Aptamer-Mediated Proximity Labeling (ApMPL) for Spatially Resolved Deciphering of Cell Membrane Protein Interactomes

Cell membrane protein-protein interactions (PPIs) play pivotal roles in maintaining cellular homeostasis and physiological balance. Deciphering these interactions is crucial to understanding disease mechanisms and identifying therapeutic targets. While proximity labeling technologies have revolutionized PPI studies, existing methods face limitations including operational complexity, safety concerns, uncontrollable labeling radius, and poor membrane protein accessibility. To overcome these challenges, we developed an aptamer-mediated proximity labeling (ApMPL) system that enables radius-tunable labeling and capture of membrane protein interactomes. The ApMPL probe combines aptamer-based precision targeting, adjustable interaction radii through programmable DNA spacers, and efficient bioorthogonal capture of proximal proteins. Using tumor-associated membrane protein nucleolin as a model target, we demonstrated that this innovative approach leverages the unparalleled programmability of DNA nanotechnology to systematically map membrane PPIs with accurate spatial control. Meanwhile, different interacting proteins of nucleolin between the normal physiological state and apoptotic state could also be captured. Additionally, the versatility and adaptability of the platform have been confirmed on the PTK7 protein and the FGFR2 protein. The ApMPL platform will be valuable for discovering membrane protein interactions, elucidating critical signaling networks, and facilitating therapeutic target identification.