Spatial distribution of blood-brain barrier membrane proteins is controlled by sorting motifs and physiological signals in vivo.

The blood-brain barrier (BBB), formed by brain endothelial cells (BECs), creates a safe and homeostatic environment for proper brain function. While BECs are extraordinarily thin, their luminal and abluminal plasma membranes face markedly different environments: the blood and brain parenchyma, respectively. How BBB membrane proteins are spatially distributed between these membranes and the factors regulating their localization are not clear. Here, we establish a method for measuring polarized protein sorting at the BBB in vivo. We characterize the distribution of transporters and receptors on the luminal and abluminal plasma membranes and identify protein-intrinsic motifs that control polarized sorting. Finally, we observe a change in membrane protein distribution that aligns with circadian rhythms, revealing an under-appreciated dimension of BBB dynamics. This method can be broadly used for evaluating membrane protein landscape changes during development and disease and for choosing optimal molecular targets for BBB-crossing therapeutics.