Endosome-phagophore linking assemblies for the degradation of membrane/extracellular proteins.

Lysosome-targeting chimeras specifically degrade membrane/extracellular proteins with the specificity and potency highly dependent on the expression pattern and kinetics of lysosome-targeting receptors. Here we describe an endosome-phagophore linking assembly (EPLA), which is constructed by attaching a specific ligand for a protein of interest (POI) to an endosome surface-anchored phagophore-targeting peptide (ES-PTP) that consists of a pH-low insertion peptide and a phagophore-binding element. EPLAs degrade proteins by binding with POIs, being internalized into endosomes, inserting endosome membrane, anchoring the phagophore-targeting moiety onto endosome surface, and then triggering the spatial proximity of endosomes to phagophores. We show the modularity and generality of the EPLA technology by degrading membrane-bound PD-L1, RAGE, GRP94, PSMA, ICAM-1, p32, VCAM-1 and LRP1, and extracellular amyloid-β and tau. Our results establish a technology platform for autophagic degradation of the membrane/extracellular POIs, which may have broad implications for biochemical research and clinical therapeutics.