Proteomics, transcriptomics and lipidomics of exosomes and ectosomes

Choi, Dong-Sic; Kim, Dae-Kyum; Kim, Eui Chong; Gho, Yong Song

doi:10.1002/pmic.201200329

Cited by 455 publications

(419 citation statements)

References 150 publications

(314 reference statements)

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“…There are many published proteome studies on extracellular vesicles, including MP and exsosomes from cancer cells, isolated blood cells, urine, ascites, and plasma (42). We are aware of only four studies on human circulating plasma MP (5,8,18,29).…”

Section: Discussionmentioning

confidence: 99%

Robust Label-free, Quantitative Profiling of Circulating Plasma Microparticle (MP) Associated Proteins

Braga-Lagache

Buchs

Iacovache

et al. 2016

Molecular & Cellular Proteomics

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Cells of the vascular system release spherical vesicles, called microparticles, in the size range of 0.1-1 m induced by a variety of stress factors resulting in variable concentrations between health and disease. Furthermore, microparticles have intercellular communication/signaling properties and interfere with inflammation and coagulation pathways. Today's most used analytical technology for microparticle characterization, flow cytometry, is lacking sensitivity and specificity, which might have led to the publication of contradicting results in the past.We propose the use of nano-liquid chromatography two-stage mass spectrometry as a nonbiased tool for quantitative MP proteome analysis.For this, we developed an improved microparticle isolation protocol and quantified the microparticle protein composition of twelve healthy volunteers with a labelfree, data-dependent and independent proteomics approach on a quadrupole orbitrap instrument.Using aliquots of 250 l platelet-free plasma from one individual donor, we achieved excellent reproducibility with an interassay coefficient of variation of 2.7 ؎ 1.7% (mean ؎ 1 standard deviation) on individual peptide intensities across 27 acquisitions performed over a period of 3.5 months. We show that the microparticle proteome between twelve healthy volunteers were remarkably similar, and that it is clearly distinguishable from whole cell and platelet lysates. We propose the use of the proteome profile shown in this work as a quality criterion for microparticle purity in proteomics studies. Furthermore, one freeze thaw cycle damaged the microparticle integrity, articulated by a loss of cytoplasm proteins, encompassing a specific set of proteins involved in regulating dynamic structures of the cytoskeleton, and thrombin activation leading to MP clotting. On the other hand, plasma membrane protein composition was unaffected. Finally, we show that multiplexed data-independent acquisition can be used for relative quantification of target proteins using Skyline software. Mass spectrometry data are available via ProteomeXchange (identifier PXD003935) and panoramaweb.org (https://panoramaweb.org/labkey/

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Section: Discussionmentioning

confidence: 99%

Robust Label-free, Quantitative Profiling of Circulating Plasma Microparticle (MP) Associated Proteins

Braga-Lagache

Buchs

Iacovache

et al. 2016

Molecular & Cellular Proteomics

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“…microdomains, but also refl ect those occurring in intracellular vesicles, such as multivesicular bodies including sphingolipid-rich membranes (23)(24)(25).…”

Section: Preparation Of Detergent-resistant Scmsmentioning

confidence: 99%

Analysis of lipid-composition changes in plasma membrane microdomains

Ogiso

Taniguchi

Okazaki

2015

Journal of Lipid Research

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This article is available online at http://www.jlr.org and cholesterol (Chol) ( 1-5 ). These sphingolipid-rich microdomains are considered to be important sites for signal transduction and death receptor functions ( 6, 7 ). Depending on the local microenvironment, certain membrane proteins are preferentially localized inside (or outside) of the microdomains and serve as signaling platforms (8)(9)(10)(11)(12)(13)(14)(15)(16)(17). Recent data has indicated that membrane microdomains are dynamic nanometer-sized domains ( 18,19 ). Results from image analysis and single-molecule tracking studies have shown that these metastable membrane assemblies can be stabilized locally by lipid-lipid and lipidprotein interactions to coalesce and form functional domains and facilitate cell surface receptor signal transduction. A commonly held view is that microdomains regulate membrane protein functions by recruiting signaling molecules to the spatially limited region ( 7,20,21 ).Tight interactions between Chol and SM result in the formation of domains that are resistant to solubilization with detergents ( 22 ). This property is often used to prepare membrane microdomains. The typical preparation method involves the treatment of postnuclear lysates, generated by the removal of nuclei from cell lysates, with a nonionic detergent at low temperature, followed by separation of the low-density lipid fraction in a sucrose gradient ( 1 ). However, this fraction may contain a broad range of detergent-resistant membranes other than plasma membrane microdomains. Therefore, concerns have been raised that results obtained using this conventional method are not limited to events occurring on plasma membrane Membrane microdomains, including caveolae or lipid rafts, are plasma membrane domains that contain enhanced levels of sphingolipids, saturated fatty-acyl glycerophospholipids,

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“…Cell membranes and cell membrane derived vesicles are an increasing field of interest, considering studies of composition, morphology, and membrane interactions for the better understanding of physiological and pathological processes and therapeutic possibilities [1][2][3][4]. Because of the complex and variable composition of biological membranes, they are often substituted with model membranes for primal investigations.…”

Section: Introductionmentioning

confidence: 99%

Physicochemical characterization of artificial nanoerythrosomes derived from erythrocyte ghost membranes

Deák

Mihály

Szigyártó

et al. 2015

Colloids and Surfaces B: Biointerfaces

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Colloidal stabile nanoerythrosomes with 200 nm average diameter were formed from hemoglobin-free erythrocyte ghost membrane via sonication and membrane extrusion. The incorporation of extra lipid (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC), added to the sonicated ghosts, caused significant changes in the thermotropic character of the original membranes. As a result of the increased DPPC ratio the chain melting of the hydrated DPPC system and the characteristic small angle X-ray scattering (SAXS) of the lipid bilayers appeared. Significant morphological changes were followed by transmission electron microscopy combined with freeze fracture method (FF-TEM). After the ultrasonic treatment the large entities of erythrocyte ghosts transformed into nearly spherical nanoerythrosomes with diameters between 100-300 nm and at the same time a great number of 10-30 nm large membrane proteins or protein clusters were dispersed in the aqueous medium. The infrared spectroscopy (FT-IR) pointed out, that the sonication did not cause changes in the secondary structures of the membrane proteins under our preparation conditions. About fivefold of extra lipid -compared to the lipid content of the original membrane -caused homogeneous dispersion of nanoerythrosomes however the shape of the vesicles was not uniform. After the addition of about tenfold of DPPC, monoform and monodisperse nanoerythrosomes became typical. The outer surfaces of these roughly spherical objects were frequently polygonal, consisting of a net of pentagons and hexagons..

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Proteomics, transcriptomics and lipidomics of exosomes and ectosomes

Cited by 455 publications

References 150 publications

Robust Label-free, Quantitative Profiling of Circulating Plasma Microparticle (MP) Associated Proteins

Robust Label-free, Quantitative Profiling of Circulating Plasma Microparticle (MP) Associated Proteins

Analysis of lipid-composition changes in plasma membrane microdomains

Physicochemical characterization of artificial nanoerythrosomes derived from erythrocyte ghost membranes

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