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1. Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research

Author

Mateescu, Bogdan, Jones, Jennifer C, Alexander, Roger P, Alsop, Eric, An, Ji Yeong, Asghari, Mohammad, Boomgarden, Alex, Bouchareychas, Laura, Cayota, Alfonso, Chang, Hsueh-Chia, Charest, Al, Chiu, Daniel T, Coffey, Robert J, Das, Saumya, De Hoff, Peter, deMello, Andrew, D’Souza-Schorey, Crislyn, Elashoff, David, Eliato, Kiarash R, Franklin, Jeffrey L, Galas, David J, Gerstein, Mark B, Ghiran, Ionita H, Go, David B, Gould, Stephen, Grogan, Tristan R, Higginbotham, James N, Hladik, Florian, Huang, Tony Jun, Huo, Xiaoye, Hutchins, Elizabeth, Jeppesen, Dennis K, Jovanovic-Talisman, Tijana, Kim, Betty YS, Kim, Sung, Kim, Kyoung-Mee, Kim, Yong, Kitchen, Robert R, Knouse, Vaughan, LaPlante, Emily L, Lebrilla, Carlito B, Lee, L James, Lennon, Kathleen M, Li, Guoping, Li, Feng, Li, Tieyi, Liu, Tao, Liu, Zirui, Maddox, Adam L, McCarthy, Kyle, Meechoovet, Bessie, Maniya, Nalin, Meng, Yingchao, Milosavljevic, Aleksandar, Min, Byoung-Hoon, Morey, Amber, Ng, Martin, Nolan, John, De Oliveira, Getulio P, Paulaitis, Michael E, Phu, Tuan Anh, Raffai, Robert L, Reátegui, Eduardo, Roth, Matthew E, Routenberg, David A, Rozowsky, Joel, Rufo, Joseph, Senapati, Satyajyoti, Shachar, Sigal, Sharma, Himani, Sood, Anil K, Stavrakis, Stavros, Stürchler, Alessandra, Tewari, Muneesh, Tosar, Juan P, Tucker-Schwartz, Alexander K, Turchinovich, Andrey, Valkov, Nedyalka, Van Keuren-Jensen, Kendall, Vickers, Kasey C, Vojtech, Lucia, Vreeland, Wyatt N, Wang, Ceming, Wang, Kai, Wang, ZeYu, Welsh, Joshua A, Witwer, Kenneth W, Wong, David TW, Xia, Jianping, Xie, Ya-Hong, Yang, Kaichun, Zaborowski, Mikołaj P, Zhang, Chenguang, Zhang, Qin, Zivkovic, Angela M, and Laurent, Louise C

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Biochemistry, Biological sciences, Cell biology, Molecular biology
Abstract

The extracellular RNA communication consortium (ERCC) is an NIH-funded program aiming to promote the development of new technologies, resources, and knowledge about exRNAs and their carriers. After Phase 1 (2013-2018), Phase 2 of the program (ERCC2, 2019-2023) aims to fill critical gaps in knowledge and technology to enable rigorous and reproducible methods for separation and characterization of both bulk populations of exRNA carriers and single EVs. ERCC2 investigators are also developing new bioinformatic pipelines to promote data integration through the exRNA atlas database. ERCC2 has established several Working Groups (Resource Sharing, Reagent Development, Data Analysis and Coordination, Technology Development, nomenclature, and Scientific Outreach) to promote collaboration between ERCC2 members and the broader scientific community. We expect that ERCC2's current and future achievements will significantly improve our understanding of exRNA biology and the development of accurate and efficient exRNA-based diagnostic, prognostic, and theranostic biomarker assays.

Published
2022

2. Towards defining reference materials for extracellular vesicle size, concentration, refractive index and epitope abundance

Author

Welsh, Joshua A., van der Pol, Edwin, Bettin, Britta A., Carter, David R. F., Hendrix, An, Lenassi, Metka, Langlois, Marc-André, Llorente, Alicia, van de Nes, Arthur S., Nieuwland, Rienk, Tang, Vera, Wang, Lili, Witwer, Kenneth W., and Jones, Jennifer C.

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Accurate characterization of extracellular vesicles (EVs) is critical to explore their diagnostic and therapeutic applications. As the EV research field has developed, so too have the techniques used to characterize them. The development of reference materials is required for the standardization of these techniques. This work, initiated from the ISEV 2017 Biomarker Workshop in Birmingham, UK, and with further discussion during the ISEV 2019 Standardization Workshop in Ghent, Belgium, sets out to elucidate which reference materials are required and which are currently available to standardize commonly used analysis platforms for characterizing EV size, concentration, refractive index, and epitope expression. Due to their predominant use, a particular focus is placed on the optical methods nanoparticle tracking analysis and flow cytometry., Comment: 30 pages, 6 figures, 2 tables

Published
2020
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4. Lysosomal processing of sulfatide analogs alters target NKT cell specificity and immune responses in cancer

Author

Nishio, Kumiko, Camara, Lise PasqueKaddy, DiSapio, Julia, Hsu, Kevin S., Kato, Shingo, Bloom, Anja, Richardson, Stewart K., Welsh, Joshua A., Jiang, Tianbo, Jones, Jennifer C., Cardell, Susanna, Watarai, Hiroshi, Terabe, Masaki, Olkhanud, Purevdorj B., Howell, Amy R., and Berzofsky, Jay A.

