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54. Characterisation of microRNA expression in post-natal mouse mammary gland development

Author

Karagavriilidou Konstantina, Spiteri Inmaculada, Le Quesne John, Blenkiron Cherie, Stingl John, Goldstein Leonard D, Avril-Sassen Stefanie, Watson Christine J, Tavaré Simon, Miska Eric A, and Caldas Carlos

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

Abstract Background The differential expression pattern of microRNAs (miRNAs) during mammary gland development might provide insights into their role in regulating the homeostasis of the mammary epithelium. Our aim was to analyse these regulatory functions by deriving a comprehensive tissue-specific combined miRNA and mRNA expression profile of post-natal mouse mammary gland development. We measured the expression of 318 individual murine miRNAs by bead-based flow-cytometric profiling of whole mouse mammary glands throughout a 16-point developmental time course, including juvenile, puberty, mature virgin, gestation, lactation, and involution stages. In parallel whole-genome mRNA expression data were obtained. Results One third (n = 102) of all murine miRNAs analysed were detected during mammary gland development. MicroRNAs were represented in seven temporally co-expressed clusters, which were enriched for both miRNAs belonging to the same family and breast cancer-associated miRNAs. Global miRNA and mRNA expression was significantly reduced during lactation and the early stages of involution after weaning. For most detected miRNA families we did not observe systematic changes in the expression of predicted targets. For miRNA families whose targets did show changes, we observed inverse patterns of miRNA and target expression. The data sets are made publicly available and the combined expression profiles represent an important community resource for mammary gland biology research. Conclusion MicroRNAs were expressed in likely co-regulated clusters during mammary gland development. Breast cancer-associated miRNAs were significantly enriched in these clusters. The mechanism and functional consequences of this miRNA co-regulation provide new avenues for research into mammary gland biology and generate candidates for functional validation.

Published
2009
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55. Differential expression of selected histone modifier genes in human solid cancers

Author

Bowtell David, Collins V Peter, Arends Mark J, Subkhankulova Tanya, Burtt Glynn, Veerakumarasivam Abhi, Bobrow Linda, Blenkiron Cherie, Hyland Sarah J, Ahmed Ahmed, Teschendorff Andrew E, Özdağ Hilal, Kouzarides Tony, Brenton James D, and Caldas Carlos

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

Abstract Background Post-translational modification of histones resulting in chromatin remodelling plays a key role in the regulation of gene expression. Here we report characteristic patterns of expression of 12 members of 3 classes of chromatin modifier genes in 6 different cancer types: histone acetyltransferases (HATs)- EP300, CREBBP, and PCAF; histone deacetylases (HDACs)- HDAC1, HDAC2, HDAC4, HDAC5, HDAC7A, and SIRT1; and histone methyltransferases (HMTs)- SUV39H1and SUV39H2. Expression of each gene in 225 samples (135 primary tumours, 47 cancer cell lines, and 43 normal tissues) was analysedby QRT-PCR, normalized with 8 housekeeping genes, and given as a ratio by comparison with a universal reference RNA. Results This involved a total of 13,000 PCR assays allowing for rigorous analysis by fitting a linear regression model to the data. Mutation analysis of HDAC1, HDAC2, SUV39H1, and SUV39H2 revealed only two out of 181 cancer samples (both cell lines) with significant coding-sequence alterations. Supervised analysis and Independent Component Analysis showed that expression of many of these genes was able to discriminate tumour samples from their normal counterparts. Clustering based on the normalized expression ratios of the 12 genes also showed that most samples were grouped according to tissue type. Using a linear discriminant classifier and internal cross-validation revealed that with as few as 5 of the 12 genes, SIRT1, CREBBP, HDAC7A, HDAC5 and PCAF, most samples were correctly assigned. Conclusion The expression patterns of HATs, HDACs, and HMTs suggest these genes are important in neoplastic transformation and have characteristic patterns of expression depending on tissue of origin, with implications for potential clinical application.

Published
2006
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57. A pilot study of exome sequencing in a diverse New Zealand cohort with undiagnosed disorders and cancer

Author

McKeown, Colina, primary, Connors, Samantha, additional, Stapleton, Rachel, additional, Morgan, Tim, additional, Hayes, Ian, additional, Neas, Katherine, additional, Dixon, Joanne, additional, Gibson, Kate, additional, Markie, David M., additional, Tsai, Peter, additional, Blenkiron, Cherie, additional, Fitzgerald, Sandra, additional, Shields, Paula, additional, Yap, Patrick, additional, Lawrence, Ben, additional, Print, Cristin, additional, and Robertson, Stephen P., additional

Published
2018
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59. Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer

Author

Lawrence, Ben, primary, Blenkiron, Cherie, additional, Parker, Kate, additional, Tsai, Peter, additional, Fitzgerald, Sandra, additional, Shields, Paula, additional, Robb, Tamsin, additional, Yeong, Mee Ling, additional, Kramer, Nicole, additional, James, Sarah, additional, Black, Mik, additional, Fan, Vicky, additional, Poonawala, Nooriyah, additional, Yap, Patrick, additional, Coats, Esther, additional, Woodhouse, Braden, additional, Ramsaroop, Reena, additional, Yozu, Masato, additional, Robinson, Bridget, additional, Henare, Kimiora, additional, Koea, Jonathan, additional, Johnston, Peter, additional, Carroll, Richard, additional, Connor, Saxon, additional, Morrin, Helen, additional, Elston, Marianne, additional, Jackson, Christopher, additional, Reid, Papaarangi, additional, Windsor, John, additional, MacCormick, Andrew, additional, Babor, Richard, additional, Bartlett, Adam, additional, Damianovich, Dragan, additional, Knowlton, Nicholas, additional, Grimmond, Sean, additional, Findlay, Michael, additional, and Print, Cristin, additional

Published
2017
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67. MiR-210 is induced by Oct-2, regulates B-cells and inhibits autoantibody production1

Author

Mok, Yingting, Schwierzeck, Vera, Thomas, David C., Vigorito, Elena, Rayner, Tim F., Jarvis, Lorna B., Prosser, Haydn M., Bradley, Allan, Withers, David R., Mårtensson, Inga-Lill, Corcoran, Lynn M., Blenkiron, Cherie, Miska, Eric A., Lyons, Paul A., and Smith, Kenneth G.C.

Subjects
B-Lymphocytes, Chromatin Immunoprecipitation, Fluorescent Antibody Technique, Enzyme-Linked Immunosorbent Assay, Mice, Transgenic, Cell Separation, Lymphocyte Activation, Polymerase Chain Reaction, Article, Mice, Inbred C57BL, Mice, MicroRNAs, Animals, Octamer Transcription Factor-2, Transcriptome, Autoantibodies, Oligonucleotide Array Sequence Analysis
Abstract

MicroRNAs (MiRs) are small, noncoding RNAs that regulate gene expression posttranscriptionally. In this study, we show that MiR-210 is induced by Oct-2, a key transcriptional mediator of B cell activation. Germline deletion of MiR-210 results in the development of autoantibodies from 5 mo of age. Overexpression of MiR-210 in vivo resulted in cell autonomous expansion of the B1 lineage and impaired fitness of B2 cells. Mice overexpressing MiR-210 exhibited impaired class-switched Ab responses, a finding confirmed in wild-type B cells transfected with a MiR-210 mimic. In vitro studies demonstrated defects in cellular proliferation and cell cycle entry, which were consistent with the transcriptomic analysis demonstrating downregulation of genes involved in cellular proliferation and B cell activation. These findings indicate that Oct-2 induction of MiR-210 provides a novel inhibitory mechanism for the control of B cells and autoantibody production.

