EVpedia: a community web portal for extracellular vesicles research

MOTIVATION Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. RESULTS We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research. AVAILABILITY AND IMPLEMENTATION The web site was implemented in PHP, Java, MySQL and Apache, and is freely available at http://evpedia.info.

Antonella Bongiovanni | Ji Hyun Kim | Dong Soo Lee | Andrew F. Hill | Bernd Giebel | An Hendrix | Rienk Nieuwland | Antonio Marcilla | François Mullier | Susmita Sahoo | Si-Hyun Kim | Allan Stensballe | Dae-Kyum Kim | Jaewook Lee | Sae Rom Kim | Dong-Sic Choi | Yae Jin Yoon | Gyeongyun Go | Dinh Nhung | Kahye Hong | Su Chul Jang | Kyong-Su Park | Oh Youn Kim | Hyun Taek Park | Ji Hye Seo | Elena Aikawa | Monika Baj-Krzyworzeka | Bas W. M. van Balkom | Mattias Belting | Lionel Blanc | Vincent Bond | Francesc E. Borràs | Luc Buée | Edit I. Buzás | Lesley Cheng | Aled Clayton | Emanuele Cocucci | Charles S. Dela Cruz | Dominic M. Desiderio | Dolores Di Vizio | Karin Ekström | Juan M. Falcon-Perez | Chris Gardiner | David W. Greening | Julia Christina Gross | Dwijendra Gupta | Michelle M. Hill | Esther Nolte-'t Hoen | Do Won Hwang | Jameel Inal | Medicharla V. Jagannadham | Muthuvel Jayachandran | Young-Koo Jee | Malene Jørgensen | Kwang Pyo Kim | Yoon-Keun Kim | Thomas Kislinger | Cecilia Lässer | Hakmo Lee | Johannes van Leeuwen | Thomas Lener | Ming-Lin Liu | Jan Lötvall | Suresh Mathivanan | Andreas Möller | Jess Morhayim | Irina Nazarenko | Diana N. Nunes | Ken C. Pang | Jaesung Park | Tushar Patel | Gabriella Pocsfalvi | Hernando del Portillo | Ulrich Putz | Marcel I. Ramirez | Marcio L. Rodrigues | Tae-Young Roh | Felix Royo | Raymond Schiffelers | Shivani Sharma | Pia Siljander | Richard J. Simpson | Carolina Soekmadji | Philip Stahl | Ewa Stepien | Hidetoshi Tahara | Arne Trummer | Hadi Valadi | Laura J. Vella | Sun Nyunt Wai | Kenneth W. Witwer | María Yáñez-Mó | Hyewon Youn | Reinhard Zeidler | Yong Song Gho | H. T. Park | Tae-Young Roh | S. Mathivanan | L. Buée | J. Lötvall | K. Pang | Lesley Cheng | A. Hill | T. Kislinger | Jaesung Park | J. Kim | T. Patel | M. Yáñez-Mó | D. Hwang | D. S. Lee | H. Valadi | K. Ekström | E. Cocucci | Cecilia Lässer | E. Buzás | R. Simpson | E. Aikawa | V. Bond | F. Borràs | A. Clayton | J. Falcón-Pérez | Y. Gho | D. Gupta | A. Hendrix | J. Inal | A. Marcilla | I. Nazarenko | R. Nieuwland | R. Schiffelers | P. Siljander | A. Stensballe | A. Möller | Hakmo Lee | S. Wai | D. Desiderio | E. Stępień | M. Belting | P. Stahl | H. Youn | M. Rodrigues | K. Witwer | Yoon-Keun Kim | T. Lener | D. Greening | S. Sahoo | Dae-Kyum Kim | B. Giebel | E. N. Hoen | M. Jagannadham | H. Tahara | K. Kim | D. Nunes | L. Blanc | Ming-Lin Liu | S. Jang | H. Portillo | R. Zeidler | M. Hill | Y. Jee | Shivani Sharma | U. Putz | F. Mullier | F. Royo | J. V. Leeuwen | O. Y. Kim | Kahye Hong | Dong-Sic Choi | Gyeongyun Go | M. Jayachandran | M. Jørgensen | C. Soekmadji | M. Baj-Krzyworzeka | G. Pocsfalvi | M. Ramirez | L. Vella | S. Kim | Jess Morhayim | J. Gross | A. Bongiovanni | Y. Yoon | Jaewook Lee | C. Gardiner | J. Seo | Kyong-Su Park | A. Trummer | B. Balkom | D. D. Vizio | D. Nhung | S. Kim | C. D. Cruz | Cecilia Lässer | J. Falcón‐Pérez | M. Yáñez‐Mó | Emanuele Cocucci | Carolina Soekmadji

[1]  Y. Gho,et al.  Proteomics of extracellular vesicles: Exosomes and ectosomes. , 2015, Mass spectrometry reviews.