Subjects
United States. National Cancer Institute, Lipids -- Comparative analysis, Colon cancer -- Comparative analysis, Metastasis -- Comparative analysis, Sphingosine -- Comparative analysis, Immune response -- Comparative analysis, Immunotherapy -- Comparative analysis, B cells -- Comparative analysis, Antigens -- Comparative analysis, Cancer -- Comparative analysis, Sulfates -- Comparative analysis, Health care industry
Abstract

In a structure-function study of sulfatides that typically stimulate type II NKT cells, we made an unexpected discovery. We compared analogs with sphingosine or phytosphingosine chains and 24-carbon acyl chains with 0-1-2 double bonds (C or pC24:0, 24:1, or 24:2). C24:1 and C24:2 sulfatide presented by the CD1d monomer on plastic stimulated type II, not type I, NKT cell hybridomas, as expected. Unexpectedly, when presented by bone marrow- derived DCs (BMDCs), C24:2 reversed specificity to stimulate type I, not type II, NKT cell hybridomas, mimicking the corresponding [beta]-galactosylceramide ([beta]GalCer) without sulfate. C24:2 induced IFN-[gamma]-dependent immunoprotection against CT26 colon cancer lung metastases, skewed the cytokine profile, and activated conventional DC subset 1 cells (cDC1s). This was abrogated by blocking lysosomal processing with bafilomycin A1, or by sulfite blocking of arylsulfatase or deletion of this enyzme that cleaves off sulfate. Thus, C24:2 was unexpectedly processed in BMDCs from a type II to a type I NKT cell- stimulating ligand, promoting tumor immunity. We believe this is the first discovery showing that antigen processing of glycosylceramides alters the specificity for the target cell, reversing the glycolipid's function from stimulating type II NKT cells to stimulating type I NKT cells, thereby introducing protective functional activity in cancer. We also believe our study uncovers a new role for antigen processing that does not involve MHC loading but rather alteration of which type of cell is responding., Introduction The recent clinical success of checkpoint inhibitors, which manipulate T cell function and extend patient survival in many cases, provides strong motivation to treat cancer by modulating immunity. However, [...]

Published
2024
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5. High‐fidelity detection and sorting of nanoscale vesicles in viral disease and cancer

Author

Morales‐Kastresana, Aizea, Musich, Thomas A, Welsh, Joshua A, Telford, William, Demberg, Thorsten, Wood, James CS, Bigos, Marty, Ross, Carley D, Kachynski, Aliaksander, Dean, Alan, Felton, Edward J, Van Dyke, Jonathan, Tigges, John, Toxavidis, Vasilis, Parks, David R, Overton, W Roy, Kesarwala, Aparna H, Freeman, Gordon J, Rosner, Ariel, Perfetto, Stephen P, Pasquet, Lise, Terabe, Masaki, McKinnon, Katherine, Kapoor, Veena, Trepel, Jane B, Puri, Anu, Kobayashi, Hisataka, Yung, Bryant, Chen, Xiaoyuan, Guion, Peter, Choyke, Peter, Knox, Susan J, Ghiran, Ionita, Robert‐Guroff, Marjorie, Berzofsky, Jay A, and Jones, Jennifer C

Subjects
Biochemistry and Cell Biology, Biological Sciences, Nanotechnology, Bioengineering, Cancer, Nanofacs, sorting, flow cytometry, phenotyping, extracellular vesicles, Biochemistry and cell biology
Abstract

Biological nanoparticles, including viruses and extracellular vesicles (EVs), are of interest to many fields of medicine as biomarkers and mediators of or treatments for disease. However, exosomes and small viruses fall below the detection limits of conventional flow cytometers due to the overlap of particle-associated scattered light signals with the detection of background instrument noise from diffusely scattered light. To identify, sort, and study distinct subsets of EVs and other nanoparticles, as individual particles, we developed nanoscale Fluorescence Analysis and Cytometric Sorting (nanoFACS) methods to maximise information and material that can be obtained with high speed, high resolution flow cytometers. This nanoFACS method requires analysis of the instrument background noise (herein defined as the "reference noise"). With these methods, we demonstrate detection of tumour cell-derived EVs with specific tumour antigens using both fluorescence and scattered light parameters. We further validated the performance of nanoFACS by sorting two distinct HIV strains to >95% purity and confirmed the viability (infectivity) and molecular specificity (specific cell tropism) of biological nanomaterials sorted with nanoFACS. This nanoFACS method provides a unique way to analyse and sort functional EV- and viral-subsets with preservation of vesicular structure, surface protein specificity and RNA cargo activity.

Published
2019

6. Neoliberal Sexual Entrepreneurial Subjects: Student Sex Workers Responding to Twenty-first-Century Economic Demands in the US

Author

Jones, Jennifer C., Sanders, Teela, Series Editor, Jones, Angela, Series Editor, Shih, Elena, Series Editor, Ahearne, Gemma, Editorial Board Member, Armstrong, Lynzi, Editorial Board Member, Blewett, Lindsay, Editorial Board Member, Berg, Heather, Editorial Board Member, Brooks, Siobhan, Editorial Board Member, Callander, Denton, Editorial Board Member, Costales, Cocoa, Editorial Board Member, Gerasimov, Borislav, Editorial Board Member, Huysamen, Monique, Editorial Board Member, Lakkimsetti, Chaitanya, Editorial Board Member, Lister, Kate, Editorial Board Member, Macioti, Paola Gioia, Editorial Board Member, Miller-Young, Mireille, Editorial Board Member, Okyere, Samuel, Editorial Board Member, Parrenas, Rhacel, Editorial Board Member, Raguparan, Menaka, Editorial Board Member, Sinha, Sunny, Editorial Board Member, Velthuis, Olav, Editorial Board Member, Sparks, Kassandra, Editorial Board Member, Jackson, Crystal, Editorial Board Member, Kinoco, Allen, Editorial Board Member, Mwangi, Peninah, Editorial Board Member, Wotton, Rachel, Editorial Board Member, and Jones, Debbie, editor

