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4. Vesiclepedia:A Compendium for Extracellular Vesicles with Continuous Community Annotation

Author

Kalra, H., Simpson, R.J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V.C., Borras, F.E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton, A., Cocucci, E., Falcon-Perez, J.M., Gabrielsson, S., Gho, Y.S., Gupta, D., Harsha, H.C., Hendrix, A., Hill, A.F., Inal, J.M., Jenster, G., Kramer-Albers, E.M., Lim, S.K., Llorente, A., Lotvall, J., Marcilla, A., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t Hoen, E.N.M., Pandey, A, Patel, T., Piper, M.G., Pluchino, S., Prasad, T.S., Rajendran, L., Raposo, G., Record, M., Reid, G.E., Sanchez-Madrid, F., Schiffelers, R.M., Siljander, P., Stensballe, A., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B.W.M., Vazquez, J., Vidal, M., Wauben, M.H.M., Yanez-Mo, M., Zoeller, M., Mathivanan, S., Strategic Infection Biology, Dep Biochemie en Celbiologie, Sub Atmospheric physics and chemistry, dB&C I&I, LS Celbiologie-Algemeen, Urology, Medical Microbiology & Infectious Diseases, University of Zurich, Mathivanan, Suresh, Strategic Infection Biology, Dep Biochemie en Celbiologie, Sub Atmospheric physics and chemistry, dB&C I&I, LS Celbiologie-Algemeen, ACS - Amsterdam Cardiovascular Sciences, CCA -Cancer Center Amsterdam, and Laboratory Specialized Diagnostics & Research

Subjects
human proteinpedia, exosomal proteins, delivery-system, breast-milk, url decay, cells, microvesicles, update, rna, biogenesis, QH301-705.5, Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy), 610 Medicine & health, Apoptosis, Computational biology, 1100 General Agricultural and Biological Sciences, Biology, Vesiclepedia, Exosomes, Exosome, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Annotation, 0302 clinical medicine, SDG 3 - Good Health and Well-being, 1300 General Biochemistry, Genetics and Molecular Biology, 2400 General Immunology and Microbiology, Community Page, ExoCarta, Biology (General), Medicinsk bioteknologi (med inriktning mot cellbiologi (inklusive stamcellsbiologi), molekylärbiologi, mikrobiologi, biokemi eller biofarmaci), Biología y Biomedicina, 030304 developmental biology, Uncategorized, 0303 health sciences, General Immunology and Microbiology, General Neuroscience, Microvesicle, Research, 2800 General Neuroscience, Extracellular vesicle, 11359 Institute for Regenerative Medicine (IREM), Extracellular vesicles, Microvesicles, Compendium, Cell biology, Data sharing, Databases as Topic, 030220 oncology & carcinogenesis, General Agricultural and Biological Sciences, Extracellular Space
Abstract

Vesiclepedia is a community-annotated compendium of molecular data on extracellular vesicles., Extracellular vesicles (EVs) are membraneous vesicles released by a variety of cells into their microenvironment. Recent studies have elucidated the role of EVs in intercellular communication, pathogenesis, drug, vaccine and gene-vector delivery, and as possible reservoirs of biomarkers. These findings have generated immense interest, along with an exponential increase in molecular data pertaining to EVs. Here, we describe Vesiclepedia, a manually curated compendium of molecular data (lipid, RNA, and protein) identified in different classes of EVs from more than 300 independent studies published over the past several years. Even though databases are indispensable resources for the scientific community, recent studies have shown that more than 50% of the databases are not regularly updated. In addition, more than 20% of the database links are inactive. To prevent such database and link decay, we have initiated a continuous community annotation project with the active involvement of EV researchers. The EV research community can set a gold standard in data sharing with Vesiclepedia, which could evolve as a primary resource for the field.

Published
2012
Full Text
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6. Vesiclepedia: A Compendium for Extracellular Vesicles with Continuous Community Annotation