Published
2013

76. MiR-210 Is Induced by Oct-2, Regulates B Cells, and Inhibits Autoantibody Production

Author

Mok, Yingting, primary, Schwierzeck, Vera, additional, Thomas, David C., additional, Vigorito, Elena, additional, Rayner, Tim F., additional, Jarvis, Lorna B., additional, Prosser, Haydn M., additional, Bradley, Allan, additional, Withers, David R., additional, Mårtensson, Inga-Lill, additional, Corcoran, Lynn M., additional, Blenkiron, Cherie, additional, Miska, Eric A., additional, Lyons, Paul A., additional, and Smith, Kenneth G. C., additional

Published
2013
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78. Erratum: A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans

Author

Jovanovic, Marko, primary, Reiter, Lukas, additional, Picotti, Paola, additional, Lange, Vinzenz, additional, Bogan, Erica, additional, Hurschler, Benjamin A, additional, Blenkiron, Cherie, additional, Lehrbach, Nicolas J, additional, Ding, Xavier C, additional, Weiss, Manuel, additional, Schrimpf, Sabine P, additional, Miska, Eric A, additional, Groβhans, Helge, additional, Aebersold, Ruedi, additional, and Hengartner, Michael O, additional

Published
2010
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79. A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans

Author

Jovanovic, Marko, primary, Reiter, Lukas, additional, Picotti, Paola, additional, Lange, Vinzenz, additional, Bogan, Erica, additional, A Hurschler, Benjamin, additional, Blenkiron, Cherie, additional, J Lehrbach, Nicolas, additional, C Ding, Xavier, additional, Weiss, Manuel, additional, P Schrimpf, Sabine, additional, A Miska, Eric, additional, Großhans, Helge, additional, Aebersold, Ruedi, additional, and O Hengartner, Michael, additional

Published
2010
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84. MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype

Author

Blenkiron, Cherie, primary, Goldstein, Leonard D, additional, Thorne, Natalie P, additional, Spiteri, Inmaculada, additional, Chin, Suet-Feung, additional, Dunning, Mark J, additional, Barbosa-Morais, Nuno L, additional, Teschendorff, Andrew E, additional, Green, Andrew R, additional, Ellis, Ian O, additional, Tavaré, Simon, additional, Caldas, Carlos, additional, and Miska, Eric A, additional

Published
2007
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85. Differential expression of selected histone modifier genes in human solid cancers

Author

Özdağ, Hilal, primary, Teschendorff, Andrew E, additional, Ahmed, Ahmed Ashour, additional, Hyland, Sarah J, additional, Blenkiron, Cherie, additional, Bobrow, Linda, additional, Veerakumarasivam, Abhi, additional, Burtt, Glynn, additional, Subkhankulova, Tanya, additional, Arends, Mark J, additional, Collins, V Peter, additional, Bowtell, David, additional, Kouzarides, Tony, additional, Brenton, James D, additional, and Caldas, Carlos, additional

Published
2006
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88. miR-124 acts through CoREST to control onset of Sema3A sensitivity in navigating retinal growth cones.

Author

Baudet, Marie-Laure, Zivraj, Krishna H, Abreu-Goodger, Cei, Muldal, Alistair, Armisen, Javier, Blenkiron, Cherie, Goldstein, Leonard D, Miska, Eric A, and Holt, Christine E

Subjects
XENOPUS laevis, RETINAL ganglion cells, AXONS, SEMAPHORINS, NEUROPILINS
Abstract

During axon pathfinding, growth cones commonly show changes in sensitivity to guidance cues that follow a cell-intrinsic timetable. The cellular timer mechanisms that regulate such changes are, however, poorly understood. Here we have investigated microRNAs (miRNAs) in the timing control of sensitivity to the semaphorin Sema3A in Xenopus laevis retinal ganglion cell (RGC) growth cones. A developmental profiling screen identified miR-124 as a candidate timer. Loss of miR-124 delayed the onset of Sema3A sensitivity and concomitant neuropilin-1 (NRP1) receptor expression and caused cell-autonomous pathfinding errors. CoREST, a cofactor of a NRP1 repressor, was newly identified as a target and mediator of miR-124 for this highly specific temporal aspect of RGC growth cone responsiveness. Our findings indicate that miR-124 is important in regulating the intrinsic temporal changes in RGC growth cone sensitivity and suggest that miRNAs may act broadly as linear timers in vertebrate neuronal development. [ABSTRACT FROM AUTHOR]

Published
2012
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89. High-Resolution Magic Angle Spinning 1H NMR Spectroscopy and Reverse Transcription-PCR Analysis of Aoo&3x00F8;tosis in a Rat Glioma.

Author

Griffin, Julian L., Blenkiron, Cherie, Valonen, Piia K., Caldas, Carlos, and Kauppinen, Risto A.

Subjects
*GENOMICS, *PROTEOMICS, *PROTEINS, *METABOLITES, *SPECTRUM analysis, *GLIOMAS, *RATS, *TUMORS, *APOPTOSIS, *THYMIDINE, *GANCICLOVIR
Abstract

The functional genomic approaches of transcriptomics, proteomics and metabolomics aim to measure the mRNA, protein or metabolite complement of a cell, tissue or organism. In this study we have investigated the compatibility of transcriptional analysis, using Reverse Transcription (RT)-PCR, and metabolite analysis, by high-resolution magic angle spinning (HRMAS) ¹H NMR spectroscopy, in BT4C rat glioma following the induction of programmed cell death. The metabolite and transcriptional changes that accompanied apoptosis were examined at 0, 4 and 8 days of ganciclovir/thymidine kinase gene therapy. Despite the high spinning speeds employed during HRMAS ¹H NMR spectroscopy of one-half of the tumor samples, RT-PCR analysis of the pro-apoptotic transcripts Bcl-2, BAK-1, caspase-9 and FAS was possible, producing similar results to those detected in the unspun half of the tumors. Furthermore, the expression of FAS was inversely correlated with some of the key metabolic changes across the time period examined including the increases CH=CH and CH=CHCH2 lipid resonances which accompany apoptosis. This study demonstrates how combined transcriptomic and metabolomic studies of tumors can be used to understand the molecular events that accompany well documented metabolic perturbations during cell death processes. [ABSTRACT FROM AUTHOR]

Published
2006
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90. Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