Published
2022
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7. The EV antibody database: An interactive database of curated antibodies for extracellular vesicle and nanoparticle research

Author

Morey, Amber, primary, Ng, Martin, additional, Spanos, Michail, additional, Zhang, Piyan, additional, Xu, Tuoye, additional, Cheung, Willi, additional, Chatterjee, Emeli, additional, Gokulnath, Priyanka, additional, Carnel-Amar, Natacha, additional, Soares Chiaretti, Ana Luisa, additional, Nelson, Collin, additional, George, Jubin, additional, Luo, Michelle, additional, Chakraborty, Abhik, additional, Perucci, Luiza, additional, Jones, Jennifer C., additional, De Hoff, Peter, additional, Franklin, Jeffrey L., additional, Raffai, Robert L., additional, Das, Saumya, additional, Routenberg, David A., additional, Nolan, John P., additional, Charest, Al, additional, Laurent, Louise C., additional, and Alexander, Roger P., additional

Published
2024
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8. exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

Author

Murillo, Oscar D, Thistlethwaite, William, Rozowsky, Joel, Subramanian, Sai Lakshmi, Lucero, Rocco, Shah, Neethu, Jackson, Andrew R, Srinivasan, Srimeenakshi, Chung, Allen, Laurent, Clara D, Kitchen, Robert R, Galeev, Timur, Warrell, Jonathan, Diao, James A, Welsh, Joshua A, Hanspers, Kristina, Riutta, Anders, Burgstaller-Muehlbacher, Sebastian, Shah, Ravi V, Yeri, Ashish, Jenkins, Lisa M, Ahsen, Mehmet E, Cordon-Cardo, Carlos, Dogra, Navneet, Gifford, Stacey M, Smith, Joshua T, Stolovitzky, Gustavo, Tewari, Ashutosh K, Wunsch, Benjamin H, Yadav, Kamlesh K, Danielson, Kirsty M, Filant, Justyna, Moeller, Courtney, Nejad, Parham, Paul, Anu, Simonson, Bridget, Wong, David K, Zhang, Xuan, Balaj, Leonora, Gandhi, Roopali, Sood, Anil K, Alexander, Roger P, Wang, Liang, Wu, Chunlei, Wong, David TW, Galas, David J, Van Keuren-Jensen, Kendall, Patel, Tushar, Jones, Jennifer C, Das, Saumya, Cheung, Kei-Hoi, Pico, Alexander R, Su, Andrew I, Raffai, Robert L, Laurent, Louise C, Roth, Matthew E, Gerstein, Mark B, and Milosavljevic, Aleksandar

Subjects
Biological Sciences, Genetics, Human Genome, Biotechnology, Adult, Body Fluids, Cell Communication, Cell-Free Nucleic Acids, Circulating MicroRNA, Extracellular Vesicles, Female, Humans, Male, RNA, Reproducibility of Results, Sequence Analysis, RNA, Software, ERCC, deconvolution, exRNA, exosomes, extracellular RNA, extracellular vesicles, lipoproteins, ribonucleoproteins, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

To develop a map of cell-cell communication mediated by extracellular RNA (exRNA), the NIH Extracellular RNA Communication Consortium created the exRNA Atlas resource (https://exrna-atlas.org). The Atlas version 4P1 hosts 5,309 exRNA-seq and exRNA qPCR profiles from 19 studies and a suite of analysis and visualization tools. To analyze variation between profiles, we apply computational deconvolution. The analysis leads to a model with six exRNA cargo types (CT1, CT2, CT3A, CT3B, CT3C, CT4), each detectable in multiple biofluids (serum, plasma, CSF, saliva, urine). Five of the cargo types associate with known vesicular and non-vesicular (lipoprotein and ribonucleoprotein) exRNA carriers. To validate utility of this model, we re-analyze an exercise response study by deconvolution to identify physiologically relevant response pathways that were not detected previously. To enable wide application of this model, as part of the exRNA Atlas resource, we provide tools for deconvolution and analysis of user-provided case-control studies.

Published
2019

9. MPAPASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays

Author

Welsh, Joshua A., Killingsworth, Bryce, Kepley, Julia, Traynor, Tim, Cook, Sean, Savage, Jason, Marte, Jenn, Lee, Min-Jung, Maeng, Hoyoung M., Pleet, Michelle L., Magana, Setty, Gorgens, André, Maire, Cecile L., Lamszus, Katrin, Ricklefs, Franz L., Merino, Maria J., Linehan, W. Marston, Greten, Tim, Cooks, Tomer, Harris, Curtis C., Apolo, Andrea, Abdel-Mageed, Asim, Ivanov, Alexander R., Trepel, Jane B., Roth, Matthew, Tkach, Mercedes, Milosavljevic, Aleksandar, Théry, Clotilde, LeBlanc, Amy, Berzofsky, Jay A., Ruppin, Eytan, Aldape, Kenneth, Camphausen, Kevin, Gulley, James L., Ghiran, Ionita, Jacobson, Steve, and Jones, Jennifer C.

