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1. EVpedia: a community web portal for extracellular vesicles research

Author

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

Subjects
Biomedical Research, Computational Biology, Database Management Systems, Databases, Factual, Exosomes, Extracellular Space, Humans, Software, User-Computer Interface, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

MotivationExtracellular 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.ResultsWe 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 implementationThe web site was implemented in PHP, Java, MySQL and Apache, and is freely available at http://evpedia.info.

Published
2015

5. Colorectal cancer cell-derived microvesicles are enriched in cell cycle-related mRNAs that promote proliferation of endothelial cells

Author

Kim Yoon-Keun, Choi Dong-Sic, Kim Ji, Kim Jongmin, Rho Sangchul, Choi Eun-Jeong, Kim Hyunjung, Cho Ji-Hoon, Hong Bok, Hwang Daehee, and Gho Yong

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Various cancer cells, including those of colorectal cancer (CRC), release microvesicles (exosomes) into surrounding tissues and peripheral circulation. These microvesicles can mediate communication between cells and affect various tumor-related processes in their target cells. Results We present potential roles of CRC cell-derived microvesicles in tumor progression via a global comparative microvesicular and cellular transcriptomic analysis of human SW480 CRC cells. We first identified 11,327 microvesicular mRNAs involved in tumorigenesis-related processes that reflect the physiology of donor CRC cells. We then found 241 mRNAs enriched in the microvesicles above donor cell levels, of which 27 were involved in cell cycle-related processes. Network analysis revealed that most of the cell cycle-related microvesicle-enriched mRNAs were associated with M-phase activities. The integration of two mRNA datasets showed that these M-phase-related mRNAs were differentially regulated across CRC patients, suggesting their potential roles in tumor progression. Finally, we experimentally verified the network-driven hypothesis by showing a significant increase in proliferation of endothelial cells treated with the microvesicles. Conclusion Our study demonstrates that CRC cell-derived microvesicles are enriched in cell cycle-related mRNAs that promote proliferation of endothelial cells, suggesting that microvesicles of cancer cells can be involved in tumor growth and metastasis by facilitating angiogenesis-related processes. This information will help elucidate the pathophysiological functions of tumor-derived microvesicles, and aid in the development of cancer diagnostics, including colorectal cancer.

Published
2009
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6. EVpedia: a community web portal for extracellular vesicles research

Author

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

Abstract

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. CONTACT: ysgho@postech.ac.kr.

Published
2014

7. EVpedia : A community web portal for extracellular vesicles research

Author

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

Published
2015

8. EVpedia: A community web portal for extracellular vesicles research

Author

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

Published
2015

11. Outer Membrane Vesicles: In vivo Kinetic Biodistribution of Nano-Sized Outer Membrane Vesicles Derived from Bacteria (Small 4/2015)

Author

Jang, Su Chul, primary, Kim, Sae Rom, additional, Yoon, Yae Jin, additional, Park, Kyong-Su, additional, Kim, Ji Hyun, additional, Lee, Jaewook, additional, Kim, Oh Youn, additional, Choi, Eun-Jeong, additional, Kim, Dae-Kyum, additional, Choi, Dong-Sic, additional, Kim, Yoon-Keun, additional, Park, Jaesung, additional, Di Vizio, Dolores, additional, and Gho, Yong Song, additional

Published
2015
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12. MicroRNA in exosomes isolated directly from the liver circulation in patients with metastatic uveal melanoma

Author

Eldh, Maria, Olofsson Bagge, Roger, Lässer, Cecilia, Svanvik, Joar, Sjöstrand, Margareta, Mattsson, Jan, Lindnér, Per, Choi, Dong-Sic, Gho, Yong Song, Lötvall, Jan, Eldh, Maria, Olofsson Bagge, Roger, Lässer, Cecilia, Svanvik, Joar, Sjöstrand, Margareta, Mattsson, Jan, Lindnér, Per, Choi, Dong-Sic, Gho, Yong Song, and Lötvall, Jan

Abstract

BACKGROUND: Uveal melanoma is a tumour arising from melanocytes of the eye, and 30 per cent of these patients develop liver metastases. Exosomes are small RNA containing nano-vesicles released by most cells, including malignant melanoma cells. This clinical translational study included patients undergoing isolated hepatic perfusion (IHP) for metastatic uveal melanoma, from whom exosomes were isolated directly from liver perfusates. The objective was to determine whether exosomes are present in the liver circulation, and to ascertain whether these may originate from melanoma cells. METHODS: Exosomes were isolated from the liver perfusate of twelve patients with liver metastases from uveal melanoma undergoing IHP. Exosomes were visualised by electron microscopy, and characterised by flow cytometry, Western blot and real-time PCR. Furthermore, the concentration of peripheral blood exosomes were measured and compared to healthy controls. RESULTS: The liver perfusate contained Melan-A positive and RNA containing exosomes, with similar miRNA profiles among patients, but dissimilar miRNA compared to exosomes isolated from tumor cell cultures. Patients with metastatic uveal melanoma had a higher concentration of exosomes in their peripheral venous blood compared to healthy controls. CONCLUSIONS: Melanoma exosomes are released into the liver circulation in metastatic uveal melanoma, and is associated with higher concentrations of exosomes in the systemic circulation. The exosomes isolated directly from liver circulation contain miRNA clusters that are different from exosomes from other cellular sources.