Author

Kalra, H., Simpson, R.J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V.C., Borras, F.E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton, A., Cocucci, E., Falcon-Perez, J.M., Gabrielsson, S., Gho, Y.S., Gupta, D., Harsha, H.C., Hendrix, A., Hill, A.F., Inal, J.M., Jenster, G., Kramer-Albers, E.M., Lim, S.K., Llorente, A., Lotvall, J., Marcilla, A., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t Hoen, E.N.M., Pandey, A, Patel, T., Piper, M.G., Pluchino, S., Prasad, T.S., Rajendran, L., Raposo, G., Record, M., Reid, G.E., Sanchez-Madrid, F., Schiffelers, R.M., Siljander, P., Stensballe, A., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B.W.M., Vazquez, J., Vidal, M., Wauben, M.H.M., Yanez-Mo, M., Zoeller, M., Mathivanan, S., Kalra, H., Simpson, R.J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V.C., Borras, F.E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton, A., Cocucci, E., Falcon-Perez, J.M., Gabrielsson, S., Gho, Y.S., Gupta, D., Harsha, H.C., Hendrix, A., Hill, A.F., Inal, J.M., Jenster, G., Kramer-Albers, E.M., Lim, S.K., Llorente, A., Lotvall, J., Marcilla, A., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t Hoen, E.N.M., Pandey, A, Patel, T., Piper, M.G., Pluchino, S., Prasad, T.S., Rajendran, L., Raposo, G., Record, M., Reid, G.E., Sanchez-Madrid, F., Schiffelers, R.M., Siljander, P., Stensballe, A., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B.W.M., Vazquez, J., Vidal, M., Wauben, M.H.M., Yanez-Mo, M., Zoeller, M., and Mathivanan, S.

Abstract

Extracellular vesicles (EVs) are membraneous vesicles released by a variety of cells into their microenvironment. Recent studies have elucidated the role of EVs in intercellular communication, pathogenesis, drug, vaccine and gene-vector delivery, and as possible reservoirs of biomarkers. These findings have generated immense interest, along with an exponential increase in molecular data pertaining to EVs. Here, we describe Vesiclepedia, a manually curated compendium of molecular data (lipid, RNA, and protein) identified in different classes of EVs from more than 300 independent studies published over the past several years. Even though databases are indispensable resources for the scientific community, recent studies have shown that more than 50% of the databases are not regularly updated. In addition, more than 20% of the database links are inactive. To prevent such database and link decay, we have initiated a continuous community annotation project with the active involvement of EV researchers. The EV research community can set a gold standard in data sharing with Vesiclepedia, which could evolve as a primary resource for the field.

Published
2012

7. Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation.

Author

Strategic Infection Biology, Dep Biochemie en Celbiologie, Sub Atmospheric physics and chemistry, dB&C I&I, LS Celbiologie-Algemeen, Kalra, H., Simpson, R.J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V.C., Borras, F.E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton, A., Cocucci, E., Falcon-Perez, J.M., Gabrielsson, S., Gho, Y.S., Gupta, D., Harsha, H.C., Hendrix, A., Hill, A.F., Inal, J.M., Jenster, G., Kramer-Albers, E.M., Lim, S.K., Llorente, A., Lotvall, J., Marcilla, A., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t Hoen, E.N.M., Pandey, A, Patel, T., Piper, M.G., Pluchino, S., Prasad, T.S., Rajendran, L., Raposo, G., Record, M., Reid, G.E., Sanchez-Madrid, F., Schiffelers, R.M., Siljander, P., Stensballe, A., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B.W.M., Vazquez, J., Vidal, M., Wauben, M.H.M., Yanez-Mo, M., Zoeller, M., Mathivanan, S., Strategic Infection Biology, Dep Biochemie en Celbiologie, Sub Atmospheric physics and chemistry, dB&C I&I, LS Celbiologie-Algemeen, Kalra, H., Simpson, R.J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V.C., Borras, F.E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton, A., Cocucci, E., Falcon-Perez, J.M., Gabrielsson, S., Gho, Y.S., Gupta, D., Harsha, H.C., Hendrix, A., Hill, A.F., Inal, J.M., Jenster, G., Kramer-Albers, E.M., Lim, S.K., Llorente, A., Lotvall, J., Marcilla, A., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t Hoen, E.N.M., Pandey, A, Patel, T., Piper, M.G., Pluchino, S., Prasad, T.S., Rajendran, L., Raposo, G., Record, M., Reid, G.E., Sanchez-Madrid, F., Schiffelers, R.M., Siljander, P., Stensballe, A., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B.W.M., Vazquez, J., Vidal, M., Wauben, M.H.M., Yanez-Mo, M., Zoeller, M., and Mathivanan, S.