Published
2022
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12. Obstacles and opportunities in the functional analysis of extracellular vesicle RNA – an ISEV position paper

Author

Mateescu, Bogdan, Kowal, Emma J. K., Van Balkom, Bas W. M. Emma J. K., Bartel, Sabine, Bhattacharyya, Suvendra N., Buzás, Edit I., Buck, Amy H., Candia, Paola de, Chow, Franklin W. N., Das, Saumya, Driedonks, Tom A. P., Fernández Messina, Lola María, Haderk, Franziska, Hill, Andrew F., Jones, Jennifer C., Van Keuren‐Jensen, Kendall R., Lai, Charles P., Lässer, Cecilia, di Liegro, Italia, Lunavat, Taral R., Lorenowicz, Magdalena J., Maas, Sybren L. N., Mäger, Imre, Mittelbrunn, Maria, Momma, Stefan, Mukherjee, Kamalika, Nawaz, Muhammad, Pegtel, D. Michiel, Pfaffl, Michael W., Schiffelers, Raymond M., Tahara, Hidetoshi, Théry, Clotilde, Tosar, Juan Pablo, Wauben, Marca H. M., Witwer, Kenneth W., Nolte‐'t Hoen, Esther N. M., Mateescu, Bogdan, Kowal, Emma J. K., Van Balkom, Bas W. M. Emma J. K., Bartel, Sabine, Bhattacharyya, Suvendra N., Buzás, Edit I., Buck, Amy H., Candia, Paola de, Chow, Franklin W. N., Das, Saumya, Driedonks, Tom A. P., Fernández Messina, Lola María, Haderk, Franziska, Hill, Andrew F., Jones, Jennifer C., Van Keuren‐Jensen, Kendall R., Lai, Charles P., Lässer, Cecilia, di Liegro, Italia, Lunavat, Taral R., Lorenowicz, Magdalena J., Maas, Sybren L. N., Mäger, Imre, Mittelbrunn, Maria, Momma, Stefan, Mukherjee, Kamalika, Nawaz, Muhammad, Pegtel, D. Michiel, Pfaffl, Michael W., Schiffelers, Raymond M., Tahara, Hidetoshi, Théry, Clotilde, Tosar, Juan Pablo, Wauben, Marca H. M., Witwer, Kenneth W., and Nolte‐'t Hoen, Esther N. M.

Abstract

Acknowledgements We thank all participants of the 2015 ISEV workshop on EV-RNA for their valuable input in roundtable discussions, which formed the basis for this position paper. We are grateful to Dr P. Vader for preparing Figure 3., The release of RNA-containing extracellular vesicles (EV) into the extracellular milieu has been demonstrated in a multitude of different in vitro cell systems and in a variety of body fluids. RNA-containing EV are in the limelight for their capacity to communicate genetically encoded messages to other cells, their suitability as candidate biomarkers for diseases, and their use as therapeutic agents. Although EV-RNA has attracted enormous interest from basic researchers, clinicians, and industry, we currently have limited knowledge on which mechanisms drive and regulate RNA incorporation into EV and on how RNA-encoded messages affect signalling processes in EV-targeted cells. Moreover, EV-RNA research faces various technical challenges, such as standardisation of EV isolation methods, optimisation of methodologies to isolate and characterise minute quantities of RNA found in EV, and development of approaches to demonstrate functional transfer of EV-RNA in vivo. These topics were discussed at the 2015 EV-RNA workshop of the International Society for Extracellular Vesicles. This position paper was written by the participants of the workshop not only to give an overview of the current state of knowledge in the field, but also to clarify that our incomplete knowledge – of the nature of EV(-RNA)s and of how to effectively and reliably study them – currently prohibits the implementation of gold standards in EV-RNA research. In addition, this paper creates awareness of possibilities and limitations of currently used strategies to investigate EV-RNA and calls for caution in interpretation of the obtained data., Depto. de Biología Celular, Fac. de Ciencias Biológicas, TRUE, pub

Published
2024

13. 'It's Complex:' Student Sex Workers Constructing Their Lives in the 21st Century: A Modified Qualitative Content Analysis

Author

Jones, Jennifer C.

Abstract

Individuals in the United States who work in the sex industry while in undergraduate or graduate school are in the unique position of straddling between the two seemingly disparate worlds of academia and the sex industry. This position has the potential to put them at greater risk of isolation due to stigmatization and the threat of criminalization. Limited empirical data has been gathered regarding student sex workers' financial, personal, and professional goals; how they manage life challenges and who they turn to for support, or what student sex workers need. To address this gap, a qualitative content analysis was conducted with 17 cisgender female student sex workers, ages 19 to 33 years. Using semi-structured interviews, demographic surveys, and contextual interviews with five key informants, this study sought to understand how the participants constructed their lives as students and as sex workers and how 21st century neoliberal economic policies and sensibilities factored into their constructions. Four themes emerged: 1) Doing what is socially expected; 2) Doing what the 21st century economy demands; 3) Embracing a stigmatized identity: "I am a sex worker" while also resisting the stigma attached to it; and 4) Needing and deserving acknowledgement rather than being saved or judged by social workers and academic institutions. With knowledge gained from this study, social workers are in a position to support student sex workers and raise staff awareness on campuses, as well as impact national policy debates regarding sex work criminalization. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Published
2019

14. Inter‐laboratory multiplex bead‐based surface protein profiling of MSC‐derived EV preparations identifies MSC‐EV surface marker signatures.

