Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR

Verdaguer, Mireia Pérez; Zhang, Tian; Surve, Sachin; Paulo, João A.; Wallace, Callen T.; Watkins, Simon C.; Gygi, Steven P.; Sorkin, Alexander

doi:10.1016/j.celrep.2022.110950

Cited by 20 publications

(25 citation statements)

References 44 publications

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“…Alternatively, TFG may possess additional roles in endolysosomal protein trafficking that contribute to lysosome activity. Indeed, recent studies using immortalized cell lines suggest that TFG accumulates transiently with a subset of early endosomes that harbor the ESCRT-0 subunit Hrs following exposure to Wnt3a or epidermal growth factor (EGF) to regulate downstream signal transduction pathways ( 85 , 86 ). The mechanisms by which TFG contributes to Wnt and EGF signaling remain unclear, and further studies will be necessary to determine whether TFG functions analogously in neuronal cells.…”

Section: Discussionmentioning

confidence: 99%

TFG regulates secretory and endosomal sorting pathways in neurons to promote their activity and maintenance

Peotter

Pustova

Lettman

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Molecular pathways that intrinsically regulate neuronal maintenance are poorly understood, but rare pathogenic mutations that underlie neurodegenerative disease can offer important insights into the mechanisms that facilitate lifelong neuronal function. Here, we leverage a rat model to demonstrate directly that the TFG p.R106C variant implicated previously in complicated forms of hereditary spastic paraplegia (HSP) underlies progressive spastic paraparesis with accompanying ventriculomegaly and thinning of the corpus callosum, consistent with disease phenotypes identified in adolescent patients. Analyses of primary cortical neurons obtained from CRISPR-Cas9–edited animals reveal a kinetic delay in biosynthetic secretory protein transport from the endoplasmic reticulum (ER), in agreement with prior induced pluripotent stem cell–based studies. Moreover, we identify an unexpected role for TFG in the trafficking of Rab4A-positive recycling endosomes specifically within axons and dendrites. Impaired TFG function compromises the transport of at least a subset of endosomal cargoes, which we show results in down-regulated inhibitory receptor signaling that may contribute to excitation-inhibition imbalances. In contrast, the morphology and trafficking of other organelles, including mitochondria and lysosomes, are unaffected by the TFG p.R106C mutation. Our findings demonstrate a multifaceted role for TFG in secretory and endosomal protein sorting that is unique to cells of the central nervous system and highlight the importance of these pathways to maintenance of corticospinal tract motor neurons.

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Section: Discussionmentioning

confidence: 99%

TFG regulates secretory and endosomal sorting pathways in neurons to promote their activity and maintenance

Peotter

Pustova

Lettman

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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“…Based on the high labeling efficiency of APEX, the spatiotemporal-resolved EGFR interactome has been systematically analyzed. A novel protein TFG that regulates EGFR endosomal sorting has been identified [ 116 ]. We have systematically studied the PTK7 spatial interactome and found that its mechanism in drug resistance is related to NDRG1 [ 117 ].…”

Section: Potential Strategies In Kinase Spatial Assaymentioning

confidence: 99%

Mapping the Protein Kinome: Current Strategy and Future Direction

Hou

Liu²

2023

Cells

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The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.

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“…The ideal platform should meet the following three requirements: (1) rapid and specific response to H 2 O 2 ; (2) conversion of H 2 O 2 signals into proximity covalent labeling; and (3) broad applicability to a variety of cell types. Inspired by the boom in proximity labeling (PL) technologies, − we believe that peroxidase is the perfect tool to meet the first two requirements. Peroxidase-dependent proximity labeling technology converts tyramine derivatives into phenoxy radicals with very short lifetimes (<1 ms) and small diffusion radius (<20 nm) in the presence of H 2 O 2 , allowing the labeling of amino acids (e.g., tyrosine, tryptophan, etc.)…”

Section: Introductionmentioning

confidence: 99%

“…Peroxidase-dependent proximity labeling technology converts tyramine derivatives into phenoxy radicals with very short lifetimes (<1 ms) and small diffusion radius (<20 nm) in the presence of H 2 O 2 , allowing the labeling of amino acids (e.g., tyrosine, tryptophan, etc.) adjacent to the enzyme anchor site. − In combination with quantitative proteomics, this technique has become a powerful tool for dissecting the interaction networks in dynamic biological processes. − Recently, peroxidase (APEX2 or APEX) has been expressed intracellularly to detect endogenous H 2 O 2 and to identify the targets of H 2 O 2 oxidation by proximity labeling . To meet the third requirement, peroxidase can be mounted to the glycocalyx on the cell surface.…”

Section: Introductionmentioning

confidence: 99%

Interception Proximity Labeling for Interrogating Cell Efflux Microenvironment

Wang,

Li,

Guo

et al. 2023

Anal. Chem.

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The difficulty in elucidating the microenvironment of extracellular H2O2 efflux has led to the lack of a critical extracellular link in studies of the mechanisms of redox signaling pathways. Herein, we mounted horseradish peroxidase (HRP) to glycans expressed globally on the living cell surface and constructed an interception proximity labeling (IPL) platform for H2O2 efflux. The release of endogenous H2O2 is used as a “physiological switch” for HRP to enable proximity labeling. Using this platform, we visualize the oxidative stress state of tumor cells under the condition of nutrient withdrawal, as well as that of macrophages exposed to nonparticulate stimuli. Furthermore, in combination with a proteomics technique, we identify candidate proteins at the invasion interface between fungal mimics (zymosan) and macrophages by interception labeling of locally accumulated H2O2 and confirm that Toll-like receptor 2 binds zymosan in a glycan-dependent manner. The IPL platform has great potential to elucidate the mechanisms underlying biological processes involving redox pathways.

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Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR

Cited by 20 publications

References 44 publications

TFG regulates secretory and endosomal sorting pathways in neurons to promote their activity and maintenance

TFG regulates secretory and endosomal sorting pathways in neurons to promote their activity and maintenance

Mapping the Protein Kinome: Current Strategy and Future Direction

Interception Proximity Labeling for Interrogating Cell Efflux Microenvironment

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