[2]  Lesley Cheng,et al.  Characterization and deep sequencing analysis of exosomal and non-exosomal miRNA in human urine. , 2014, Kidney international.

[3]  J. Dogné,et al.  Platelet microparticle generation assay: a valuable test for immune heparin-induced thrombocytopenia diagnosis. , 2014, Thrombosis research.

[4]  M. Epple,et al.  MSC-derived exosomes: a novel tool to treat therapy-refractory graft-versus-host disease , 2014, Leukemia.

[5]  S. Chisholm,et al.  Bacterial Vesicles in Marine Ecosystems , 2014, Science.

[6]  Lesley Cheng,et al.  Exosomes provide a protective and enriched source of miRNA for biomarker profiling compared to intracellular and cell-free blood , 2014, Journal of extracellular vesicles.

[7]  Romaric Lacroix,et al.  Plasmatic level of leukocyte-derived microparticles is associated with unstable plaque in asymptomatic patients with high-grade carotid stenosis. , 2013, Journal of the American College of Cardiology.

[8]  S. Wai,et al.  Role of the Vibrio cholerae Matrix Protein Bap1 in Cross-Resistance to Antimicrobial Peptides , 2013, PLoS pathogens.

[9]  Jaesung Park,et al.  Bioinspired exosome-mimetic nanovesicles for targeted delivery of chemotherapeutics to malignant tumors. , 2013, ACS nano.

[10]  Y. Gho,et al.  Circulating Extracellular Vesicles in Cancer Diagnosis and Monitoring , 2013, Molecular Diagnosis & Therapy.

[11]  Y. Gho,et al.  Proteomics, transcriptomics and lipidomics of exosomes and ectosomes , 2013, Proteomics.

[12]  Lynne T. Bemis,et al.  Standardization of sample collection, isolation and analysis methods in extracellular vesicle research , 2013, Journal of extracellular vesicles.

[13]  J. Lötvall,et al.  EVpedia: an integrated database of high-throughput data for systemic analyses of extracellular vesicles , 2013, Journal of extracellular vesicles.

[14]  G. Raposo,et al.  As we wait: coping with an imperfect nomenclature for extracellular vesicles , 2013, Journal of extracellular vesicles.

[15]  P. Altevogt,et al.  Vesiclepedia: A Compendium for Extracellular Vesicles with Continuous Community Annotation , 2012, PLoS biology.

[16]  James W. Clancy,et al.  Tumor-derived microvesicles: shedding light on novel microenvironment modulators and prospective cancer biomarkers. , 2012, Genes & development.

[17]  G. Capasso,et al.  A multiplex quantitative proteomics strategy for protein biomarker studies in urinary exosomes. , 2012, Kidney international.

[18]  Andrew F. Hill,et al.  Exosomes: Vehicles for the Transfer of Toxic Proteins Associated with Neurodegenerative Diseases? , 2012, Front. Physio..

[19]  Y. Gho,et al.  Therapeutic Effects of Autologous Tumor-Derived Nanovesicles on Melanoma Growth and Metastasis , 2012, PloS one.

[20]  B. Cookson,et al.  Membrane Vesicle Release in Bacteria, Eukaryotes, and Archaea: a Conserved yet Underappreciated Aspect of Microbial Life , 2012, Infection and Immunity.

[21]  R. Schiffelers,et al.  Cellular stress conditions are reflected in the protein and RNA content of endothelial cell-derived exosomes , 2012, Journal of extracellular vesicles.

[22]  Richard J. Simpson,et al.  ExoCarta as a resource for exosomal research , 2012, Journal of extracellular vesicles.

