Proteomics of extracellular vesicle after SDCBP knockout
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Brain, Glioblast
DISEASE(S): Brain Glioblastoma Multiforme
SUBMITTER: 
Dae-Kyum Kim
LAB HEAD: Frederick P. Roth
PROVIDER: PXD012321 | Pride | 2019-12-02
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 20161020_SP_HUMAN_R201609.fasta | Fasta | |||
| U373V3_KO1.raw | Raw | |||
| U373V3_KO2.raw | Raw | |||
| U373V3_KO3.raw | Raw | |||
| U373V3_WT1.raw | Raw |
Items per page: 5 1 - 5 of 9 |
Publications
A reference map of the human binary protein interactome.
Luck Katja K Kim Dae-Kyum DK Lambourne Luke L Spirohn Kerstin K Begg Bridget E BE Bian Wenting W Brignall Ruth R Cafarelli Tiziana T Campos-Laborie Francisco J FJ Charloteaux Benoit B Choi Dongsic D Coté Atina G AG Daley Meaghan M Deimling Steven S Desbuleux Alice A Dricot Amélie A Gebbia Marinella M Hardy Madeleine F MF Kishore Nishka N Knapp Jennifer J JJ Kovács István A IA Lemmens Irma I Mee Miles W MW Mellor Joseph C JC Pollis Carl C Pons Carles C Richardson Aaron D AD Schlabach Sadie S Teeking Bridget B Yadav Anupama A Babor Mariana M Balcha Dawit D Basha Omer O Bowman-Colin Christian C Chin Suet-Feung SF Choi Soon Gang SG Colabella Claudia C Coppin Georges G D'Amata Cassandra C De Ridder David D De Rouck Steffi S Duran-Frigola Miquel M Ennajdaoui Hanane H Goebels Florian F Goehring Liana L Gopal Anjali A Haddad Ghazal G Hatchi Elodie E Helmy Mohamed M Jacob Yves Y Kassa Yoseph Y Landini Serena S Li Roujia R van Lieshout Natascha N MacWilliams Andrew A Markey Dylan D Paulson Joseph N JN Rangarajan Sudharshan S Rasla John J Rayhan Ashyad A Rolland Thomas T San-Miguel Adriana A Shen Yun Y Sheykhkarimli Dayag D Sheynkman Gloria M GM Simonovsky Eyal E Taşan Murat M Tejeda Alexander A Tropepe Vincent V Twizere Jean-Claude JC Wang Yang Y Weatheritt Robert J RJ Weile Jochen J Xia Yu Y Yang Xinping X Yeger-Lotem Esti E Zhong Quan Q Aloy Patrick P Bader Gary D GD De Las Rivas Javier J Gaudet Suzanne S Hao Tong T Rak Janusz J Tavernier Jan J Hill David E DE Vidal Marc M Roth Frederick P FP Calderwood Michael A MA
Nature 20200408 7803
Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships<sup>1,2</sup>. Here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'HuRI'. With approximately 53,000 protein-protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integra ...[more]
Similar Datasets
Project description:Glioblastoma multiforme (GBM) is a highly aggressive and heterogeneous form of primary brain tumors, driven by a complex repertoire of oncogenic alterations, including the constitutively active epidermal growth factor receptor (EGFRvIII). EGFRvIII impacts both cell-intrinsic and non-cell autonomous aspects of GBM progression, including cell invasion, angiogenesis and modulation of the tumor microenvoiront, this is, at least in part, attributable to the release and intercellular trafficking of extracellular vesicles (EVs), heterogeneous membrane structures containing multiple bioactive macromolecules. Here we analyzed the impact of EGFRvIII on the profile of glioma EVs using a series of isogenic tumor cell lines, in which this oncogene exhibits a strong transforming activity. Thus, we observed that EGFRvIII expression alters several properties of glioma EVs, including their output and global protein composition. Using mass spectrometry, quantitative proteomic analysis and Gene Ontology terms filters, we observed that EVs released by EGFRVIII-transformed cells were enriched for extracellular exosome and focal adhesion related proteins. Among them, we validated the association of pro-invasive proteins (CD44, BSG, CD151) with EVs of EGFRvIII expressing cells, and down-regulation of exosomal markers (CD81 and CD82) in EVs of their indolent counterparts. Nano-flow cytometry revealed that the EV output from individual glioma cell lines was highly heterogeneous, such that only a fraction of EVs contained specific proteins such as EGFR, CD9, or others. Notably, cells expressing EGFRvIII released ample EVs double positive for CD44/BSG, and these proteins also co-localized in cellular filopodia. We also detected the expression of homophilic adhesion molecules and increased homologous EV uptake by EGFRvIII-positive glioma cells. These results suggest that oncogenic EGFRvIII reprograms the proteome of GBM-related EVs, a notion with considerable implications for their biological activity and properties relevant for development of EV-based cancer biomarkers.