Author

Nguyen, Vivian V. T., Welsh, Joshua A., Tertel, Tobias, Choo, Andre, van de Wakker, Simonides I., Defourny, Kyra A. Y., Giebel, Bernd, Vader, Pieter, Padmanabhan, Jayanthi, Lim, Sai Kiang, Nolte‐'t Hoen, Esther N. M., Verhaar, Marianne C., Bostancioglu, R. Beklem, Zickler, Antje M., Hong, Jia Mei, Jones, Jennifer C., EL Andaloussi, Samir, van Balkom, Bas W. M., and Görgens, André

Subjects
EXTRACELLULAR vesicles, STROMAL cells, MANUFACTURED products, HIERARCHICAL clustering (Cluster analysis), CD19 antigen, LABORATORIES
Abstract

Mesenchymal stromal cells (MSCs) are promising regenerative therapeutics that primarily exert their effects through secreted extracellular vesicles (EVs). These EVs – being small and non‐living – are easier to handle and possess advantages over cellular products. Consequently, the therapeutic potential of MSC‐EVs is increasingly investigated. However, due to variations in MSC‐EV manufacturing strategies, MSC‐EV products should be considered as highly diverse. Moreover, the diverse array of EV characterisation technologies used for MSC‐EV characterisation further complicates reliable interlaboratory comparisons of published data. Consequently, this study aimed to establish a common method that can easily be used by various MSC‐EV researchers to characterise MSC‐EV preparations to facilitate interlaboratory comparisons. To this end, we conducted a comprehensive inter‐laboratory assessment using a novel multiplex bead‐based EV flow cytometry assay panel. This assessment involved 11 different MSC‐EV products from five laboratories with varying MSC sources, culture conditions, and EV preparation methods. Through this assay panel covering a range of mostly MSC‐related markers, we identified a set of cell surface markers consistently positive (CD44, CD73 and CD105) or negative (CD11b, CD45 and CD197) on EVs of all explored MSC‐EV preparations. Hierarchical clustering analysis revealed distinct surface marker profiles associated with specific preparation processes and laboratory conditions. We propose CD73, CD105 and CD44 as robust positive markers for minimally identifying MSC‐derived EVs and CD11b, CD14, CD19, CD45 and CD79 as reliable negative markers. Additionally, we highlight the influence of culture medium components, particularly human platelet lysate, on EV surface marker profiles, underscoring the influence of culture conditions on resulting EV products. This standardisable approach for MSC‐EV surface marker profiling offers a tool for routine characterisation of manufactured EV products in pre‐clinical and clinical research, enhances the quality control of MSC‐EV preparations, and hopefully paves the way for higher consistency and reproducibility in the emerging therapeutic MSC‐EV field. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Lysosomal processing of sulfatide analogues alters target NKT cell specificity and immune responses in cancer

Author

Nishio, Kumiko, primary, Pasquet, Lise, additional, Camara, Kaddy, additional, DiSapio, Julia, additional, Kato, Shingo, additional, Hsu, Kevin S., additional, Bloom, Anja, additional, Richardson, Stewart K., additional, Welsh, Joshua A., additional, Jiang, Tianbo, additional, Jones, Jennifer C., additional, Cardell, Susanna, additional, Watarai, Hiroshi, additional, Terabe, Masaki, additional, Olkhanud, Purevdorj B., additional, Howell, Amy R., additional, and Berzofsky, Jay A., additional

Published
2023
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16. MIBlood‐EV: Minimal information to enhance the quality and reproducibility of blood extracellular vesicle research

Author

Lucien, Fabrice, primary, Gustafson, Dakota, additional, Lenassi, Metka, additional, Li, Bo, additional, Teske, Jacob J., additional, Boilard, Eric, additional, von Hohenberg, Katharina Clemm, additional, Falcón‐Perez, Juan Manual, additional, Gualerzi, Alice, additional, Reale, Antonia, additional, Jones, Jennifer C., additional, Lässer, Cecilia, additional, Lawson, Charlotte, additional, Nazarenko, Irina, additional, O'Driscoll, Lorraine, additional, Pink, Ryan, additional, Siljander, Pia R‐M, additional, Soekmadji, Carolina, additional, Hendrix, An, additional, Welsh, Joshua A, additional, Witwer, Kenneth W., additional, and Nieuwland, Rienk, additional

Published
2023
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19. Melanocytes derived from transgene-free human induced pluripotent stem cells.

Author

Jones, Jennifer C, Sabatini, Karen, Liao, Xiaoyan, Tran, Ha T, Lynch, Candace L, Morey, Robert E, Glenn-Pratola, Victoria, Boscolo, Francesca S, Yang, Qinghong, Parast, Mana M, Liu, Ying, Peterson, Suzanne E, Laurent, Louise C, Loring, Jeanne F, and Wang, Yu-Chieh

Subjects
Melanocytes, Animals, Humans, Mice, Cell Culture Techniques, Coculture Techniques, Cell Differentiation, Transgenes, Induced Pluripotent Stem Cells, Feeder Cells, Dermatology & Venereal Diseases, Clinical Sciences, Oncology and Carcinogenesis
Published
2013

20. Viral Immune signatures from cerebrospinal fluid extracellular vesicles and particles in HAM and other chronic neurological diseases