Author

Théry, Clotilde, Witwer, Kenneth W., Aikawa, Elena, Alcaraz, Maria Jose, Anderson, Johnathon D., Andriantsitohaina, Ramaroson, Antoniou, Anna, Arab, Tanina, Archer, Fabienne, Atkin-Smith, Georgia K., Ayre, D Craig, Bach, Jean-Marie, Bachurski, Daniel, Baharvand, Hossein, Balaj, Leonora, Baldacchino, Shawn, Bauer, Natalie N., Baxter, Amy A., Bebawy, Mary, Beckham, Carla, Bedina Zavec, Apolonija, Benmoussa, Abderrahim, Berardi, Anna C., Bergese, Paolo, Bielska, Ewa, Blenkiron, Cherie, Bobis-Wozowicz, Sylwia, Boilard, Eric, Boireau, Wilfrid, Bongiovanni, Antonella, Borràs, Francesc E., Bosch, Steffi, Boulanger, Chantal M., Breakefield, Xandra, Breglio, Andrew M., Brennan, Meadhbh Á., Brigstock, David R., Brisson, Alain, Broekman, Marike Ld., Bromberg, Jacqueline F., Bryl-Górecka, Paulina, Buch, Shilpa, Buck, Amy H., Burger, Dylan, Busatto, Sara, Buschmann, Dominik, Bussolati, Benedetta, Buzás, Edit I., Byrd, James Bryan, Camussi, Giovanni, Carter, David Rf., Caruso, Sarah, Chamley, Lawrence W., Chang, Yu-Ting, Chen, Chihchen, Chen, Shuai, Cheng, Lesley, Chin, Andrew R., Clayton, Aled, Clerici, Stefano P., Cocks, Alex, Cocucci, Emanuele, Coffey, Robert J., Cordeiro-Da-Silva, Anabela, Couch, Yvonne, Coumans, Frank Aw., Coyle, Beth, Crescitelli, Rossella, Criado, Miria Ferreira, D'Souza-Schorey, Crislyn, Das, Saumya, Datta Chaudhuri, Amrita, De Candia, Paola, De Santana, Eliezer F., De Wever, Olivier, Del Portillo, Hernando A., Demaret, Tanguy, Deville, Sarah, Devitt, Andrew, Dhondt, Bert, Di Vizio, Dolores, Dieterich, Lothar C., Dolo, Vincenza, Dominguez Rubio, Ana Paula, Dominici, Massimo, Dourado, Mauricio R., Driedonks, Tom Ap., Duarte, Filipe V., Duncan, Heather M., Eichenberger, Ramon M., Ekström, Karin, El Andaloussi, Samir, Elie-Caille, Celine, Erdbrügger, Uta, Falcón-Pérez, Juan M., Fatima, Farah, Fish, Jason E., Flores-Bellver, Miguel, Försönits, András, Frelet-Barrand, Annie, Fricke, Fabia, Fuhrmann, Gregor, Gabrielsson, Susanne, Gámez-Valero, Ana, Gardiner, Chris, Gärtner, Kathrin, Gaudin, Raphael, Gho, Yong Song, Giebel, Bernd, Gilbert, Caroline, Gimona, Mario, Giusti, Ilaria, Goberdhan, Deborah Ci, Görgens, André, Gorski, Sharon M., Greening, David W., Gross, Julia Christina, Gualerzi, Alice, Gupta, Gopal N., Gustafson, Dakota, Handberg, Aase, Haraszti, Reka A., Harrison, Paul, Hegyesi, Hargita, Hendrix, An, Hill, Andrew F., Hochberg, Fred H., Hoffmann, Karl F., Holder, Beth, Holthofer, Harry, Hosseinkhani, Baharak, Hu, Guoku, Huang, Yiyao, Huber, Veronica, Hunt, Stuart, Ibrahim, Ahmed Gamal-Eldin, Ikezu, Tsuneya, Inal, Jameel M., Isin, Mustafa, Ivanova, Alena, Jackson, Hannah K., Jacobsen, Soren, Jay, Steven M, Jayachandran, Muthuvel, Jenster, Guido, Jiang, Lanzhou, Johnson, Suzanne M., Jones, Jennifer C., Jong, Ambrose, Jovanovic-Talisman, Tijana, Jung, Stephanie, Kalluri, Raghu, Kano, Shin-Ichi, Kaur, Sukhbir, Kawamura, Yumi, Keller, Evan T., Khamari, Delaram, Khomyakova, Elena, Khvorova, Anastasia, Kierulf, Peter, Kim, Kwang Pyo, Kislinger, Thomas, Klingeborn, Mikael, Klinke, David J., Kornek, Miroslaw, Kosanović, Maja M., Kovács, Árpád Ferenc, Krämer-Albers, Eva-Maria, Krasemann, Susanne, Krause, Mirja, Kurochkin, Igor V., Kusuma, Gina D., Kuypers, Sören, Laitinen, Saara, Langevin, Scott M., Languino, Lucia R., Lannigan, Joanne, Lässer, Cecilia, Laurent, Louise C., Lavieu, Gregory, Lázaro-Ibáñez, Elisa, Le Lay, Soazig, Lee, Myung-Shin, Lee, Yi Xin Fiona, Lemos, Debora S., Lenassi, Metka, Leszczynska, Aleksandra, Li, Isaac Ts, Liao, Ke, Libregts, Sten F., Ligeti, Erzsebet, Lim, Rebecca, Lim, Sai Kiang, Linē, Aija, Linnemannstöns, Karen, Llorente, Alicia, Lombard, Catherine A., Lorenowicz, Magdalena J., Lörincz, Ákos M., Lötvall, Jan, Lovett, Jason, Lowry, Michelle C., Loyer, Xavier, Lu, Quan, Lukomska, Barbara, Lunavat, Taral R., Maas, Sybren Ln, Malhi, Harmeet, Marcilla, Antonio, Mariani, Jacopo, Mariscal, Javier, Martens-Uzunova, Elena S., Martin-Jaular, Lorena, Martinez, M Carmen, Martins, Vilma Regina, Mathieu, Mathilde, Mathivanan, Suresh, Maugeri, Marco, McGinnis, Lynda K., McVey, Mark J., Meckes, David G., Meehan, Katie L., Mertens, Inge, Minciacchi, Valentina R., Möller, Andreas, Møller Jørgensen, Malene, Morales-Kastresana, Aizea, Morhayim, Jess, Mullier, François, Muraca, Maurizio, Musante, Luca, Mussack, Veronika, Muth, Dillon C., Myburgh, Kathryn H., Najrana, Tanbir, Nawaz, Muhammad, Nazarenko, Irina, Nejsum, Peter, Neri, Christian, Neri, Tommaso, Nieuwland, Rienk, Nimrichter, Leonardo, Nolan, John P., Nolte-'T Hoen, Esther Nm, Noren Hooten, Nicole, O'Driscoll, Lorraine, O'Grady, Tina, O'Loghlen, Ana, Ochiya, Takahiro, Olivier, Martin, Ortiz, Alberto, Ortiz, Luis A., Osteikoetxea, Xabier, Østergaard, Ole, Ostrowski, Matias, Park, Jaesung, Pegtel, D Michiel, Peinado, Hector, Perut, Francesca, Pfaffl, Michael W., Phinney, Donald G., Pieters, Bartijn Ch., Pink, Ryan C., Pisetsky, David S., Pogge Von Strandmann, Elke, Polakovicova, Iva, Poon, Ivan Kh, Powell, Bonita H., Prada, Ilaria, Pulliam, Lynn, Quesenberry, Peter, Radeghieri, Annalisa, Raffai, Robert L., Raimondo, Stefania, Rak, Janusz, Ramirez, Marcel I., Raposo, Graça, Rayyan, Morsi S., Regev-Rudzki, Neta, Ricklefs, Franz L., Robbins, Paul D., Roberts, David D., Rodrigues, Silvia C., Rohde, Eva, Rome, Sophie, Rouschop, Kasper Ma, Rughetti, Aurelia, Russell, Ashley E., Saá, Paula, Sahoo, Susmita, Salas-Huenuleo, Edison, Sánchez, Catherine, Saugstad, Julie A., Saul, Meike J., Schiffelers, Raymond M., Schneider, Raphael, Schøyen, Tine Hiorth, Scott, Aaron, Shahaj, Eriomina, Sharma, Shivani, Shatnyeva, Olga, Shekari, Faezeh, Shelke, Ganesh Vilas, Shetty, Ashok K., Shiba, Kiyotaka, Siljander, Pia R-M, Silva, Andreia M., Skowronek, Agata, Snyder, Orman L., Soares, Rodrigo Pedro, Sódar, Barbara W., Soekmadji, Carolina, Sotillo, Javier, Stahl, Philip D., Stoorvogel, Willem, Stott, Shannon L., Strasser, Erwin F., Swift, Simon, Tahara, Hidetoshi, Tewari, Muneesh, Timms, Kate, Tiwari, Swasti, Tixeira, Rochelle, Tkach, Mercedes, Toh, Wei Seong, Tomasini, Richard, Torrecilhas, Ana Claudia, Tosar, Juan Pablo, Toxavidis, Vasilis, Urbanelli, Lorena, Vader, Pieter, Van Balkom, Bas Wm, Van Der Grein, Susanne G., Van Deun, Jan, Van Herwijnen, Martijn Jc, Van Keuren-Jensen, Kendall, Van Niel, Guillaume, Van Royen, Martin E., Van Wijnen, Andre J., Vasconcelos, M Helena, Vechetti, Ivan J., Veit, Tiago D., Vella, Laura J., Velot, Émilie, Verweij, Frederik J., Vestad, Beate, Viñas, Jose L., Visnovitz, Tamás, Vukman, Krisztina V., Wahlgren, Jessica, Watson, Dionysios C., Wauben, Marca Hm, Weaver, Alissa, Webber, Jason P., Weber, Viktoria, Wehman, Ann M., Weiss, Daniel J., Welsh, Joshua A., Wendt, Sebastian, Wheelock, Asa M., Wiener, Zoltán, Witte, Leonie, Wolfram, Joy, Xagorari, Angeliki, Xander, Patricia, Xu, Jing, Yan, Xiaomei, Yáñez-Mó, María, Yin, Hang, Yuana, Yuana, Zappulli, Valentina, Zarubova, Jana, Žėkas, Vytautas, Zhang, Jian-Ye, Zhao, Zezhou, Zheng, Lei, Zheutlin, Alexander R., Zickler, Antje M., Zimmermann, Pascale, Zivkovic, Angela M., Zocco, Davide, and Zuba-Surma, Ewa K.