[23]  M. Wood,et al.  Delivery of siRNA to the mouse brain by systemic injection of targeted exosomes , 2011, Nature Biotechnology.

[24]  F. Magni,et al.  Advances in membranous vesicle and exosome proteomics improving biological understanding and biomarker discovery , 2011, Proteomics.

[25]  J. Lötvall,et al.  Human saliva, plasma and breast milk exosomes contain RNA: uptake by macrophages , 2011, Journal of Translational Medicine.

[26]  Dongmei Sun,et al.  A novel nanoparticle drug delivery system: the anti-inflammatory activity of curcumin is enhanced when encapsulated in exosomes. , 2010, Molecular therapy : the journal of the American Society of Gene Therapy.

[27]  Gerard Pasterkamp,et al.  Exosome secreted by MSC reduces myocardial ischemia/reperfusion injury. , 2010, Stem cell research.

[28]  W. Koh,et al.  Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha , 2010, BMC Genomics.

[29]  Y. Gho,et al.  Gram‐positive bacteria produce membrane vesicles: Proteomics‐based characterization of Staphylococcus aureus‐derived membrane vesicles , 2009, Proteomics.

[30]  Graça Raposo,et al.  Exosomes--vesicular carriers for intercellular communication. , 2009, Current opinion in cell biology.

[31]  C. Théry,et al.  Membrane vesicles as conveyors of immune responses , 2009, Nature Reviews Immunology.

[32]  Manuel Mayr,et al.  Proteomics, Metabolomics, and Immunomics on Microparticles Derived From Human Atherosclerotic Plaques , 2009, Circulation. Cardiovascular genetics.

[33]  Robert L Moritz,et al.  Exosomes: proteomic insights and diagnostic potential , 2009, Expert review of proteomics.

[34]  Jacopo Meldolesi,et al.  Shedding microvesicles: artefacts no more. , 2009, Trends in cell biology.

[35]  Michael S. Spilman,et al.  Structural heterogeneity and protein composition of exosome‐like vesicles (prostasomes) in human semen , 2009, The Prostate.

[36]  Y. Gho,et al.  Proteomics in gram-negative bacterial outer membrane vesicles. , 2008, Mass spectrometry reviews.

[37]  R. Simpson,et al.  Proteomic profiling of exosomes: Current perspectives , 2008, Proteomics.

[38]  D. Skupski,et al.  Heat shock protein-containing exosomes in mid-trimester amniotic fluids. , 2008, Journal of reproductive immunology.

[39]  Dong Wei,et al.  Phase I Clinical Trial of Autologous Ascites-derived Exosomes Combined With GM-CSF for Colorectal Cancer , 2008, Molecular Therapy.

[40]  J. Lötvall,et al.  Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells , 2007, Nature Cell Biology.

[41]  M. Record,et al.  Exosome lipidomics unravels lipid sorting at the level of multivesicular bodies. , 2007, Biochimie.

[42]  Graça Raposo,et al.  Exosomal-like vesicles are present in human blood plasma. , 2005, International immunology.

[43]  L. Zitvogel,et al.  The potential of exosomes in immunotherapy , 2005, Expert opinion on biological therapy.

[44]  Agneta Richter-Dahlfors,et al.  Vesicle-Mediated Export and Assembly of Pore-Forming Oligomers of the Enterobacterial ClyA Cytotoxin , 2003, Cell.

[45]  K. Shedden,et al.  Expulsion of small molecules in vesicles shed by cancer cells: association with gene expression and chemosensitivity profiles. , 2003, Cancer research.

[46]  P. Shannon,et al.  Proteomic analysis of human prostasomes , 2003, The Prostate.

[47]  G. FitzGerald,et al.  Transcellular activation of platelets and endothelial cells by bioactive lipids in platelet microparticles. , 1997, The Journal of clinical investigation.

[48]  J. George,et al.  Isolation of human platelet membrane microparticles from plasma and serum. , 1982, Blood.

[49]  Toshiyuki Yamamoto,et al.  CONFLICT OF INTEREST: None declared. , 2013 .

[50]  H. Schwarz,et al.  Proteomic analysis of secreted membrane vesicles of archaeal Sulfolobus species reveals the presence of endosome sorting complex components , 2008, Extremophiles.