Author

Pleet, Michelle L., primary, Welsh, Joshua A., additional, Stack, Emily H., additional, Cook, Sean, additional, Johnson, Dove-Anna, additional, Killingsworth, Bryce, additional, Traynor, Tim, additional, Clauze, Annaliese, additional, Hughes, Randall, additional, Monaco, Maria Chiara, additional, Ngouth, Nyater, additional, Ohayon, Joan, additional, Enose-Akahata, Yoshimi, additional, Nath, Avindra, additional, Cortese, Irene, additional, Reich, Daniel S., additional, Jones, Jennifer C., additional, and Jacobson, Steven, additional

Published
2023
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21. The NanoFlow Repository

Author

Arce, Jessie E, primary, Welsh, Joshua A, additional, Cook, Sean, additional, Tigges, John, additional, Ghiran, Ionita, additional, Jones, Jennifer C, additional, Jackson, Andrew, additional, Roth, Matthew, additional, and Milosavljevic, Aleksandar, additional

Published
2023
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24. Supplementary Figure from Immune Checkpoint Blockade in Combination with Stereotactic Body Radiotherapy in Patients with Metastatic Pancreatic Ductal Adenocarcinoma

Author

Xie, Changqing, primary, Duffy, Austin G., primary, Brar, Gagandeep, primary, Fioravanti, Suzanne, primary, Mabry-Hrones, Donna, primary, Walker, Melissa, primary, Bonilla, Cecilia Monge, primary, Wood, Bradford J., primary, Citrin, Deborah E., primary, Gil Ramirez, Elizabeth M., primary, Escorcia, Freddy E., primary, Redd, Bernadette, primary, Hernandez, Jonathan M., primary, Davis, Jeremy L., primary, Gasmi, Billel, primary, Kleiner, David, primary, Steinberg, Seth M., primary, Jones, Jennifer C., primary, and Greten, Tim F., primary

Published
2023
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25. Exosomes, microvesicles, and other extracellular vesicles—a Keystone Symposia report

Author

Cable, Jennifer, primary, Witwer, Kenneth W., additional, Coffey, Robert J., additional, Milosavljevic, Aleksandar, additional, von Lersner, Ariana K., additional, Jimenez, Lizandra, additional, Pucci, Ferdinando, additional, Barr, Maureen M., additional, Dekker, Niek, additional, Barman, Bahnisikha, additional, Humphrys, Daniel, additional, Williams, Justin, additional, de Palma, Michele, additional, Guo, Wei, additional, Bastos, Nuno, additional, Hill, Andrew F., additional, Levy, Efrat, additional, Hantak, Michael P., additional, Crewe, Clair, additional, Aikawa, Elena, additional, Adamczyk, Alan M., additional, Zanotto, Tamires M., additional, Ostrowski, Matias, additional, Arab, Tanina, additional, Rabe, Daniel C., additional, Sheikh, Aadil, additional, da Silva, Danilo Rodrigues, additional, Jones, Jennifer C., additional, Okeoma, Chioma, additional, Gaborski, Thomas, additional, Zhang, Qin, additional, and Gololobova, Olesia, additional

Published
2023
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26. A compendium of single extracellular vesicle flow cytometry

Author

IOV Facs, Celbiologie, Welsh, Joshua A, Arkesteijn, Ger J A, Bremer, Michel, Cimorelli, Michael, Dignat-George, Françoise, Giebel, Bernd, Görgens, André, Hendrix, An, Kuiper, Martine, Lacroix, Romaric, Lannigan, Joanne, van Leeuwen, Ton G, Lozano-Andrés, Estefanía, Rao, Shoaib, Robert, Stéphane, de Rond, Leonie, Tang, Vera A, Tertel, Tobias, Yan, Xiaomei, Wauben, Marca H M, Nolan, John P, Jones, Jennifer C, Nieuwland, Rienk, van der Pol, Edwin, IOV Facs, Celbiologie, Welsh, Joshua A, Arkesteijn, Ger J A, Bremer, Michel, Cimorelli, Michael, Dignat-George, Françoise, Giebel, Bernd, Görgens, André, Hendrix, An, Kuiper, Martine, Lacroix, Romaric, Lannigan, Joanne, van Leeuwen, Ton G, Lozano-Andrés, Estefanía, Rao, Shoaib, Robert, Stéphane, de Rond, Leonie, Tang, Vera A, Tertel, Tobias, Yan, Xiaomei, Wauben, Marca H M, Nolan, John P, Jones, Jennifer C, Nieuwland, Rienk, and van der Pol, Edwin

Published
2023

28. Lymph Nodes, Thymus, Spleen, and Lymphatics

Author

Jones, Jennifer C., Knox, Susan J., Brady, Luther W., Series editor, Molls, Michael, Series editor, Heilmann, Hans-Peter, Series editor, Nieder, Carsten, Series editor, Rubin, Philip, editor, Constine, Louis S., editor, and Marks, Lawrence B., editor

Published
2014
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29. A compendium of single extracellular vesicle flow cytometry

Author

Welsh, Joshua A., primary, Arkesteijn, Ger J. A., additional, Bremer, Michel, additional, Cimorelli, Michael, additional, Dignat‐George, Françoise, additional, Giebel, Bernd, additional, Görgens, André, additional, Hendrix, An, additional, Kuiper, Martine, additional, Lacroix, Romaric, additional, Lannigan, Joanne, additional, van Leeuwen, Ton G., additional, Lozano‐Andrés, Estefanía, additional, Rao, Shoaib, additional, Robert, Stéphane, additional, de Rond, Leonie, additional, Tang, Vera A., additional, Tertel, Tobias, additional, Yan, Xiaomei, additional, Wauben, Marca H. M., additional, Nolan, John P., additional, Jones, Jennifer C., additional, Nieuwland, Rienk, additional, and van der Pol, Edwin, additional

