A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos

Rosenthal, Shimon M.; Misra, Tvisha; Abdouni, Hala; Branon, Tess C; Ting, Alice Y.; Scott, Ian C.; Gingras, Anne‐Claude

doi:10.1016/j.mcpro.2021.100128

Cited by 12 publications

(6 citation statements)

References 70 publications

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“…Proteomics based on proximity-labeling strategies using biotin ligases ( e.g. , BioID, TurboID-NES) are being increasingly used in in vitro and in vivo experimental contexts and in model systems ranging from plants ( 17 , 64 , 65 , 66 ), yeast ( 67 ), zebrafish ( 68 , 69 ), Drosophila ( 70 , 71 ), Caenorhabditis elegans ( 16 , 72 ), to mouse models ( 18 , 21 , 22 , 73 ). TurboID is one of the most efficient biotin ligases that can effectively label several proteins within a 10 nm labeling radius in mammalian cells.…”

Section: Discussionmentioning

confidence: 99%

Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines

Sunna¹,

Bowen²,

Zeng³

et al. 2023

Molecular & Cellular Proteomics

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Section: Discussionmentioning

confidence: 99%

Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines

Sunna¹,

Bowen²,

Zeng³

et al. 2023

Molecular & Cellular Proteomics

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“…More work is needed to unravel the ineluctable complexity of GREM1 biology and signaling in human health and disease. We look forward to emerging reports and data that will shed "bright light" on our understanding of GREM1 biology, providing studies, for example using sensitive BioID proximity labelling methods in which the bait protein is fused to a promiscuous biotin ligase (Rosenthal et al 2021). Delineation of the BMP versus non-BMP binding functions of GREM1 is also critical.…”

Section: Discussionmentioning

confidence: 99%

“…However, care needs to be taken in interpreting data from transgenic/knockout mice using diverse CRE recombinase constructs and purported tissue-specific promotors that may lead to off-target effects (Gooding and Leedham 2020 ). Moreover, CRISPR/Cas9 techniques can be used to epitope tag GREM1 or its binding partners and allow for endogenous protein interaction studies, for example using sensitive BioID proximity labelling methods in which the bait protein is fused to a promiscuous biotin ligase (Rosenthal et al 2021 ). Delineation of the BMP versus non-BMP binding functions of GREM1 is also critical.…”

Section: Future Perspectivesmentioning

confidence: 99%

GREM1 signaling in cancer: tumor promotor and suppressor?

Gao,

Houthuijzen,

ten Dijke

et al. 2023

J. Cell Commun. Signal.

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GREMLIN1 (GREM1) is member of a family of structurally and functionally related secreted cysteine knot proteins, which act to sequester and inhibit the action of multifunctional bone morphogenetic proteins (BMPs). GREM1 binds directly to BMP dimers, thereby preventing BMP-mediated activation of BMP type I and type II receptors. Multiple reports identify the overexpression of GREM1 as a contributing factor in a broad range of cancers. Additionally, the GREM1 gene is amplified in a rare autosomal dominant inherited form of colorectal cancer. The inhibitory effects of GREM1 on BMP signaling have been linked to these tumor-promoting effects, including facilitating cancer cell stemness and the activation of cancer-associated fibroblasts. Moreover, GREM1 has been described to bind and signal to vascular endothelial growth factor receptor (VEGFR) and stimulate angiogenesis, as well as epidermal and fibroblast growth factor receptor (EGFR and FGFR) to elicit tumor-promoting effects in breast and prostate cancer, respectively. In contrast, a 2022 report revealed that GREM1 can promote an epithelial state in pancreatic cancers, thereby inhibiting pancreatic tumor growth and metastasis. In this commentary, we will review these disparate findings and attempt to provide clarity around the role of GREM1 signaling in cancer. Graphical Abstract

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“…Proteomics based on proximity-labeling strategies using biotin ligases (e.g. BioID, TurboID-NES) are being increasingly used in in vitro and in vivo experimental contexts and in model systems ranging from plants 17,[51][52][53] , yeast 54 , zebrafish 55,56 , Drosophila 57,58 , C. elegans 16,59 , to mouse models 18,21,22,60 . TurboID is one of the most efficient biotin ligases that can effectively label several proteins within a 10nm labeling radius in mammalian cells.…”

Section: Discussionmentioning

confidence: 99%

Cellular proteomic profiling using proximity labelling by TurboID-NES in microglial and neuronal cell lines

Sunna

Bowen

Zeng

et al. 2022

Preprint

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Different brain cell types play distinct roles in brain development and disease. Molecular characterization of cell-specific mechanisms using cell type-specific approaches at the protein (proteomic) level, can provide biological and therapeutic insights. Conventional approaches to investigate cell type-specific proteomes from brain are incompatible with the survival of adult murine neurons and contamination from non-target cell-types and experimental artifacts confound the data. To overcome these barriers, in vivo proteomic labeling with proximity dependent biotinylation of cytosolic proteins using TurboID with a Nuclear Export Sequence (TurboID-NES), coupled with mass spectrometry (MS) of labeled proteins, emerged as a powerful strategy to sample cell type-specific proteomes in the native state of cells without need for cellular isolation. To complement in vivo proximity labeling approaches, in vitro studies are needed to ensure that cellular proteomes using the TurboID-NES approach are representative of the whole cell proteome, and capture cellular responses to stimuli without disruption of cellular processes. To address this, we generated murine neuroblastoma (N2A) and microglial (BV2) lines stably expressing TurboID-NES to biotinylate the cellular proteome for downstream purification and analysis using MS. TurboID-NES expression and biotinylation did not significantly impact homeostatic cellular proteomes of BV2 and N2A cells, and did not affect cytokine production or mitochondrial respiration of BV2 cells under resting or lipopolysaccharide (LPS)-stimulated conditions. TurboID-NES mediated biotinylation captured 59% of BV2 and 65% of N2A proteomes under homeostatic conditions. Acute LPS treatment significantly altered microglial proteomes, but not N2A proteomes. LPS treatment induced >500 differentially expressed proteins in transduced BV2 proteomes, including an increase in canonical M1 proteins (IL1a, Irg1, Oasl1) and a decrease in canonical M2 proteins (Arg1, MGl2).

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A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos

Cited by 12 publications

References 70 publications

Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines

Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines

GREM1 signaling in cancer: tumor promotor and suppressor?

Cellular proteomic profiling using proximity labelling by TurboID-NES in microglial and neuronal cell lines

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