hollow tubes with central lumens. Posterior neural tube formation during secondary neurulation requires tightly coordinated membrane remodeling for de novo lumen formation and resolution, yet the role of autophagy in this process remains unclear. Autophagy operates through canonical and noncanonical pathways. While canonical autophagy is primarily degradative, the V-ATPase/ATG16L1-dependent Conjugation of ATG8 to Single Membranes (CASM) regulates LC3 lipidation on endocytic compartments. Using human neural tube organoids, MDCK cysts, and epithelial tube micropatterns selectively deficient in canonical or noncanonical autophagy, we demonstrate that CASM is essential for epithelial lumen resolution. Mechanistically, the V-ATPase/ATG16L1 axis coordinates junctional remodeling, phosphoinositide transitions, and Rab-dependent endocytic and recycling pathways to ensure single-lumen formation. These findings identify noncanonical autophagy as a spatially restricted membrane-remodeling mechanism that governs epithelial morphogenesis and reveal distinct, hierarchically balanced contributions of autophagy pathways during development. Here they show that, during lumenogenesis, noncanonical autophagy drives formation of a single central cavity by controlling membrane recycling, while canonical autophagy supports its growth, and provide insights into tissue development from neural tube organoids.