Published
2023
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30. A compendium of single extracellular vesicle flow cytometry

Author

Welsh, Joshua A., Arkesteijn, Ger J. A., Bremer, Michel, Cimorelli, Michael, Dignat-George, Françoise, Giebel, Bernd, Görgens, André, Hendrix, An, Kuiper, Martine, Lacroix, Romaric, Lannigan, Joanne, van Leeuwen, Ton G., Lozano-Andrés, Estefanía, Rao, Shoaib, Robert, Stéphane, de Rond, Leonie, Tang, Vera A., Tertel, Tobias, Yan, Xiaomei, Wauben, Marca H. M., Nolan, John P., Jones, Jennifer C., Nieuwland, Rienk, and van der Pol, Edwin

Subjects
Medizin
Abstract

Flow cytometry (FCM) offers a multiparametric technology capable of characterizing single extracellular vesicles (EVs). However, most flow cytometers are designed to detect cells, which are larger than EVs. Whereas cells exceed the background noise, signals originating from EVs partly overlap with the background noise, thereby making EVs more difficult to detect than cells. This technical mismatch together with complexity of EV-containing fluids causes limitations and challenges with conducting, interpreting and reproducing EV FCM experiments. To address and overcome these challenges, researchers from the International Society for Extracellular Vesicles (ISEV), International Society for Advancement of Cytometry (ISAC), and the International Society on Thrombosis and Haemostasis (ISTH) joined forces and initiated the EV FCM working group. To improve the interpretation, reporting, and reproducibility of future EV FCM data, the EV FCM working group published an ISEV position manuscript outlining a framework of minimum information that should be reported about an FCM experiment on single EVs (MIFlowCyt-EV). However, the framework contains limited background information. Therefore, the goal of this compendium is to provide the background information necessary to design and conduct reproducible EV FCM experiments. This compendium contains background information on EVs, the interaction between light and EVs, FCM hardware, experimental design and preanalytical procedures, sample preparation, assay controls, instrument data acquisition and calibration, EV characterization, and data reporting. Although this compendium focuses on EVs, many concepts and explanations could also be applied to FCM detection of other particles within the EV size range, such as bacteria, lipoprotein particles, milk fat globules, and viruses. CA extern

Published
2023

33. Identification of markers for tumor- and immune-derived extracellular vesicles (EVs) in preclinical models.

Author

Johnson, Dove-Anna, primary, Pleet, Michelle, additional, Welsh, Joshua Aden, additional, Cook, Sean, additional, Savage, Jason, additional, Mirza Nasiri, Nooshin, additional, Camphausen, Kevin A., additional, Aldape, Kenneth D., additional, Gulley, James L., additional, Mock, Beverly A, additional, Berzofsky, Jay A., additional, Jacobson, Steve, additional, and Jones, Jennifer C, additional

Published
2022
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36. Use of Psychotropic Medication in Oklahoma: A Statewide Survey.

Author

Spreat, Scott, Conroy, James W., and Jones, Jennifer C.

Abstract

Analysis of statewide (Oklahoma) survey data revealed that 22.5% of individuals with mental retardation who were served by the Oklahoma mental retardation system were receiving antipsychotic medication. Higher levels of medication use were found in institutional settings and Intermediate Care Facility settings. (Author/DB)

Published
1997

39. A phase I study of bintrafusp alfa (M7824) and NHS-IL12 (M9241) alone and in combination with stereotactic body radiation therapy (SBRT) in adults with metastatic non-prostate genitourinary malignancies.

Author

Niglio, Scot Anthony, primary, Girardi, Daniel da Motta, additional, Cordes, Lisa M., additional, Ley, Lisa, additional, Mallek, Marissa, additional, Sierra Ortiz, Olena, additional, Cadena, Jacqueline, additional, Diaz, Carlos, additional, Chalfin, Heather, additional, Kydd, Andre, additional, Costello, Rene, additional, Marciscano, Ariel E., additional, Jones, Jennifer C, additional, Salerno, Kilian Elizabeth, additional, Valera, Vladimir, additional, Figg, William Douglas, additional, Dahut, William L., additional, Gulley, James L., additional, Schlom, Jeffrey, additional, and Apolo, Andrea B., additional

Published
2021
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40. MIFlowCyt-EV: a framework for standardized reporting of extracellular vesicle flow cytometry experiments

Author

LS Celbiologie-Algemeen, Celbiologie, dB&C I&I, Welsh, Joshua A, Van Der Pol, Edwin, Arkesteijn, Ger J A, Bremer, Michel, Brisson, Alain, Coumans, Frank, Dignat-George, Françoise, Duggan, Erika, Ghiran, Ionita, Giebel, Bernd, Görgens, André, Hendrix, An, Lacroix, Romaric, Lannigan, Joanne, Libregts, Sten F W M, Lozano-Andrés, Estefanía, Morales-Kastresana, Aizea, Robert, Stephane, De Rond, Leonie, Tertel, Tobias, Tigges, John, De Wever, Olivier, Yan, Xiaomei, Nieuwland, Rienk, Wauben, Marca H M, Nolan, John P, Jones, Jennifer C, LS Celbiologie-Algemeen, Celbiologie, dB&C I&I, Welsh, Joshua A, Van Der Pol, Edwin, Arkesteijn, Ger J A, Bremer, Michel, Brisson, Alain, Coumans, Frank, Dignat-George, Françoise, Duggan, Erika, Ghiran, Ionita, Giebel, Bernd, Görgens, André, Hendrix, An, Lacroix, Romaric, Lannigan, Joanne, Libregts, Sten F W M, Lozano-Andrés, Estefanía, Morales-Kastresana, Aizea, Robert, Stephane, De Rond, Leonie, Tertel, Tobias, Tigges, John, De Wever, Olivier, Yan, Xiaomei, Nieuwland, Rienk, Wauben, Marca H M, Nolan, John P, and Jones, Jennifer C