Subjects
3. Good health

91. Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

Author

Théry, Clotilde, Witwer, Kenneth W, Aikawa, Elena, Alcaraz, Maria Jose, Anderson, Johnathon D, Andriantsitohaina, Ramaroson, Antoniou, Anna, Arab, Tanina, Archer, Fabienne, Atkin-Smith, Georgia K, Ayre, D Craig, Bach, Jean-Marie, Bachurski, Daniel, Baharvand, Hossein, Balaj, Leonora, Baldacchino, Shawn, Bauer, Natalie N, Baxter, Amy A, Bebawy, Mary, Beckham, Carla, Bedina Zavec, Apolonija, Benmoussa, Abderrahim, Berardi, Anna C, Bergese, Paolo, Bielska, Ewa, Blenkiron, Cherie, Bobis-Wozowicz, Sylwia, Boilard, Eric, Boireau, Wilfrid, Bongiovanni, Antonella, Borràs, Francesc E, Bosch, Steffi, Boulanger, Chantal M, Breakefield, Xandra, Breglio, Andrew M, Brennan, Meadhbh Á, Brigstock, David R, Brisson, Alain, Broekman, Marike LD, Bromberg, Jacqueline F, Bryl-Górecka, Paulina, Buch, Shilpa, Buck, Amy H, Burger, Dylan, Busatto, Sara, Buschmann, Dominik, Bussolati, Benedetta, Buzás, Edit I, Byrd, James Bryan, Camussi, Giovanni, Carter, David RF, Caruso, Sarah, Chamley, Lawrence W, Chang, Yu-Ting, Chen, Chihchen, Chen, Shuai, Cheng, Lesley, Chin, Andrew R, Clayton, Aled, Clerici, Stefano P, Cocks, Alex, Cocucci, Emanuele, Coffey, Robert J, Cordeiro-Da-Silva, Anabela, Couch, Yvonne, Coumans, Frank AW, Coyle, Beth, Crescitelli, Rossella, Criado, Miria Ferreira, D’Souza-Schorey, Crislyn, Das, Saumya, Datta Chaudhuri, Amrita, De Candia, Paola, De Santana, Eliezer F, De Wever, Olivier, Del Portillo, Hernando A, Demaret, Tanguy, Deville, Sarah, Devitt, Andrew, Dhondt, Bert, Di Vizio, Dolores, Dieterich, Lothar C, Dolo, Vincenza, Dominguez Rubio, Ana Paula, Dominici, Massimo, Dourado, Mauricio R, Driedonks, Tom AP, Duarte, Filipe V, Duncan, Heather M, Eichenberger, Ramon M, Ekström, Karin, EL Andaloussi, Samir, Elie-Caille, Celine, Erdbrügger, Uta, Falcón-Pérez, Juan M, Fatima, Farah, Fish, Jason E, Flores-Bellver, Miguel, Försönits, András, Frelet-Barrand, Annie, Fricke, Fabia, Fuhrmann, Gregor, Gabrielsson, Susanne, Gámez-Valero, Ana, Gardiner, Chris, Gärtner, Kathrin, Gaudin, Raphael, Gho, Yong Song, Giebel, Bernd, Gilbert, Caroline, Gimona, Mario, Giusti, Ilaria, Goberdhan, Deborah CI, Görgens, André, Gorski, Sharon M, Greening, David W, Gross, Julia Christina, Gualerzi, Alice, Gupta, Gopal N, Gustafson, Dakota, Handberg, Aase, Haraszti, Reka A, Harrison, Paul, Hegyesi, Hargita, Hendrix, An, Hill, Andrew F, Hochberg, Fred H, Hoffmann, Karl F, Holder, Beth, Holthofer, Harry, Hosseinkhani, Baharak, Hu, Guoku, Huang, Yiyao, Huber, Veronica, Hunt, Stuart, Ibrahim, Ahmed Gamal-Eldin, Ikezu, Tsuneya, Inal, Jameel M, Isin, Mustafa, Ivanova, Alena, Jackson, Hannah K, Jacobsen, Soren, Jay, Steven M, Jayachandran, Muthuvel, Jenster, Guido, Jiang, Lanzhou, Johnson, Suzanne M, Jones, Jennifer C, Jong, Ambrose, Jovanovic-Talisman, Tijana, Jung, Stephanie, Kalluri, Raghu, Kano, Shin-Ichi, Kaur, Sukhbir, Kawamura, Yumi, Keller, Evan T, Khamari, Delaram, Khomyakova, Elena, Khvorova, Anastasia, Kierulf, Peter, Kim, Kwang Pyo, Kislinger, Thomas, Klingeborn, Mikael, Klinke, David J, Kornek, Miroslaw, Kosanović, Maja M, Kovács, Árpád Ferenc, Krämer-Albers, Eva-Maria, Krasemann, Susanne, Krause, Mirja, Kurochkin, Igor V, Kusuma, Gina D, Kuypers, Sören, Laitinen, Saara, Langevin, Scott M, Languino, Lucia R, Lannigan, Joanne, Lässer, Cecilia, Laurent, Louise C, Lavieu, Gregory, Lázaro-Ibáñez, Elisa, Le Lay, Soazig, Lee, Myung-Shin, Lee, Yi Xin Fiona, Lemos, Debora S, Lenassi, Metka, Leszczynska, Aleksandra, Li, Isaac TS, Liao, Ke, Libregts, Sten F, Ligeti, Erzsebet, Lim, Rebecca, Lim, Sai