Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

TurboID-EV: a proximity-labeling proteomic approach to dissect the uptake mechanism of extracellular vesicles

ABSTRACT: Extracellular vesicles (EVs), including exosomes, have been recognized as key mediators of intercellular communications through donor EV and recipient cell interaction. Until now, most studies have focused on the development of analytical tools to separate EVs and their applications for molecular profiling of EV cargo. However, we lack a complete picture of the mechanism of uptake of EVs by recipient cells. Here, we developed the TurboID-EV system with the engineered biotin ligase, TurboID, tethered to the EV membrane, which allowed us to track the footprints of EVs during and after EV uptake by proximity-dependent biotinylation of recipient cellular proteins. To enrich and analyze biotinylated recipient proteins from low amounts of input cells (corresponding to ~10 µg proteins), we developed an integrated proteomic workflow that combined SILAC labeling, fluorescence-activated cell sorting, spintip-based streptavidin affinity purification, and mass spectrometry. Using the method, we successfully identified 456 biotinylated recipient proteins, including not only well-known proteins involved in endocytosis and macropinocytosis but also previously unappreciated membrane-associated proteins such as DSP and JUP. The TurboID-EV system should be readily applicable to various EV subtypes and recipient cell types, providing a promising tool to dissect the specificity of EV uptake mechanisms on a proteome-wide scale.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Yasushi Ishihama

PROVIDER: PXD040569 | JPOST Repository | Mon Aug 21 00:00:00 BST 2023

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	211119YL_HS_10_T1.raw	Raw
	211119YL_HS_11_T2.raw	Raw
	211119YL_HS_12_T3.raw	Raw
	211119YL_HS_13_T4.raw	Raw
	211119YL_HS_14_T5.raw	Raw

Items per page:

1 - 5 of 20

Similar Datasets

Proteomic signatures of extracellular vesicles secreted by non-mineralizing and mineralizing human osteoblasts and stimulation of tumor cell growth

Project description:Beyond forming bone, osteoblasts play pivotal roles in various biological processes, including hematopoiesis and bone metastasis. Extracellular vesicles (EVs) have recently been implicated in intercellular communication via transfer of proteins and nucleic acids between cells. Here, we focused on the proteomic characterization of non-mineralizing (NMOBs) and mineralizing (MOBs) human osteoblast (SV-HFOs) EVs and investigated their effect on human prostate cancer (PC3) cells by microscopic, proteomic and gene expression analyses. Proteomic analysis showed that 97% of the proteins were shared among NMOB and MOB EVs, and 30% were novel osteoblast-specific EV proteins. Label-free quantification demonstrated mineralization stage-dependent five-fold enrichment of 59 and 451 EV proteins in NMOBs and MOBs, respectively. Interestingly, bioinformatic analyses of the osteoblast EV proteomes and EV-regulated prostate cancer gene expression profiles showed that they converged on pathways involved in cell survival and growth. This was verified by in vitro proliferation assays where osteoblast EV uptake led to two-fold increase in PC3 cell growth compared to cell-free culture medium-derived vesicle controls. Our findings elucidate the mineralization stage-specific protein content of osteoblast-secreted EVs, show a novel way by which osteoblasts communicate with prostate cancer, and open up innovative avenues for therapeutic intervention. PC3 cells were treated with extracellular vesicles from non-mineralizing and mineralizing SV-HFOs for three different incubation times (4hrs, 24hrs, 48hr)

2014-10-28 | E-GEOD-56172 | biostudies-arrayexpress

Proteomic signatures of extracellular vesicles secreted by non-mineralizing and mineralizing human osteoblasts and stimulation of tumor cell growth

2014-10-28 | GSE56172 | GEO

Novel Mouse Model for Tissue-specific Extracellular Vesicle Isolation and Characterization

Project description:Extracellular vesicles (EVs) are key mediators of intercellular communication, with important roles in numerous physiological and pathological processes, including profound effects on bone metabolism. These small membrane-bound vesicles are produced and released in the extracellular environment by virtually all cell types, including cells in the osteogenic lineage such as bone marrow-derived mesenchymal stem cells (MSCs), osteoblasts, osteoclasts and osteocytes. EVs serve as potent carriers of bioactive molecules, such as nucleic acids, proteins, lipids and metabolites, where they can influence recipient cells through fusion with target cell membranes to deliver these functional biomolecules. However, once released, the source cell of the EV is difficult to ascertain with any certainty. To overcome this obstacle, we developed a conditional (e.g. Cre-mediated) mouse model that expresses an EV tag, containing a fusion of CD81 and multiple C-terminal tags, termed the “Snorkel-tag”. By crossing with a Cre of interest, representing a specific cell-type or tissue, the specific EV subpopulations that are released can be isolated using antibody affinity columns. We crossed the CAGS-Snorkel mouse with Prx1- and Ocn-Cre, representing cell-types in the early vs late stages of osteoblast differentiation, isolated EVs from bone marrow plasma, and treated mouse bone marrow stromal cells (mBMSCs) with Prx1-EVs, Ocn-EVs or All-EVs (isolated using a Pan EV Isolation Kit [Miltenyi Biotec]) for 3 days and performed bulk RNA-sequencing. We found unique transcriptional and pathway signatures elicited by the different EV subpopulations in the mBMSCs, suggesting that EVs from diverse sources have distinct biological activities.

