Phospholipid‐flippase chaperone CDC50A is required for synapse maintenance by regulating phosphatidylserine exposure

Synaptic refinement is a critical physiological process that removes excess synapses to establish and maintain functional neuronal circuits. Recent studies have shown that focal exposure of phosphatidylserine (PS) on synapses acts as an “eat me” signal to mediate synaptic pruning. However, the molecular mechanism underlying PS externalization at synapses remains elusive. Here, we find that murine CDC50A, a chaperone of phospholipid flippases, localizes to synapses, and that its expression depends on neuronal activity. Cdc50a knockdown leads to phosphatidylserine exposure at synapses and subsequent erroneous synapse removal by microglia partly via the GPR56 pathway. Taken together, our data support that CDC50A safeguards synapse maintenance by regulating focal phosphatidylserine exposure at synapses. Synopsis CDC50A, a chaperone of phospholipid flippases, plays an important role in the maintenance of synapses. Cdc50a knockdown causes phosphatidylserine exposure at synapse and subsequent synaptic removal by microglia. CDC50A is present at synapses and its expression is regulated by neuronal activity CDC50A knockdown leads to PS exposure at synapses CDC50A knockdown induces aberrant synaptic elimination by microglia Microglial GPR56 in part mediates CDC50A knockdown‐induced synaptic removal Graphical Abstract Neuronal activity‐dependent downregulation of CDC50A leads to phosphatidylserine exposure and aberrant synaptic removal by microglia.