Kiang, Linē, Aija, Linnemannstöns, Karen, Llorente, Alicia, Lombard, Catherine A, Lorenowicz, Magdalena J, Lörincz, Ákos M, Lötvall, Jan, Lovett, Jason, Lowry, Michelle C, Loyer, Xavier, Lu, Quan, Lukomska, Barbara, Lunavat, Taral R, Maas, Sybren LN, Malhi, Harmeet, Marcilla, Antonio, Mariani, Jacopo, Mariscal, Javier, Martens-Uzunova, Elena S, Martin-Jaular, Lorena, Martinez, M Carmen, Martins, Vilma Regina, Mathieu, Mathilde, Mathivanan, Suresh, Maugeri, Marco, McGinnis, Lynda K, McVey, Mark J, Meckes, David G, Meehan, Katie L, Mertens, Inge, Minciacchi, Valentina R, Möller, Andreas, Møller Jørgensen, Malene, Morales-Kastresana, Aizea, Morhayim, Jess, Mullier, François, Muraca, Maurizio, Musante, Luca, Mussack, Veronika, Muth, Dillon C, Myburgh, Kathryn H, Najrana, Tanbir, Nawaz, Muhammad, Nazarenko, Irina, Nejsum, Peter, Neri, Christian, Neri, Tommaso, Nieuwland, Rienk, Nimrichter, Leonardo, Nolan, John P, Nolte-’T Hoen, Esther NM, Noren Hooten, Nicole, O’Driscoll, Lorraine, O’Grady, Tina, O’Loghlen, Ana, Ochiya, Takahiro, Olivier, Martin, Ortiz, Alberto, Ortiz, Luis A, Osteikoetxea, Xabier, Ostegaard, Ole, Ostrowski, Matias, Park, Jaesung, Pegtel, D. Michiel, Peinado, Hector, Perut, Francesca, Pfaffl, Michael W, Phinney, Donald G, Pieters, Bartijn CH, Pink, Ryan C, Pisetsky, David S, Pogge Von Strandmann, Elke, Polakovicova, Iva, Poon, Ivan KH, Powell, Bonita H, Prada, Ilaria, Pulliam, Lynn, Quesenberry, Peter, Radeghieri, Annalisa, Raffai, Robert L, Raimondo, Stefania, Rak, Janusz, Ramirez, Marcel I, Raposo, Graça, Rayyan, Morsi S, Regev-Rudzki, Neta, Ricklefs, Franz L, Robbins, Paul D, Roberts, David D, Rodrigues, Silvia C, Rohde, Eva, Rome, Sophie, Rouschop, Kasper MA, Rughetti, Aurelia, Russell, Ashley E, Saá, Paula, Sahoo, Susmita, Salas-Huenuleo, Edison, Sánchez, Catherine, Saugstad, Julie A, Saul, Meike J, Schiffelers, Raymond M, Schneider, Raphael, Schøyen, Tine Hiorth, Scott, Aaron, Shahaj, Eriomina, Sharma, Shivani, Shatnyeva, Olga, Shekari, Faezeh, Shelke, Ganesh Vilas, Shetty, Ashok K, Shiba, Kiyotaka, Siljander, Pia R-M, Silva, Andreia M, Skowronek, Agata, Snyder, Orman L, Soares, Rodrigo Pedro, Sódar, Barbara W, Soekmadji, Carolina, Sotillo, Javier, Stahl, Philip D, Stoorvogel, Willem, Stott, Shannon L, Strasser, Erwin F, Swift, Simon, Tahara, Hidetoshi, Tewari, Muneesh, Timms, Kate, Tiwari, Swasti, Tixeira, Rochelle, Tkach, Mercedes, Toh, Wei Seong, Tomasini, Richard, Torrecilhas, Ana Claudia, Tosar, Juan Pablo, Toxavidis, Vasilis, Urbanelli, Lorena, Vader, Pieter, Van Balkom, Bas WM, Van Der Grein, Susanne G, Van Deun, Jan, Van Herwijnen, Martijn JC, Van Keuren-Jensen, Kendall, Van Niel, Guillaume, Van Royen, Martin E, Van Wijnen, Andre J, Vasconcelos, M Helena, Vechetti, Ivan J, Veit, Tiago D, Vella, Laura J, Velot, Émilie, Verweij, Frederik J, Vestad, Beate, Viñas, Jose L, Visnovitz, Tamás, Vukman, Krisztina V, Wahlgren, Jessica, Watson, Dionysios C, Wauben, Marca HM, Weaver, Alissa, Webber, Jason P, Weber, Viktoria, Wehman, Ann M, Weiss, Daniel J, Welsh, Joshua A, Wendt, Sebastian, Wheelock, Asa M, Wiener, Zoltán, Witte, Leonie, Wolfram, Joy, Xagorari, Angeliki, Xander, Patricia, Xu, Jing, Yan, Xiaomei, Yáñez-Mó, María, Yin, Hang, Yuana, Yuana, Zappulli, Valentina, Zarubova, Jana, Žėkas, Vytautas, Zhang, Jian-Ye, Zhao, Zezhou, Zheng, Lei, Zheutlin, Alexander R, Zickler, Antje M, Zimmermann, Pascale, Zivkovic, Angela M, Zocco, Davide, and Zuba-Surma, Ewa K

Subjects
3. Good health
Abstract

Journal of extracellular vesicles 7(1), 1535750 (2018). doi:10.1080/20013078.2018.1535750, Published by Co-Action Publ., [S.l.]

92. Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

Author

Thery, Clotilde, Witwer, Kenneth W, Aikawa, Elena, Alcaraz, Maria Jose, Anderson, Johnathon D, Andriantsitohaina, Ramaroson, Antoniou, Anna, Arab, Tanina, Archer, Fabienne, Atkin-Smith, Georgia, Ayre, D Craig, Bach, Jean-Marie, Bachurski, Daniel, Baharvand, Hossein, Balaj, Leonora, Baldacchino, Shawn, Bauer, Natalie N, Baxter, Amy, Bebawy, Mary, Beckham, Carla, Zavec, Apolonija Bedina, Benmoussa, Abderrahim, Berardi, Anna C, Bergese, Paolo, Bielska, Ewa, Blenkiron, Cherie, Bobis-Wozowicz, Sylwia, Boilard, Eric, Boireau, Wilfrid, Bongiovanni, Antonella, Borras, Francesc E, Bosch, Steffi, Boulanger, Chantal M, Breakefield, Xandra, Breglio, Andrew M, Brennan, Meadhbh A, Brigstock, David R, Brisson, Alain, Broekman, Marike LD, Bromberg, Jacqueline F, Bryl-Gorecka, Paulina, Buch, Shilpa, Buck, Amy H, Burger, Dylan, Busatto, Sara, Buschmann, Dominik, Bussolati, Benedetta, Buzas, Edit, Byrd, James Bryan, Camussi, Giovanni, Carter, David RF, Caruso, Sarah, Chamley, Lawrence W, Chang, Yu-Ting, Chen, Chihchen, Chen, Shuai, Sim, Lesley, Chin, Andrew R, Clayton, Aled, Clerici, Stefano P, Cocks, Alex, Cocucci, Emanuele, Coffey, Robert J, Cordeiro-da-Silva, Anabela, Couch, Yvonne, Coumans, Frank AW, Coyle, Beth, Crescitelli, Rossella, Criado, Miria Ferreira, D'Souza-Schorey, Crislyn, Das, Saumya, Chaudhuri, Amrita Datta, de Candia, Paola, De Santana Junior, Eliezer F, De Wever, Olivier, del Portillo, Hernando A, Demaret, Tanguy, Deville, Sarah, Devitt, Andrew, Dhondt, Bert, Di Vizio, Dolores, Dieterich, Lothar C, Dolo, Vincenza, Rubio, Ana Paula Dominguez, Dominici, Massimo, Dourado, Mauricio R, Driedonks, Tom AP, Duarte, Filipe, Duncan, Heather M, Eichenberger, Ramon M, Ekstrom, Karin, Andaloussi, Samir EL, Elie-Caille, Celine, Erdbrugger, Uta, Falcon-Perez, Juan M, Fatima, Farah, Fish, Jason E, Flores-Bellver, Miguel, Forsonits, Andras, Frelet-Barrand, Annie, Fricke, Fabia, Fuhrmann, Gregor, Gabrielsson, Susanne, Gamez-Valero, Ana, Gardiner, Chris, Gaertner, Kathrin, Gaudin, Raphael, Gho, Yong Song, Giebel, Bernd, Gilbert, Caroline, Gimona, Mario, Giusti, Ilaria, Goberdhan, Deborah C, Goergens, Andre, Gorski, Sharon M, Greening, David, Gross, Julia Christina, Gualerzi, Alice, Gupta, Gopal N, Gustafson, Dakota, Handberg, Aase, Haraszti, Reka A, Harrison, Paul, Hegyesi, Hargita, Hendrix, An, Hill, Andrew, Hochberg, Fred H, Hoffmann, Karl F, Holder, Beth, Holthofer, Harry, Hosseinkhani, Baharak, Hu, Guoku, Huang, Yiyao, Huber, Veronica, Hunt, Stuart, Ibrahim, Ahmed Gamal-Eldin, Ikezu, Tsuneya, Inal, Jameel M, Isin, Mustafa, Ivanova, Alena, Jackson, Hannah K, Jacobsen, Soren, Jay, Steven M, Jayachandran, Muthuvel, Jenster, Guido, Jiang, Lanzhou, Johnson, Suzanne M, Jones, Jennifer C, Jong, Ambrose, Jovanovic-Talisman, Tijana, Jung, Stephanie, Kalluri, Raghu, Kano, Shin-ichi, Kaur, Sukhbir, Kawamura, Yumi, Keller, Evan T, Khamari, Delaram, Khomyakova, Elena, Khvorova, Anastasia, Kierulf, Peter, Kim, Kwang Pyo, Kislinger, Thomas, Klingeborn, Mikael, Klinke, David J, Kornek, Miroslaw, Kosanovic, Maja M, Kovacs, Arpad Ferenc, Kraemer-Albers, Eva-Maria, Krasemann, Susanne, Krause, Mirja, Kurochkin, Igor, Kusuma, Gina D, Kuypers, Soren, Laitinen, Saara, Langevin, Scott M, Languino, Lucia R, Lannigan, Joanne, Lasser, Cecilia, Laurent, Louise C, Lavieu, Gregory, Lazaro-Ibanez, Elisa, Le Lay, Soazig, Lee, Myung-Shin, Lee, Yi Xin Fiona, Lemos, Debora S, Lenassi, Metka, Leszczynska, Aleksandra, Li, Isaac TS, Liao, Ke, Libregts, Sten F, Ligeti, Erzsebet, Lim, Rebecca, Lim, Sai Kiang, Line, Aija, Linnemannstoens, Karen, Llorente, Alicia, Lombard, Catherine A, Lorenowicz, Magdalena J, Lorincz, Akos M, Lotvall, Jan, Lovett, Jason, Lowry, Michelle C, Loyer, Xavier, Lu, Quan, Lukomska, Barbara, Lunavat, Taral R, Maas, Sybren LN, Malhi, Harmeet, Marcilla, Antonio, Mariani, Jacopo, Mariscal, Javier, Martens-Uzunova, Elena S, Martin-Jaular, Lorena, Martinez, M Carmen, Martins, Vilma Regina, Mathieu, Mathilde, Mathivanan, Suresh, Maugeri, Marco, McGinnis, Lynda K, McVey, Mark J, Meckes, David G, Meehan, Katie L, Mertens, Inge, Minciacchi, Valentina R, Moller, Andreas, Jorgensen, Malene Moller, Morales-Kastresana, Aizea, Morhayim, Jess, Mullier, Francois, Muraca, Maurizio, Musante, Luca, Mussack, Veronika, Muth, Dillon C, Myburgh, Kathryn H, Najrana, Tanbir, Nawaz, Muhammad, Nazarenko, Irina, Nejsum, Peter, Neri, Christian, Neri, Tommaso, Nieuwland, Rienk, Nimrichter, Leonardo, Nolan, John P, Hoen, Esther NM Nolte-'t, Hooten, Nicole Noren, O'Driscoll, Lorraine, O'Grady, Tina, O'Loghlen, Ana, Ochiya, Takahiro, Olivier, Martin, Ortiz, Alberto, Ortiz, Luis A, Osteikoetxea, Xabier, Ostegaard, Ole, Ostrowski, Matias, Park, Jaesung, Pegtel, D Michiel, Peinado, Hector, Perut, Francesca, Pfaffl, Michael W, Phinney, Donald G, Pieters, Bartijn CH, Pink, Ryan C, Pisetsky, David S, von Strandmann, Elke Pogge, Polakovicova, Iva, Poon, Ivan, Powell, Bonita H, Prada, Ilaria, Pulliam, Lynn, Quesenberry, Peter, Radeghieri, Annalisa, Raffai, Robert L, Raimondo, Stefania, Rak, Janusz, Ramirez, Marcel, Raposo, Graca, Rayyan, Morsi S, Regev-Rudzki, Neta, Ricklefs, Franz L, Robbins, Paul D, Roberts, David D, Rodrigues, Silvia C, Rohde, Eva, Rome, Sophie, Rouschop, Kasper MA, Rughetti, Aurelia, Russell, Ashley E, Saa, Paula, Sahoo, Susmita, Salas-Huenuleo, Edison, Sanchez, Catherine, Saugstad, Julie A, Saul, Meike J, Schiffelers, Raymond M, Schneider, Raphael, Schoyen, Tine Hiorth, Scott, Aaron, Shahaj, Eriomina, Sharma, Shivani, Shatnyeva, Olga, Shekari, Faezeh, Shelke, Ganesh Vilas, Shetty, Ashok K, Shiba, Kiyotaka, Siljander, Pia R-M, Silva, Andreia M, Skowronek, Agata, Snyder, Orman L, Soares, Rodrigo Pedro, Sodar, Barbara W, Soekmadji, Carolina, Sotillo, Javier, Stahl, Philip D, Stoorvogel, Willem, Stott, Shannon L, Strasser, Erwin F, Swift, Simon, Tahara, Hidetoshi, Tewari, Muneesh, Timms, Kate, Tiwari, Swasti, Tixeira, Rochelle, Tkach, Mercedes, Toh, Wei Seong, Tomasini, Richard, Torrecilhas, Ana Claudia, Tosar, Juan Pablo, Toxavidis, Vasilis, Urbanelli, Lorena, Vader, Pieter, van Balkom, Bas WM, van der Grein, Susanne G, Van Deun, Jan, van Herwijnen, Martijn JC, Van Keuren-Jensen, Kendall, van Niel, Guillaume, van Royen, Martin E, van Wijnen, Andre J, Vasconcelos, M Helena, Vechetti, Ivan J, Veit, Tiago D, Vella, Laura J, Velot, Emilie, Verweij, Frederik J, Vestad, Beate, Vinas, Jose L, Visnovitz, Tamas, Vukman, Krisztina V, Wahlgren, Jessica, Watson, Dionysios C, Wauben, Marca HM, Weaver, Alissa, Webber, Jason P, Weber, Viktoria, Wehman, Ann M, Weiss, Daniel J, Welsh, Joshua A, Wendt, Sebastian, Wheelock, Asa M, Wiener, Zoltan, Witte, Leonie, Wolfram, Joy, Xagorari, Angeliki, Xander, Patricia, Xu, Jing, Yan, Xiaomei, Yanez-Mo, Maria, Yin, Hang, Yuana, Yuana, Zappulli, Valentina, Zarubova, Jana, Zekas, Vytautas, Zhang, Jian-ye, Zhao, Zezhou, Zheng, Lei, Zheutlin, Alexander R, Zickler, Antje M, Zimmermann, Pascale, Zivkovic, Angela M, Zocco, Davide, and Zuba-Surma, Ewa K