2024-11-06 | GSE256087 | GEO

Crosstalk between the effects of extracellular vesicles (Evs) and TNF on U937 human monocyte cell line

Project description:Under physiological conditions, extracellular vesicles (EVs) are present simultaneously in the extracellular compartment together with cytokines. Thus, we hypothesized that EVs in combination with cytokines induce different responses of monocyte cells compared to EVs or cytokines alone. Human monocyte U937 cells were incubated with EV-containing or EV-free CCRF human T-cell supernatant, with or without the addition of TNF. U937 cells cultured in EV-free supernatant, supernatant containing CCRF t-cell derived EVs, TNF or both. Each treatment option was measured in 3 replicates.

2013-06-19 | E-GEOD-47897 | biostudies-arrayexpress

The ESCRT-III protein CHMP1A mediates secretion of sonic hedgehog on a novel class of extracellular vesicles

Project description:Extracellular vesicles (EVs) enable cell-to-cell communication in the nervous system essential for development and adult function. Endosomal Sorting Complex Required for Transport (ESCRT) complex proteins regulate EV formation and release. Recent work shows loss of function (LOF) mutations in, CHMP1A, which encodes one ESCRT-III member, cause autosomal recessive microcephaly with pontocerebellar hypoplasia in humans (Mochida et al., 2012). Here we show CHMP1A is required for maintenance of progenitors in human cerebral organoids and that mouse Chmp1a is required for progenitor proliferation in cortex and cerebellum and specifically for sonic hedgehog (SHH) mediated proliferation through SHH secretion. CHMP1A mutation reduces intraluminal vesicle (ILV) formation in multivesicular bodies (MVBs), and EV release. SHH protein is present on a subset of EVs marked by a unique set of proteins we call ART-EVs. CHMP1A’s requirement in formation of ART-EVs and other EVs provides a model to elucidate EV functions in multiple brain processes.

2018-06-16 | GSE115867 | GEO

Novel Mouse Model for Tissue-specific Extracellular Vesicle Isolation and Characterization

Project description:Extracellular vesicles (EVs) are key mediators of intercellular communication, with important roles in numerous physiological and pathological processes, including profound effects on bone metabolism. These small membrane-bound vesicles are produced and released in the extracellular environment by virtually all cell types, including cells in the osteogenic lineage such as bone marrow-derived mesenchymal stem cells (MSCs), osteoblasts, osteoclasts and osteocytes. EVs serve as potent carriers of bioactive molecules, such as nucleic acids, proteins, lipids and metabolites, where they can influence recipient cells through fusion with target cell membranes to deliver these functional biomolecules. However, once released, the source cell of the EV is difficult to ascertain with any certainty. To overcome this obstacle, we developed a conditional (e.g. Cre-mediated) mouse model that expresses an EV tag, containing a fusion of CD81 and multiple C-terminal tags, termed the “Snorkel-tag”. By crossing with a Cre of interest, representing a specific cell-type or tissue, the specific EV subpopulation that is released can be isolated using antibody affinity columns. We crossed the CAGS-Snorkel mouse with Prx1-Cre and Ocn-Cre, representing cell-types in the early vs late stages of osteoblast differentiation. Isolation of Prx1-EVs and Ocn-EVs was performed from the mouse bone marrow plasma. We performed miRNA-sequencing to determine the specific miRNA cargo in these different EV subpopulations and found miRNAs involved in bone metabolism and function to be expressed, some of which are enriched in the Ocn-EVs. In summary, the CAGS-Snorkel mouse model will be useful in the characterization of EVs from diverse cell- and tissue-types in the mouse.

