EVpedia: an integrated database of high‐throughput data for systemic analyses of extracellular vesicles

Kim, Dae-Kyum; Kang, Byeongsoo; Kim, Oh Youn; Choi, Dong-Sic; Lee, Jae‐Wook; Kim, Sae Rom; Go, Gyeongyun; Yoon, Yae Jin; Kim, Ji Hyun; Jang, Su Chul; Park, Kyong Su; Choi, Eun Jeong; Kim, Kwang Pyo; Desiderio, Dominic M.; Kim, Yoon Keun; Lötvall, Jan; Hwang, Daehee; Gho, Yong Song

doi:10.3402/jev.v2i0.20384

Cited by 444 publications

(353 citation statements)

References 23 publications

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“…Therefore, the subpopulation of CD9-single positive sEVs probably forms at the PM and early endocytic locations. described in sEVs (i.e., 100K pellets) secreted by mouse DCs (20) and other cells (21,22), and listed by us as components of "canonical exosomes" (23), but our results now show that only a restricted subset of these proteins represent sEV-specific markers, among which a subfraction is associated to tetraspaninenriched EVs corresponding to endosome-derived exosomes.…”

Section: Separation Of Sev Subtypes By Immuno-isolation With Antitetrmentioning

confidence: 65%

Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes

Kowal

Arras

Colombo

et al. 2016

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

2,773

188

2,965

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Extracellular vesicles (EVs) have become the focus of rising interest because of their numerous functions in physiology and pathology. Cells release heterogeneous vesicles of different sizes and intracellular origins, including small EVs formed inside endosomal compartments (i.e., exosomes) and EVs of various sizes budding from the plasma membrane. Specific markers for the analysis and isolation of different EV populations are missing, imposing important limitations to understanding EV functions. Here, EVs from human dendritic cells were first separated by their sedimentation speed, and then either by their behavior upon upward floatation into iodixanol gradients or by immuno-isolation. Extensive quantitative proteomic analysis allowing comparison of the isolated populations showed that several classically used exosome markers, like major histocompatibility complex, flotillin, and heatshock 70-kDa proteins, are similarly present in all EVs. We identified proteins specifically enriched in small EVs, and define a set of five protein categories displaying different relative abundance in distinct EV populations. We demonstrate the presence of exosomal and nonexosomal subpopulations within small EVs, and propose their differential separation by immuno-isolation using either CD63, CD81, or CD9. Our work thus provides guidelines to define subtypes of EVs for future functional studies.exosomes | microvesicles | ectosomes | dendritic cells | extracellular vesicles

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Section: Separation Of Sev Subtypes By Immuno-isolation With Antitetrmentioning

confidence: 65%

Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes

Kowal

Arras

Colombo

et al. 2016

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

2,773

188

2,965

View full text Add to dashboard Cite

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“…Our previous work has shown that E. coliderived EVs induce systemic inflammation mimicking sepsis after entering the bloodstream (10) and that EVs from indoor dust and also from Staphylococcus aureus can induce neutrophilic pulmonary inflammation (11,12). In the current study, we hypothesized that EVs from Gram-negative bacteria, especially E. coli, are an important cause of neutrophilic inflammation and thereby emphysema in the lung.…”

mentioning

confidence: 87%

Extracellular Vesicles Derived from Gram-Negative Bacteria, such asEscherichia coli, Induce Emphysema Mainly via IL-17A–Mediated Neutrophilic Inflammation

Kim

Lee

Choi

et al. 2015

The Journal of Immunology

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Recent evidence indicates that Gram-negative bacteria–derived extracellular vesicles (EVs) in indoor dust can evoke neutrophilic pulmonary inflammation, which is a key pathology of chronic obstructive pulmonary disease (COPD). Escherichia coli is a ubiquitous bacterium present in indoor dust and secretes nanometer-sized vesicles into the extracellular milieu. In the current study, we evaluated the role of E. coli–derived EVs on the development of COPD, such as emphysema. E. coli EVs were prepared by sequential ultrafiltration and ultracentrifugation. COPD phenotypes and immune responses were evaluated in C57BL/6 wild-type (WT), IFN-γ–deficient, or IL-17A–deficient mice after airway exposure to E. coli EVs. The present study showed that indoor dust from a bed mattress harbors E. coli EVs. Airway exposure to E. coli EVs increased the production of proinflammatory cytokines, such as TNF-α and IL-6. In addition, the repeated inhalation of E. coli EVs for 4 wk induced neutrophilic inflammation and emphysema, which are associated with enhanced elastase activity. Emphysema and elastase activity enhanced by E. coli EVs were reversed by the absence of IFN-γ or IL-17A genes. In addition, during the early period, lung inflammation is dependent on IL-17A and TNF-α, but not on IFN-γ, and also on TLR4. Moreover, the production of IFN-γ is eliminated by the absence of IL-17A, whereas IL-17A production is not abolished by IFN-γ absence. Taken together, the present data suggest that E. coli–derived EVs induce IL-17A–dependent neutrophilic inflammation and thereby emphysema, possibly via upregulation of elastase activity.

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“…Lipid raft-associated proteins such as transferrin and caveolins, and other proteins involved in membrane trafficking, like the tetraspanins CD9, CD63, and CD81, which have been shown to bind to ESCRT machinery, are also enriched in exosomes [32][33][34]. There are now several databases that exist that list the assortment of materials that can be found in exosomes (Vesiclepedia, EVPedia, and Exocarta) [7,35,36].…”

Section: Exosome Biogenesismentioning

confidence: 99%

Exosomes in Viral Disease

2016

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Viruses have evolved many mechanisms by which to evade and subvert the immune system to ensure survival and persistence. However, for each method undertaken by the immune system for pathogen removal, there is a counteracting mechanism utilized by pathogens. The new and emerging role of microvesicles in immune intercellular communication and function is no different. Viruses across many different families have evolved to insert viral components in exosomes, a subtype of microvesicle, with many varying downstream effects. When assessed cumulatively, viral antigens in exosomes increase persistence through cloaking viral genomes, decoying the immune system, and even by increasing viral infection in uninfected cells. Exosomes therefore represent a source of viral antigen that can be used as a biomarker for disease and targeted for therapy in the control and eradication of these disorders. With the rise in the persistence of new and reemerging viruses like Ebola and Zika, exploring the role of exosomes become more important than ever.

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EVpedia: an integrated database of high‐throughput data for systemic analyses of extracellular vesicles

Cited by 444 publications

References 23 publications

Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes

Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes

Extracellular Vesicles Derived from Gram-Negative Bacteria, such asEscherichia coli, Induce Emphysema Mainly via IL-17A–Mediated Neutrophilic Inflammation

Exosomes in Viral Disease

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