Subjects
3. Good health, Uncategorized
Abstract

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.

93. Specialized cell-free DNA blood collection tubes can be repurposed for extracellular vesicle isolation: a pilot study

Author

Cherie Blenkiron, Yohanes Nursalim, Ben Lawrence, Jessica K. Heatlie, Cristin G. Print, Kate Parker, Vanessa Chang, Sandra Fitzgerald, Heatlie, Jessica, Chang, Vanessa, Fitzgerald, Sandra, Nursalim, Yohanes, Parker, Kate, Lawrence, Ben, Print, Cristin G., and Blenkiron, Cherie

Subjects
Medicine (miscellaneous), Nanoparticle tracking analysis, Pilot Projects, exosomes, General Biochemistry, Genetics and Molecular Biology, cancer biomarker, Blood cell, cell-free DNA, Extracellular Vesicles, medicine, Humans, Bicinchoninic acid assay, Centrifugation, Edetic Acid, Chemistry, Liquid Biopsy, Cell Biology, General Medicine, Extracellular vesicle, Molecular biology, Microvesicles, medicine.anatomical_structure, Cell-free fetal DNA, Blood Collection Tube, extracellular vesicles, Cell-Free Nucleic Acids
Abstract

Background: Liquid biopsies offer a minimally invasive approach to patient disease diagnosis and monitoring. However, these are highly affected by preprocessing variables with many protocols designed for downstream analysis of a single molecular biomarker. Here we investigate whether specialized blood tubes could be repurposed for the analysis of an increasingly valuable biomarker, extracellular vesicles (EVs). Methods: Blood was collected from three donors into K3-EDTA, Roche, or Streck cell-free DNA (cfDNA) collection tubes and processed using sequential centrifugation either immediately or after storage for 3 days. MicroEV were collected from platelet-poor plasma by 10,000 g centrifugation and NanoEVs isolated using size exclusion chromatography. Particle size and counts were assessed by Nanoparticle Tracking Analysis, protein quantitation by bicinchoninic acid assay (BCA) assay, and dot blotting for blood cell surface proteins. Results: MicroEVs and NanoEVs could be isolated from plasma collected using all three tube types. Major variations were seen with delayed time to processing. Both MicroEV particle number and protein content increased with the processing delay. The NanoEV number did not change with the time-delay but their protein quantity increased. EV-associated proteins predominantly arose from platelets (CD61) and erythrocytes (CD235a). However, leukocyte marker CD45 was only increased in NanoEVs from ethylenediaminetetraacetic acid (EDTA) tubes, suggestive of stabilization of nucleated cells by the specialized blood tubes. Epithelial cell surface marker EpCAM, often used as a marker of cancer, remained the same across conditions in both MicroEV and NanoEV preparations indicating that these EVs were stable with time. Conclusions: Specialized cfDNA collection tubes can be repurposed for MicroEV and NanoEV analysis; however, simple counting or using protein quantity as a surrogate of EV number may be confounded by preanalytical processing. The EVs would be suitable for disease selective EV subtype analysis if the molecular target of interest is not present in blood cells. Refereed/Peer-reviewed

Published
2020

94. MiR-210 Is Induced by Oct-2, Regulates B Cells, and Inhibits Autoantibody Production.

Author

Yingting Mok, Schwierzeck, Vera, Thomas, David C., Vigorito, Elena, Rayner, Tim F., Jarvis, Lorna B., Prosser, Haydn M., Bradley, Allan, Withers, David R., Mårtensson, Inga-Lill, Corcoran, Lynn M., Blenkiron, Cherie, Miska, Eric A., Lyons, Paul A., and Smith, Kenneth G. C.

Subjects
*MICRORNA, *B cells, *AUTOANTIBODIES, *TRANSCRIPTION factors, *GENETIC overexpression, *CELL proliferation, *CELL cycle
Abstract

MicroRNAs (MiRs) are small, noncoding RNAs that regulate gene expression posttranscriptionally. In this study, we show that MiR-210 is induced by Oct-2, a key transcriptional mediator of B cell activation. Germline deletion of MiR-210 results in the development of autoantibodies from 5 mo of age. Overexpression of MiR-210 in vivo resulted in cell autonomous expansion of the B1 lineage and impaired fitness of B2 cells. Mice overexpressing MiR-210 exhibited impaired class-switched Ab responses, a finding confirmed in wild-type B cells transfected with a MiR-210 mimic. In vitro studies demonstrated defects in cellular proliferation and cell cycle entry, which were consistent with the transcriptomic analysis demonstrating downregulation of genes involved in cellular proliferation and B cell activation. These findings indicate that Oct-2 induction of MiR-210 provides a novel inhibitory mechanism for the control of B cells and autoantibody production. [ABSTRACT FROM AUTHOR]

Published
2013
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95. Deep autoencoder as an interpretable tool for Raman spectroscopy investigation of chemical and extracellular vesicle mixtures.

Author

Kazemzadeh M, Martinez-Calderon M, Otupiri R, Artuyants A, Lowe M, Ning X, Reategui E, Schultz ZD, Xu W, Blenkiron C, Chamley LW, Broderick NGR, and Hisey CL

Abstract

Surface-enhanced Raman spectroscopy (SERS) is a powerful tool that provides valuable insight into the molecular contents of chemical and biological samples. However, interpreting Raman spectra from complex or dynamic datasets remains challenging, particularly for highly heterogeneous biological samples like extracellular vesicles (EVs). To overcome this, we developed a tunable and interpretable deep autoencoder for the analysis of several challenging Raman spectroscopy applications, including synthetic datasets, chemical mixtures, a chemical milling reaction, and mixtures of EVs. We compared the results with classical methods (PCA and UMAP) to demonstrate the superior performance of the proposed technique. Our method can handle small datasets, provide a high degree of generalization such that it can fill unknown gaps within spectral datasets, and even quantify relative ratios of cell line-derived EVs to fetal bovine serum-derived EVs within mixtures. This simple yet robust approach will greatly improve the analysis capabilities for many other Raman spectroscopy applications., Competing Interests: There are no conflicts to declare., (© 2024 Optica Publishing Group.)

