Precision Mapping of Direct Membrane Protein Interactions via Binding-Induced DNA Barcode Transfer Labeling

Cell-cell communication is governed by dynamic membrane protein interactions. Precise tracking of direct protein binding and its functional outcomes across cellular engagements is essential for decoding complex biological processes. While proximity-based labeling techniques convert transient interactions into stable signals, they often fail to distinguish direct binding from nonspecific associations. In this work, we developed a binding-induced labeling strategy for 1:1 DNA barcode transfer between interacting proteins at the cellular interface. Using the PD1/PD-L1 immune checkpoint as a model, we designed functionalized aptamer probes targeting PD-L1 on cancer cells, which upon PD1/PD-L1 binding were covalently transferred to PD1 on T cells via click chemistry. By incorporating barcoded primer sequences and programmable DNA signal amplification, we achieved sensitive and sequential tracking of individual PD1/PD-L1 binding events across multiple cellular interactions. Furthermore, with the integration of single-cell transcriptional profiling, this platform revealed the progressive impact of iterative PD1/PD-L1 binding on T-cell reprogramming.