Published
2012

8. Biological properties of extracellular vesicles and their physiological functions

Author

Juan M. Falcón-Pérez, Irene M. Ghobrial, Aija Linē, Eva Rohde, Francesco Cappello, Irina Nazarenko, María Yáñez-Mó, Saara Laitinen, Mayda Gursel, María Mittelbrunn, Krisztina Buzas, Mario Gimona, Erzsébet Ligeti, An Hendrix, Ihsan Gursel, Marie Stampe Ostenfeld, Antonio Marcilla, Joana Carvalho, Eva-Maria Krämer-Albers, Georg Lipps, Francisco Sánchez-Madrid, Thomas Lener, Carla Oliveira, Éva Pállinger, Francesc E. Borràs, Susanne G. van der Grein, Olivier De Wever, Veronika Kralj-Iglič, Bernd Giebel, Anabela Cordeiro da Silva, Esther N. M. Nolte-‘t Hoen, Nuno Santarém, Willem Stoorvogel, Marina Rigau, Hernando A. del Portillo, Katsutoshi Kokubun, Marca H. M. Wauben, Alicia Llorente, Apolonija Bedina Zavec, Eva Colas, Katharina Schallmoser, Maja Kosanović, Peter Kierulf, Jaume Reventós, Mireia Olivan, Jan Lötvall, Edit I. Buzás, Enriqueta Casal, Michael W. Graner, Pia Siljander, Stefano Fais, Cecilia Lässer, Marei Sammar, Niels H. H. Heegaard, Lorraine O'Driscoll, Roman Štukelj, Tuula A. Nyman, Zoraida Andreu, Mateja Manček-Keber, M. Helena Vasconcelos, Infection & Immunity, Fertility & Reproduction, dB&C I&I, LS Celbiologie-Algemeen, Yanez-Mo M., Siljander P.R.-M., Andreu Z., Zavec A.B., Borras F.E., Buzas E.I., Buzas K., Casal E., Cappello F., Carvalho J., Colas E., Cordeiro-Da Silva A., Fais S., Falcon-Perez J.M., Ghobrial I.M., Giebel B., Gimona M., Graner M., Gursel I., Gursel M., Heegaard N.H.H., Hendrix A., Kierulf P., Kokubun K., Kosanovic M., Kralj-Iglic V., Kramer-Albers E.-M., Laitinen S., Lasser C., Lener T., Ligeti E., Line A., Lipps G., Llorente A., Lotvall J., Mancek-Keber M., Marcilla A., Mittelbrunn M., Nazarenko I., Nolte-'t Hoen E.N.M., Nyman T.A., O'Driscoll L., Olivan M., Oliveira C., Pallinger E., Del Portillo H.A., Reventos J., Rigau M., Rohde E., Sammar M., Sanchez-Madrid F., Santarem N., Schallmoser K., Ostenfeld M.S., Stoorvogel W., Stukelj R., Van Der Grein S.G., Helena Vasconcelos M., Wauben M.H.M., and De Wever O.

Subjects
Proteomics, Cellular distribution, MATURE DENDRITIC CELLS, Review, Review Article, Urine, Embryo development, Monocyte, Protein processing, Vascular biology, Feces, Vesícules seminals, SYNCYTIOTROPHOBLAST MICROVILLOUS MEMBRANES, Cell selection, Pregnancy, T lymphocyte, Bile, CELL-DERIVED EXOSOMES, Biogenesis, Lung lavage, Uterus fluid, Innate immunity, Male genital system, lcsh:Cytology, Microvesicle, OUTER-MEMBRANE VESICLES, Blood clotting, prokaryote, Eukaryota, Extracellular vesicle, RNA analysis, Cell biology, Blood, Cerebrospinal fluid, Liver metabolism, microvesicle, Morphogen, Human, Nervous system, Cell signaling, Breast milk, Natural killer cell, Fisiologia, Extracellular vesicles, Exosome, lcsh:QH573-671, Saliva, Biology, Biology and Life Sciences, DNA, Plant, RNA transport, Cell function, Macrophage, Molecular biology, Physiology, Medizin, FACTOR PATHWAY INHIBITOR, eukaryote, Protein glycosylation, Extracellular space, Tissue repair, Espai extracel·lular, Reticulocyte, Seminal plasma, Mesenchymal stem cell, Antigen presenting cell, Seminal vesicles, Nose mucus, Biofilm, Neutrophil, MicroRNA, PLANT-MICROBE INTERACTIONS, Lipid, Amnion fluid, Prokaryota, microparticle, Cell interaction, Cell transport, eukaryote, exosome, extracellular vesicle, microparticle, microvesicle, physiology, prokaryote, Bone mineralization, Microorganism, Histology, Adaptive immunity, Membrane vesicle, Computational biology, Membrane receptor, Stress, Cell communication, Mast cell, MESENCHYMAL STEM-CELLS, HUMAN ENDOTHELIAL-CELLS, exosome, Cytokine, Synovial fluid, Cell Biology, Nonhuman, IMMUNE-MODULATORY FEATURES, Review article, DNA content, physiology, RNA, INTESTINAL EPITHELIAL-CELLS, extracellular vesicle, Body fluid, Lectin
Abstract

The authors wish to thank Dr R Simpson and Dr D Taylor for critical reading of the manuscript and acknowledge the Horizon 2020 European Cooperation in Science and Technology programme and its support of our European Network on Microvesicles and Exosomes in Health & Disease (ME-HaD; BM1202 www.cost.eu/COST_Actions/bmbs/Actions/BM1202). In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.

Published
2015
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