2024-11-06 | GSE255901 | GEO

Defining extracellular vesicle release, uptake, and function in wound healing

Project description:Small extracellular vesicles (EVs) are released by cells and deliver biologically active payloads important in the intercellular signaling that coordinates the response of multiple cell types in cutaneous wound healing. Here we focus on the use of EV reporters to address cell type specificity and central questions regarding EV source cells, target cells, heterogeneity, payload, and activity using a combination of molecular approaches to address some of the barriers to translation in the use of engineered EVs. We identify a role for EVs released by resident macrophages present in adipose tissue and dermis to stimulate proliferation of overlying basal layer of keratinocytes. For these studies we use an allograft model, where donor EVs are harvested from subcutaneous implants, then purified for transplantation into the wound bed of recipient mice with a defined impaired wound healing phenotype. We demonstrate that EVs isolated from diabetic obese mice decreased keratinocyte proliferation and delayed wound closure, and that EVs loaded with specific miRNAs like miR-425-5p increased proliferation and accelerated wound closure. Utilizing a CD9-GFP reporter system, we show that fibroblasts uptake macrophage-derived EVs. In this work, we show that cell type-specific approaches can be used to unravel the biochemical activity of EVs in the complex microenvironment of the wound bed and form the basis for developing targeted pro-reparative EV payloads.

2024-02-16 | GSE242497 | GEO

Defining the activity of pro-reparative extracellular vesicles in wound healing based on miRNA payloads and cell type-specific lineage mapping

2024-02-16 | GSE242496 | GEO

Extracellular vesicles from neural stem cells transfer IFN-? via Ifngr1 to activate Stat1 signalling in target cells

Project description:The idea that stem cell therapies work only via cell replacement is challenged by the observation of consistent intercellular molecule exchange between the graft and the host. Here we defined a mechanism of cellular signaling by which neural stem/precursor cells (NPCs) communicate with the microenvironment via extracellular vesicles (EVs), and we elucidated its molecular signature and function. We observed cytokine-regulated pathways that sort proteins and mRNAs into EVs. We described induction of interferon gamma (IFN-?) pathway in NPCs exposed to proinflammatory cytokines that is mirrored in EVs. We showed that IFN-? bound to EVs through Ifngr1 activates Stat1 in target cells. Finally, we demonstrated that endogenous Stat1 and Ifngr1 in target cells are indispensable to sustain the activation of Stat1 signaling by EV-associated IFN-?/Ifngr1 complexes. Our study identifies a mechanism of cellular signaling regulated by EV-associated IFN-?/Ifngr1 complexes, which grafted stem cells may use to communicate with the host immune system. polyA RNA profiling of Neural Stem/Progenitor cells (NPCs) cultured in basal/Th1/Th2 conditions, of Exosomes derived from NPCs cultured in basal/Th1/Th2 conditions and of EVs derived from NPCs cultured in Basal/Th1/Th2 conditions. Total RNA was purified using Trizol. Purity and integrity were confirmed by BioAnalyser (Agilent). Paired End library construction and poly-A selection were performed by EASIH (The Eastern Sequence and Informatics Hub, University of Cambridge, Cambridge) according to the Illumina standard protocol. Sequencing was performed by EASIH using Illumina GAII.

2014-09-22 | E-GEOD-33527 | biostudies-arrayexpress

A reductionist approach using primary and metastatic cell-derived extracellular vesicles reveals hub proteins associated with oral cancer prognosis

Project description:Oral squamous cell carcinoma (OSCC) has high mortality rates that are largely associated with lymph node metastasis. However, the molecular mechanisms that drive OSCC metastasis are unknown. Extracellular vesicles (EVs) are membrane-bound particles that play a role in intercellular communication and impact cancer development and progression. Thus, profiling EVs would be of great significance to decipher the role of EV cargo in OSCC metastasis. For that purpose, we used a reductionist approach to map the proteomic, miRNA, metabolomic, and lipidomic profiles of extracellular vesicles (EVs) derived from human primary tumor (SCC-9) cells and matched lymph node metastases (LN1) cells. Distinct omics profiles were associated with the metastatic phenotype, including 670 proteins, 217 miRNAs, 26 metabolites, and 64 lipids differentially abundant between LN1- and SCC-9-derived EVs. A multi-omics integration identified 11 ‘hub proteins’ significantly decreased at the metastatic site compared to primary tumor-derived EVs. We confirmed the validity of these findings with analysis of data from multiple public databases, and found that low abundance of seven hub proteins in metastatic EVs is correlated with reduced survival and tumor aggressiveness in cancer patients. In summary, this multi-omics approach identified proteins transported by EVs that are associated with metastasis, and which may potentially serve as prognostic markers in OSCC.

2021-04-26 | ST001755 | MetabolomicsWorkbench

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data