Published
2014
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13. EVpedia: a community web portal for extracellular vesicles research

Author

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

Published
2014

15. EVpedia: a community web portal for extracellular vesicles research

Author

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

Published
2014
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16. In vivo Kinetic Biodistribution of Nano-Sized Outer Membrane Vesicles Derived from Bacteria

Author

Jang, Su Chul, primary, Kim, Sae Rom, additional, Yoon, Yae Jin, additional, Park, Kyong-Su, additional, Kim, Ji Hyun, additional, Lee, Jaewook, additional, Kim, Oh Youn, additional, Choi, Eun-Jeong, additional, Kim, Dae-Kyum, additional, Choi, Dong-Sic, additional, Kim, Yoon-Keun, additional, Park, Jaesung, additional, Di Vizio, Dolores, additional, and Gho, Yong Song, additional

Published
2014
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20. Identification and characterization of proteins isolated from microvesicles derived from human lung cancer pleural effusions

Author

Park, Jung Ok, primary, Choi, Do-Young, additional, Choi, Dong-Sic, additional, Kim, Hee Joung, additional, Kang, Jeong Won, additional, Jung, Jae Hun, additional, Lee, Jeong Hwa, additional, Kim, Jayoung, additional, Freeman, Michael R., additional, Lee, Kye Young, additional, Gho, Yong Song, additional, and Kim, Kwang Pyo, additional

Published
2013
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23. EVpedia: an integrated database of high-throughput data for systemic analyses of extracellular vesicles

Author

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

Published
2013
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26. Erratum: Proteomic analysis of microvesicles derived from human colorectal cancer ascites

Author

Choi, Dong-Sic, primary, Park, Jung Ok, additional, Jang, Su Chul, additional, Yoon, Yae Jin, additional, Jung, Jin Woo, additional, Choi, Do-Young, additional, Kim, Jung-Wook, additional, Kang, Ji Seon, additional, Park, Jaesung, additional, Hwang, Daehee, additional, Lee, Kyung-Hee, additional, Park, Sang-Hyun, additional, Kim, Yoon-Keun, additional, Desiderio, Dominic M., additional, Kim, Kwang Pyo, additional, and Gho, Yong Song, additional

Published
2011
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28. Proteomic analysis of microvesicles derived from human colorectal cancer ascites

Author

Choi, Dong-Sic, primary, Park, Jung Ok, additional, Jang, Su Chul, additional, Yoon, Yae Jin, additional, Jung, Jin Woo, additional, Choi, Do-Young, additional, Kim, Jung-Wook, additional, Kang, Ji Seon, additional, Park, Jaesung, additional, Hwang, Daehee, additional, Lee, Kyung-Hee, additional, Park, Sang-Hyun, additional, Kim, Yoon-Keun, additional, Desiderio, Dominic M., additional, Kim, Kwang Pyo, additional, and Gho, Yong Song, additional

Published
2011
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34. Proteomics of extracellular vesicles: Exosomes and ectosomes.

Author

Choi, Dong-Sic, Kim, Dae-Kyum, Kim, Yoon-Keun, and Gho, Yong Song

Subjects
*PROTEOMICS, *VESICLES (Cytology), *EXOSOMES, *PATHOLOGICAL physiology, *MASS spectrometry
Abstract

Almost all bacteria, archaea, and eukaryotic cells shed extracellular vesicles either constitutively or in a regulated manner. These nanosized membrane vesicles are spherical, bilayered proteolipids that harbor specific subsets of proteins, DNAs, RNAs, and lipids. Recent research has facilitated conceptual advancements in this emerging field that indicate that extracellular vesicles act as intercellular communicasomes by transferring signals to their target cell via surface ligands and delivering receptors and functional molecules. Recent progress in mass spectrometry-based proteomic analyses of mammalian extracellular vesicles derived from diverse cell types and body fluids has resulted in the identification of several thousand vesicular proteins that provide us with essential clues to the molecular mechanisms involved in vesicle cargo sorting and biogenesis. Furthermore, cell-type- or disease-specific vesicular proteins help us to understand the pathophysiological functions of extracellular vesicles and contribute to the discovery of diagnostic and therapeutic target proteins. This review focuses on the high-throughput mass spectrometry-based proteomic analyses of mammalian extracellular vesicles (i.e., exosomes and ectosomes), EVpedia (a free web-based integrated database of high-throughput data for systematic analyses of extracellular vesicles; ), and the intravesicular protein-protein interaction network analyses of mammalian extracellular vesicles. The goal of this article is to encourage further studies to construct a comprehensive proteome database for extracellular vesicles that will help us to not only decode the biogenesis and cargo-sorting mechanisms during vesicle formation but also elucidate the pathophysiological roles of these complex extracellular organelles. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 34: 474-490, 2015. [ABSTRACT FROM AUTHOR]