2018-07-30 | PXD008311 | Pride
Project description:We found that a klotho protein fragment (KL-F), administered peripherally, induced cognitive enhancement and neural resilience. Here we report a proteomic analysis of whole hippocampal homogenates from mice treated with vehicle or KL-F (10 µg/kg, i.p.) four hours prior to exploration in the small Y-maze. The proteomic results showed glutamate receptor signaling as the top enriched canonical pathway by Ingenuity Pathway Analysis.
2017-08-09 | PXD007150 | Pride
Project description:Zinc (Zn) is a major elemental component of respirable ambient particulate matter (PM) detected often at alarming levels in urban air. Exposure to PM has been widely associated with increased cardiovascular morbidity and mortality, however, it is not known what components or sources of PM are causative. We recently demonstrated that long-term episodic inhalation of combustion PM, having similar amount of Zn found in urban PM, caused myocardial lesions in rats. We further demonstrated that a single pulmonary exposure to Zn at high concentration is associated with disturbances in cardiac mitochondrial function, ion channel regulation, calcium homeostasis, and cell signaling. Therefore, in this study we investigated the role of PM-associated Zn in cardiac injury using multiple exposure scenarios. Male Wistar-Kyoto (WKY) rats of 12-14 wks age were intratracheally exposed (once per wk x 8 or16 wks) to either (1) saline (control); (2) PM having no soluble Zn; (3) combustion PM suspension containing 14.5 ug/mg water-soluble Zn at high and (4) low dose levels, (5) the aqueous fraction of this suspension devoid of solid insoluble particulate fraction (14.5 ug/mg soluble Zn), or (6) Zn sulfate. Zn concentrations were identical in groups 3, 5 and 6. Pulmonary toxicity was apparent in all exposure groups when compared to saline as determined by recovery of cells in bronchoalveolar lavage fluid. Long-term exposure to PM with or without soluble Zn, or Zn sulfate caused distinct myocardial lesions characterized by subepicardial and randomly distributed myocardial inflammation, degeneration, and fibrosis. The lesion severity was higher in those groups receiving Zn PM. Because cardiac mitochondria are likely the primary target of inhaled metal or other absorbed PM components, we analyzed mitochondrial DNA damage using QPCR and found that all exposure groups except those exposed to PM without Zn caused variable degree of damage. Aconitase activity, sensitive to inhibition by oxidative stress was inhibited slightly but significantly in rats receiving zinc sulfate. Although modest, microarray (Affymetrix) analysis revealed expression changes in the heart reflective of effects on cell signaling, inflammation/oxidative stress, mitochondrial fatty acid metabolisms and cell cycle regulation in rats exposed to zinc sulfate. However, these changes were minimal following exposure to PM devoid of soluble metals. We demonstrate that episodic subchronic pulmonary exposure to zinc sulfate causes cardiac injury and mitochondrial DNA damage. Thus, water-soluble PM-associated zinc may be one of the PM components responsible for cardiovascular morbidity. Experiment Overall Design: Group 1 received Saline to serve as a control. Group 2 received Mount St. Helenâs ash, which does not contain any water-soluble zinc or other metals such that we can delineate any cardiac effect secondary to pulmonary deposition of these particles as these fine mode particles themselves are not likely to translocate to the heart. Group 3 received whole saline suspension of the same fugitive oil combustion particle sample used in the previous study, which contained insoluble components plus water-soluble zinc (Kodavanti et al., 2003; 14.5 ug/mg zinc) and also a small amount of water-soluble nickel (3.0 µg/mg). Elemental composition of this PM is comparable to Ottawa urban PM (Kodavanti et al., 2003). Group 4 also received same particle sample but at half the dose than group 3. Group 5 received saline-soluble or leachable fraction of PM-HD devoid of any solid material but contained soluble components including zinc and nickel. And, group 6 received zinc sulfate at concentration that was present in groups 3 or 5. This design allowed us to test if cardiac injury in rats was due to leached of zinc or solid particles. There were 4 replicates per treatment group.