Published
2024
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96. Isolation and Maintenance in Culture of Primary Human Trophoblast from Term Placentae.

Author

Nursalim YNS, Groom KM, Blenkiron C, and Chamley LW

Subjects
Pregnancy, Humans, Female, Consensus, Drug Contamination, Epithelial Cells, Placenta, Trophoblasts
Abstract

Trophoblasts are placenta-specific epithelial cells that play an essential role in conducting nutrient, gas, and waste exchange between the fetus and the mother. Primary culture of human trophoblasts from donated term placentae is an important tool to study placental functions. Currently, there is a lack of general consensus of the optimal culture conditions for maintaining term trophoblast cells in vitro. A key problem with culturing trophoblasts from term placentae is overgrowth of the trophoblasts by rapidly proliferating cellular contaminants. Recently we reported a system to culture trophoblasts from term placentae which differentiate into syncytiotrophoblast-like multinucleated cells that can be maintained in culture for at least 30 days with minimal contamination. This chapter details our optimized approach for long-term, contaminant-free in vitro culture of primary trophoblasts from term placentae., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2024
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97. Manifold Learning Enables Interpretable Analysis of Raman Spectra from Extracellular Vesicle and Other Mixtures.

Author

Kazemzadeh M, Martinez-Calderon M, Otupiri R, Artuyants A, Lowe MM, Ning X, Reategui E, Schultz ZD, Xu W, Blenkiron C, Chamley LW, Broderick NGR, and Hisey CL

Abstract

Extracellular vesicles (EVs) have emerged as promising diagnostic and therapeutic candidates in many biomedical applications. However, EV research continues to rely heavily on in vitro cell cultures for EV production, where the exogenous EVs present in fetal bovine (FBS) or other required serum supplementation can be difficult to remove entirely. Despite this and other potential applications involving EV mixtures, there are currently no rapid, robust, inexpensive, and label-free methods for determining the relative concentrations of different EV subpopulations within a sample. In this study, we demonstrate that surface-enhanced Raman spectroscopy (SERS) can biochemically fingerprint fetal bovine serum-derived and bioreactor-produced EVs, and after applying a novel manifold learning technique to the acquired spectra, enables the quantitative detection of the relative amounts of different EV populations within an unknown sample. We first developed this method using known ratios of Rhodamine B to Rhodamine 6G, then using known ratios of FBS EVs to breast cancer EVs from a bioreactor culture. In addition to quantifying EV mixtures, the proposed deep learning architecture provides some knowledge discovery capabilities which we demonstrate by applying it to dynamic Raman spectra of a chemical milling process. This label-free characterization and analytical approach should translate well to other EV SERS applications, such as monitoring the integrity of semipermeable membranes within EV bioreactors, ensuring the quality or potency of diagnostic or therapeutic EVs, determining relative amounts of EVs produced in complex co-culture systems, as well as many Raman spectroscopy applications.

Published
2023
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98. Production of Extracellular Vesicles Using a CELLine Adherent Bioreactor Flask.

Author

Artuyants A, Chang V, Reshef G, Blenkiron C, Chamley LW, Leung E, and Hisey CL

Subjects
Bioreactors, Culture Media, Conditioned metabolism, Serum metabolism, Extracellular Vesicles metabolism
Abstract

The efficient production of extracellular vesicles (EVs) from adherent cells in vitro can be challenging when using conventional culture flasks. Issues such as low cell density leading to low EV yield, and the inability to completely remove bovine serum EVs without starvation contribute to this challenge. By comparison, the two-chamber CELLine adherent bioreactor can produce significantly more EVs with improved time, space, and resource efficiency. Furthermore, it is highly accessible and can continually produce EVs using long term cultures without the need for passaging. Lastly, the 10 kDa semipermeable, cellulose acetate membrane separating the cell and media chambers allows for the continual use of bovine serum in the media chamber while preventing bovine EVs from contaminating the conditioned media., (© 2021. Springer Science+Business Media, LLC.)

Published
2022
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99. Circulatory exosomal miRNA following intense exercise is unrelated to muscle and plasma miRNA abundances.

Author

D'Souza RF, Woodhead JST, Zeng N, Blenkiron C, Merry TL, Cameron-Smith D, and Mitchell CJ

Subjects
Adult, Healthy Volunteers, High-Intensity Interval Training, Humans, Male, MicroRNAs blood, Young Adult, Exercise physiology, Exosomes metabolism, MicroRNAs metabolism, Muscle, Skeletal metabolism
Abstract

MicroRNAs (miRNAs) regulate gene expression via transcript degradation and translational inhibition, and they may also function as long distance signaling molecules. Circulatory miRNAs are either protein-bound or packaged within vesicles (exosomes). Ten young men (24.6 ± 4.0 yr) underwent a single bout of high-intensity interval cycling exercise. Vastus lateralis biopsies and plasma were collected immediately before and after exercise, as well as 4 h following the exercise bout. Twenty-nine miRNAs previously reported to be regulated by acute exercise were assessed within muscle, venous plasma, and enriched circulatory exosomes via qRT-PCR. Of the 29 targeted miRNAs, 11 were altered in muscle, 8 in plasma, and 9 in the exosome fraction. Although changes in muscle and plasma expression were bidirectional, all regulated exosomal miRNAs increased following exercise. Three miRNAs were altered in all three sample pools (miR-1-3p, -16-5p, and -222-3p), three in both muscle and plasma (miR-21-5p, -134-3p, and -107), three in both muscle and exosomes (miR-23a-3p, -208a-3p, and -150-5p), and three in both plasma and exosomes (miR-486-5p, -126-3p, and -378a-5p). There was a marked discrepancy between the observed alterations between sample pools. A subset of exosomal miRNAs increased in abundance following exercise, suggesting an exercise-induced release of exosomes enriched in specific miRNAs. The uniqueness of the exosomal miRNA response suggests its relevance as a sample pool that needs to be further explored in better understanding biological functions.

Published
2018
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100. Bacterial RNA as a signal to eukaryotic cells as part of the infection process.

Author

Simonov D, Swift S, Blenkiron C, and Phillips AR

Abstract

The discovery of regulatory RNA has identified an underappreciated area for microbial subversion of the host. There is increasing evidence that RNA can be delivered from bacteria to host cells associated with membrane vesicles or by direct release from intracellular bacteria. Once inside the host cell, RNA can act by activating sequence-independent receptors of the innate immune system, where recent findings suggest this can be more than simple pathogen detection, and may contribute to the subversion of immune responses. Sequence specific effects are also being proposed, with examples from nematode, plant and human models providing support for the proposition that bacteria-to-human RNA signaling and the subversion of host gene expression may occur., Competing Interests: Conflict of interests: The authors declare that there are no conflicts of interest., (Copyright: © 2016, Simonov et al. and Applied Systems.)

Published
2016
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