Published
2015
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38. Aspirin attenuates the anti-inflammatory effects of theophylline via inhibition of cAMP production in mice with non-eosinophilic asthma

Author

Moon, Hyung-Geun, Kim, You-Sun, Choi, Jun-Pyo, Choi, Dong-Sic, Yoon, Chang Min, Jeon, Seong Gyu, Gho, Yong Song, and Kim, Yoon-Keun

Abstract

Theophylline is commonly used to treat severe asthma and chronic obstructive pulmonary disease (COPD) characterized by non-eosinophilic inflammation. Acetyl salicylic acid (ASA) is one of the most widely used medications worldwide, but up to 20% of patients with asthma experience aggravated respiratory symptoms after taking ASA. Here we evaluated the adverse effect of ASA on the therapeutic effect of theophylline in mice with non-eosinophilic asthma. A non-eosinophilic asthma mouse model was induced by airway sensitization with lipopolysaccharide-containing allergen and then challenged with allergen alone. Therapeutic intervention was performed during allergen challenge. Theophylline inhibited lung inflammation partly induced by Th1 immune response. ASA attenuated the beneficial effects of theophylline. However, co-administration of the ASA metabolite salicylic acid (SA) showed no attenuating effect on theophylline treatment. The therapeutic effect of theophylline was associated with increase in cAMP levels, which was blocked by co-treatment of theophylline and ASA. ASA co-treatment also attenuated the anti-inflammatory effects of a specific phosphodiesterase 4 inhibitor. These results demonstrate that ASA reverses anti-inflammatory effects of theophylline, and that ASA exerts its adverse effects through the inhibition of cAMP production. Our data suggest that ASA reverses lung inflammation in patients taking theophylline, although clinical evidence will be needed.

Published
2009
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40. Urinary extracellular vesicles for biomarker source to monitor polycystic kidney disease.

Author

Choi DS

Subjects
Humans, Male, Extracellular Vesicles metabolism, Polycystic Kidney Diseases urine
Abstract

Extracellular vesicles (EVs) are bilayered lipid vesicles, 50-1000 nm in diameter and secreted by most types of cells. They contain many proteins, mRNAs, miRNAs, and lipids that reflect the pathophysiological state of the cells they originate from, and are therefore considered to be a rich source of potential biomarkers. In this issue (Pocsfalvi, G. et al., Proteomics Clin. Appl. 2015, 9, 552-567), Pocsfalvi et al. conducted pioneering investigations to determine whether changes in the protein content of EVs occur during progression of autosomal dominant polycystic kidney disease (ADPKD), a common genetic disorder that predominantly affects the kidneys. Most significantly, iTRAQ-based quantitative proteomics showed that cytoskeleton-regulating and Ca(2+) -binding proteins are differentially expressed in urinary EVs of ADPKD patients. Impressively, these proteins are involved in biological processes that are closely related to the pathogenic state of tubular epithelial cells in ADPKD, demonstrating the possibility to monitor the status of patients using urinary EVs., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Published
2015
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41. Isolation of extracellular vesicles for proteomic profiling.

Author

Choi DS and Gho YS

Subjects
Cell Line, Centrifugation, Density Gradient methods, Humans, Cell Fractionation methods, Extracellular Vesicles, Proteome, Proteomics methods
Abstract

Extracellular vesicles are nano-sized lipid bilayer vesicles released from most cells, including archaea, bacteria, and eukaryotic cells. These membrane vesicles play multiple roles in cell-to-cell communication, including immune modulation, angiogenesis, and transformation of cells by transferring genetic material and functional proteins. They contain specific subsets of proteins, DNA, RNA, and lipids that represent their cellular status. Furthermore, extracellular vesicles are enriched in cell type- or disease-specific vesicular proteins, especially plasma membrane proteins, which have pathophysiological functions; these vesicular proteins are considered novel diagnostic biomarkers as well as therapeutic targets. To profile the proteome, various purification methods of extracellular vesicles have been developed, but density gradient ultracentrifugation is considered the most promising. In this chapter, we describe the isolation of extracellular vesicles derived from SW480 cells and the preparation of tryptic peptides for mass-spectrometry-based proteomic analysis.

Published
2015
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