2008-06-14 | E-GEOD-6541 | biostudies-arrayexpress
Project description:This study presents a scalable method for isolating small extracellular vesicles (sEVs) according to MISEV (minimal information for studies of extracellular vesicles) guidelines from 4 mL of bovine plasma while achieving a high purity suitable for proteomics analysis. The protocol combines ultracentrifugation (UC), size-exclusion chromatography (SEC), and ultrafiltration (UF) to minimize contamination by lipoproteins and free proteins. The purified sEVs were characterized through transmission electron microscopy (TEM), tunable resistive pulse sensing (TRPS), dynamic light scattering (DLS), and flow cytometry (FC), assessing particle size, morphology, and the presence of membrane markers such as CD9. The purity assessed by the particle-to-protein ratio (4.8 × 10⁸ particles/µg in average) was improved (× 10) compared to the previous protocol. Mass spectrometry (LC-MS/MS) and Parallel Reaction Monitoring (PRM) identified 417 proteins, 93% of which are referenced in sEVs databases. Specific markers of sEVs have been identified including cytosolic (HSPA8, SDCBP, ACT, TUB, and GAPDH) and membrane (CD9 and CD81) Markers. Gene Ontology (GO) analysis revealed an enrichment of sEVs proteins. This study demonstrates that this sEVs enrichment protocol is well-suited for small plasma volumes. These results pave the way for future studies of biomarker research on animal health and performance.
2025-11-17 | PXD068315 | Pride
Project description:Chloroplasts contain a dedicated genome, which encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. In this work, a 19-subunit PEP complex from Sinapis alba was purified by glycerol gradient centrifugation. All known subunits of the complex could be identified by LC-MS and the structure of the complex was determined by cryo-electron microscopy.
2024-02-19 | PXD048976 | Pride
Project description:Spores are of high interest to the food and health sectors because of their extreme resistance to harsh conditions especially against heat. Earlier research has shown that spores prepared on solid agar plates have a higher heat resistance than those prepared in a liquid medium. It has also been shown that the more mature a spore is the higher is its heat resistance contributed most likely by the progressive cross-linking of coat proteins. The current study for the first time enlightens the effect of sporulation medium on spore proteins. The 14N spores prepared on solid agar medium and 15N metabolically labelled spores prepared in liquid medium differ in their coat protein composition as revealed by LC-FT-MS/MS analyses. The 14N:15N isotopic ratio of the 1:1 mixture of liquid and solid medium cultured spores exposes that most of the identified inner coat and crust proteins are significantly upregulated while most of the outer coat proteins are significantly downregulated for the spores prepared on solid medium relative to the spores prepared in the liquid medium. Medium specific differences in isotopic ratios between the tryptic peptides of expected cross-linked proteins suggest that also the coat protein cross-linking may be medium specific. The spores prepared on solid medium show a higher thermal resistance than the spores prepared in liquid medium. Since the core DPA content is found to be similar in both the spore populations, it appears that the difference in wet heat resistance is connected to the differences in the coat protein composition and assembly. Supporting the proteomic analyses, the electron microscopy analyses show a significantly thinner outer coat layer of the spores cultures on the solid medium.
