CNPY4 is a Lipid-Binding Regulator of Sphingolipid Homeostasis

Sphingolipids function both as signaling molecules and as organizers of cell membranes, and their dysregulation has been linked to cancer, metabolic disorders, and neurodegeneration. A central node in the sphingolipid metabolism network is ceramide, which is converted into numerous derivatives, including sphingomyelin (SM). Through interactions with cholesterol, SM forms liquid-ordered microdomains that influence membrane organization and signaling. Previously, we reported that the Saposin-like (SAPLIP) protein Canopy4 (CNPY4) negatively regulates the levels of free cholesterol in the plasma membrane. Although SAPLIPs commonly regulate lipid metabolism through direct lipid interactions, CNPY4 does not bind cholesterol directly. Here, we show that CNPY4 interacts with multiple sphingolipids in vitro, including ceramide and SM, and with ceramide in cells. We also demonstrate that CNPY4 knockdown elevates SM levels at the plasma membrane and disrupts cellular localization and abundance of ceramide, suggesting that the levels and consequently the homeostatic distribution of these sphingolipids is under control of CNPY4. Although the most pronounced effect of CNPY4 loss is on the ceramide/SM conversion pathway, it additionally impacts the levels of over 150 cellular lipids and modulates neutral sphingomyelinase activity, consistent with secondary disruptions in sphingolipid homeostasis. Collectively, our findings point to CNPY4 as a sphingolipid chaperone that regulates the abundance and localization of these lipids, modulating in turn cholesterol homeostasis and cellular signaling.