Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks

Müller, Marion; Gräbnitz, Fabienne; Barandun, Niculò; Shen, Yang; Wendt, Fabian; Steiner, Sebastian N.; Severin, Yannik; Vetterli, Stefan U.; Mondal, Milon; Prudent, James R.; Hofmann, Raphael; Oostrum, Marc van; Sarott, Roman C.; Nesvizhskii, Alexey I.; Carreira, Erick M.; Bode, Jeffrey W.; Snijder, Berend; Loessner, Martin J.; Oxenius, Annette; Wollscheid, Bernd

doi:10.1038/s41467-021-27280-x

Cited by 35 publications

(34 citation statements)

References 96 publications

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“…Indeed, anti-mouse (recognizing both heavy- and light-chains of anti-6xHis tag antibody) and streptavidin Western blot revealed robust biotinylation of heavy and light chains. Notably, we noticed self-biotinylation of miniSOG due to the 6xHis tag as well as crosslinking between light and heavy chain, presumably due to the proximal reaction between lysine and 2-oxo-histidine, which has been previously reported 34 . Taken together, we concluded that PDPL modifies histidine in a proximity-dependent manner.…”

Section: Resultssupporting

confidence: 69%

Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling

et al. 2022

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Enzymatic-based proximity labeling approaches based on activated esters or phenoxy radicals have been widely used for mapping subcellular proteome and protein interactors in living cells. However, activated esters are poorly reactive which leads to a wide labeling radius and phenoxy radicals generated by peroxide treatment may disturb redox-sensitive pathways. Herein, we report a photoactivation-dependent proximity labeling (PDPL) method designed by genetically attaching photosensitizer protein miniSOG to a protein of interest. Triggered by blue light and tunned by irradiation time, singlet oxygen is generated, thereafter enabling spatiotemporally-resolved aniline probe labeling of histidine residues. We demonstrate its high-fidelity through mapping of organelle-specific proteomes. Side-by-side comparison of PDPL with TurboID reveals more specific and deeper proteomic coverage by PDPL. We further apply PDPL to the disease-related transcriptional coactivator BRD4 and E3 ligase Parkin, and discover previously unknown interactors. Through over-expression screening, two unreported substrates Ssu72 and SNW1 are identified for Parkin, whose degradation processes are mediated by the ubiquitination-proteosome pathway.

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Section: Resultssupporting

confidence: 69%

Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling

et al. 2022

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“…HATRIC-LRC allows the identification of direct ligand–receptor interactions, but this technique does not provide any information about a receptor’s functional neighborhood. Proximity labeling technologies such as LUX-MS [ 45 ] have the potential to decipher such nanoscale organizations. Using proximity ligation experiments, we showed that MERTK and SCRB1 are close in space on the epithelial cell membrane.…”

Section: Discussionmentioning

confidence: 99%

Decoding Functional High-Density Lipoprotein Particle Surfaceome Interactions

Frey

Goetze

Rohrer

et al. 2022

IJMS

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High-density lipoprotein (HDL) is a mixture of complex particles mediating reverse cholesterol transport (RCT) and several cytoprotective activities. Despite its relevance for human health, many aspects of HDL-mediated lipid trafficking and cellular signaling remain elusive at the molecular level. During HDL’s journey throughout the body, its functions are mediated through interactions with cell surface receptors on different cell types. To characterize and better understand the functional interplay between HDL particles and tissue, we analyzed the surfaceome-residing receptor neighborhoods with which HDL potentially interacts. We applied a combination of chemoproteomic technologies including automated cell surface capturing (auto-CSC) and HATRIC-based ligand–receptor capturing (HATRIC-LRC) on four different cellular model systems mimicking tissues relevant for RCT. The surfaceome analysis of EA.hy926, HEPG2, foam cells, and human aortic endothelial cells (HAECs) revealed the main currently known HDL receptor scavenger receptor B1 (SCRB1), as well as 155 shared cell surface receptors representing potential HDL interaction candidates. Since vascular endothelial growth factor A (VEGF-A) was recently found as a regulatory factor of transendothelial transport of HDL, we next analyzed the VEGF-modulated surfaceome of HAEC using the auto-CSC technology. VEGF-A treatment led to the remodeling of the surfaceome of HAEC cells, including the previously reported higher surfaceome abundance of SCRB1. In total, 165 additional receptors were found on HAEC upon VEGF-A treatment representing SCRB1 co-regulated receptors potentially involved in HDL function. Using the HATRIC-LRC technology on human endothelial cells, we specifically aimed for the identification of other bona fide (co-)receptors of HDL beyond SCRB1. HATRIC-LRC enabled, next to SCRB1, the identification of the receptor tyrosine-protein kinase Mer (MERTK). Through RNA interference, we revealed its contribution to endothelial HDL binding and uptake. Furthermore, subsequent proximity ligation assays (PLAs) demonstrated the spatial vicinity of MERTK and SCRB1 on the endothelial cell surface. The data shown provide direct evidence for a complex and dynamic HDL receptome and that receptor nanoscale organization may influence binding and uptake of HDL.

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“…Dibromofluorescein (DBF) was chosen as our organic photocatalyst to trigger proximity labeling between interacting cells with high efficiency under mild conditions (∼520 nm irradiation). The light-controlled singlet oxygen generation and subsequent biotin labeling via an optimized aliphatic amine probe further enable the tagging of cell–cell interactions with high spatial precision. ,− Through spatiotemporally resolved interacting cells labeling within the T cell–immune cell synapse, PhoXCELL offers a valuable approach for the rapid detection of tumor antigen-specific T cells from primary tissue samples.…”

Section: Introductionmentioning

confidence: 99%

Antigen-Specific T Cell Detection via Photocatalytic Proximity Cell Labeling (PhoXCELL)

Liu

Luo

et al. 2022

J. Am. Chem. Soc.

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Quantitative detection and characterization of antigen-specific T cells are crucial to our understanding of immune responses as well as the development of new immunotherapies. Herein, we report a spatiotemporally resolved method for the detection and quantification of cell–cell interactions via Photocatalytic proXimity CELl Labeling (PhoXCELL). The biocompatible photosensitizer dibromofluorescein (DBF) was leveraged and optimized as a nongenetic alternative of enzymatic approaches for efficient generation of singlet oxygen upon photoirradiation (520 nm) on the cell surface, which allowed the subsequent labeling of nearby oxidized proteins with primary aliphatic amine-based probes. We demonstrated that DBF-functionalized dendritic cells (DCs) could spatiotemporally label interacting T cells in immune synapses via rapid photoirradiation with quantitatively discriminated interaction strength, which revealed distinct gene signatures for T cells that strongly interact with antigen-pulsed DCs. Furthermore, we employed PhoXCELL to simultaneously detect tumor antigen-specific CD8+ as well as CD4+ T cells from tumor-infiltrating lymphocytes and draining lymph nodes in murine tumor models, enabling PhoXCELL as a powerful platform to identify antigen-specific T cells in T cell receptor (TCR)-relevant personal immunotherapy.

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Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks

Cited by 35 publications

References 96 publications

Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling

Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling

Decoding Functional High-Density Lipoprotein Particle Surfaceome Interactions

Antigen-Specific T Cell Detection via Photocatalytic Proximity Cell Labeling (PhoXCELL)

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