2017-09-20 | PXD004473 | Pride
Project description:TAp63 is a transcription factor belonging to the p53 family with important tumor suppressive functions. We show that TAp63-/- mice exhibit an increased susceptibility to UVR-induced cutaneous squamous cell carcinoma (cuSCC). These tumors showed global disruption of miRNA and mRNA expression when compared to tumors arising in wild-type mice. A comparison to similarly sequenced human cuSCC tumors identified miR-30c-2* and miR-497 as being significantly underexpressed in cuSCC. Reintroduction of these miRNAs significantly inhibited the growth of cuSCC cell lines and xenografts. Proteomic profiling of cells transfected with either miRNA showed significant downregulation of proteins related to cell cycle progression and mitosis. A cross-platform comparison of the RNAseq and proteomics signatures identified 7 downregulated proteins, which are also frequently overexpressed in both mouse and human cuSCC. Knockdown of AURKA, KIF18B, PKMYT1, and ORC1 in cuSCC cell lines suppressed tumor cell proliferation and induced cell death. Additionally, we found that an investigational, oral, selective inhibitor of AURKA suppressed cuSCC cell growth and induced cell death, and showed anti-tumor effects in vivo. Our data establishes TAp63 as an essential regulator of miRNA expression during skin carcinogenesis and reveals a novel network of miRNAs and mRNAs, which include potential targets for therapeutic intervention.
2020-07-07 | PXD014261 | Pride
Project description:Breast cancer is the leading cause of death in women worldwide. Plasticity and heterogeneity of breast cancer cells make this disease extremely difficult to treat. Many reports point to metabolic shifts, mainly those carried out in o mitochondria, as key processes governing the behavior and heterogeneity of several types of breast cancer. In this study, we performed label-free proteomics analysis on mitochondria-enriched fractions from T47D and MDAMB-231 breast cancer cell lines, which have distinct molecular classifications, using bioinformatics analyses to identify differentially expressed proteins compared to MCF-12F healthy breast cells. Cancer cells exhibited down-regulated protein levels of subunits from the respiratory chain's Complex I. However, both presented differentially abundant proteins related to ligase and oxidoreductase activities, such as enzymes involved in glycolysis, pyruvate metabolism, the Krebs cycle, and gluconeogenesis. Many of these enzymes also participate in other metabolic processes, such as localization to the mitochondrion, mitochondrial gene expression, and the metabolism of amino acids, fatty acids, purines, and pyrimidines. Gene Set Enrichment Analysis revealed that OXPHOS enzymes play key roles in many neurodegenerative disease pathways. A protein set with little or no evidence in breast cancer was identified, which could lead to future research in breast cancer mitochondrial metabolism.
2026-04-27 | PXD069883 | Pride
Project description:Brachylophosaurus canadensis peptides from blood vessels isolated from within the bone were characterized using high resolution mass spectrometry. This allowed identification of actin, alpha and beta tubulin, various histones, myosin, and tropomyosin. Within the peptides, evidence of age (e.g., deamidation, oxidation, protein backbone cleavage) was present.
2015-11-30 | PXD001738 | Pride
Project description:Bacillus weihenstephanensis is a subspecies of the Bacillus cereus sensu lato group of spore forming bacteria known to cause food spoilage or food poisoning. The key distinguishing phenotype of B. weihenstephanensis is its ability to grow below 7°C or, from a food safety perspective, to grow and potentially produce toxins in a refrigerated environment. In order to gain insight into to the mechanistic basis of its psychrotolerant phenotype, as well as elucidate relevant aspects of its toxigenic profile, the proteome profiles of cells grown at either 6°C or 30°C were compared.
2015-12-01 | PXD002007 | Pride