Cocktail Chemical Labeling for In-Depth Surfaceome Profiling of Bone-Marrow Derived Dendritic Cells

Sun, S.; Liu, S.; Deng, T.; Hu, Y.; Yang, R.; Li, J. P.; GE, Y.

doi:10.1101/2025.03.15.643439

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bioRxiv · 10.1101/2025.03.15.643439

Cocktail Chemical Labeling for In-Depth Surfaceome Profiling of Bone-Marrow Derived Dendritic Cells

Sun, S.·Liu, S.·Deng, T.·Hu, Y.·Yang, R.·Li, J. P.·GE, Y.

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Abstract

Cell surface proteins (CSPs) are crucial identifiers for cell types and states, especially in dendritic cells (DCs). Current proteomic methods for profiling CSPs are limited by their hydrophobic nature and low abundance, which often require genetic or cell surface engineering and exhibit biased and insufficient labeling efficiency. Herein, we report [Ru(bpy)3]Cl2 (Ru) for effective biotinylation on the cell surfaceome via a simple "mix and lighten" method. The versatile photoredox pathways of Ru are leveraged using a probe cocktail of biotin-phenol and biotin-hydrazide for improved substrate coverage. The "cocktail" labeling strategy results in reproducible identification of up to 733 plasma membrane proteins on HeLa cells, and is further applied to map dynamic changes in the surfaceome during the differentiation of primary bone marrow-derived dendritic cells, which demonstrates a user-friendly and deep-surfaceome-coverage tool for profiling dynamic changes in primary cells, with potential implications for cell identities, functional states, and novel drug targets.

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Sun, S., Liu, S., Deng, T., Hu, Y., Yang, R., Li, J. P., GE, Y.. 2025-03-17. Cocktail Chemical Labeling for In-Depth Surfaceome Profiling of Bone-Marrow Derived Dendritic Cells. https://doi.org/10.1101/2025.03.15.643439

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