Published
2020

41. Optimisation of imaging flow cytometry for the analysis of single extracellular vesicles by using fluorescence-tagged vesicles as biological reference material

Author

Görgens, André, Bremer, Michel, Ferrer-Tur, Rita, Murke, Florian, Tertel, Tobias, Horn, Peter A., Thalmann, Sebastian, Welsh, Joshua A., Probst, Christine, Guerin, Coralié, Boulanger, Chantal M., Jones, Jennifer C., Hanenberg, Helmut, Erdbrügger, Uta, Lannigan, Joanne, Ricklefs, Franz L., El-Andaloussi, Samir, and Giebel, Bernd

Subjects
viruses, Medizin, standardisation, Medizinische Fakultät » Universitätsklinikum Essen » Institut für Transfusionsmedizin, exosomes, Exosomes, Submicron Particle Analysis, Imaging Flow Cytometry, Extracellular Vesicles, ddc:610, Flow cytometry, lcsh:QH573-671, reference material, lcsh:Cytology, Medizinische Fakultät » Universitätsklinikum Essen » Zentrum für Kinder- und Jugendmedizin » Klinik für Kinderheilkunde III, flow cytometry, cd63, submicron particle analysis, respiratory system, imaging flow cytometry, Cd63, Reference material, Standardisation, extracellular vesicles, microvesicles, Microvesicles, Research Article
Abstract

Extracellular vesicles (EVs) mediate targeted cellular interactions in normal and pathophysiological conditions and are increasingly recognised as potential biomarkers, therapeutic agents and drug delivery vehicles. Based on their size and biogenesis, EVs are classified as exosomes, microvesicles and apoptotic bodies. Due to overlapping size ranges and the lack of specific markers, these classes cannot yet be distinguished experimentally. Currently, it is a major challenge in the field to define robust and sensitive technological platforms being suitable to resolve EV heterogeneity, especially for small EVs (sEVs) with diameters below 200 nm, i.e. smaller microvesicles and exosomes. Most conventional flow cytometers are not suitable for the detection of particles being smaller than 300 nm, and the poor availability of defined reference materials hampers the validation of sEV analysis protocols. Following initial reports that imaging flow cytometry (IFCM) can be used for the characterisation of larger EVs, we aimed to investigate its usability for the characterisation of sEVs. This study set out to identify optimal sample preparation and instrument settings that would demonstrate the utility of this technology for the detection of single sEVs. By using CD63eGFP-labelled sEVs as a biological reference material, we were able to define and optimise IFCM acquisition and analysis parameters on an Amnis ImageStreamX MkII instrument for the detection of single sEVs. In addition, using antibody-labelling approaches, we show that IFCM facilitates robust detection of different EV and sEV subpopulations in isolated EVs, as well as unprocessed EV-containing samples. Our results indicate that fluorescently labelled sEVs as biological reference material are highly useful for the optimisation of fluorescence-based methods for sEV analysis. Finally, we propose that IFCM will help to significantly increase our ability to assess EV heterogeneity in a rigorous and reproducible manner, and facilitate the identification of specific subsets of sEVs as useful biomarkers in various diseases. OA Förderung 2019

Published
2019

42. Genome-wide methylation profiling of glioblastoma cell-derived extracellular vesicle DNA allows tumor classification

Author

Maire, Cecile L, primary, Fuh, Marceline M, additional, Kaulich, Kerstin, additional, Fita, Krystian D, additional, Stevic, Ines, additional, Heiland, Dieter H, additional, Welsh, Joshua A, additional, Jones, Jennifer C, additional, Görgens, André, additional, Ricklefs, Tammo, additional, Dührsen, Lasse, additional, Sauvigny, Thomas, additional, Joosse, Simon A, additional, Reifenberger, Guido, additional, Pantel, Klaus, additional, Glatzel, Markus, additional, Miklosi, Andras G, additional, Felce, James H, additional, Caselli, Marco, additional, Pereno, Valerio, additional, Reimer, Rudolph, additional, Schlüter, Hartmut, additional, Westphal, Manfred, additional, Schüller, Ulrich, additional, Lamszus, Katrin, additional, and Ricklefs, Franz L, additional

Published
2021
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43. Correction: Immune Checkpoint Blockade in Combination with Stereotactic Body Radiotherapy in Patients with Metastatic Pancreatic Ductal Adenocarcinoma

Author

Xie, Changqing, primary, Duffy, Austin G., additional, Brar, Gagandeep, additional, Fioravanti, Suzanne, additional, Mabry-Hrones, Donna, additional, Walker, Melissa, additional, Bonilla, Cecilia Monge, additional, Wood, Bradford J., additional, Citrin, Deborah E., additional, Gil Ramirez, Elizabeth M., additional, Escorcia, Freddy E., additional, Redd, Bernadette, additional, Hernandez, Jonathan M., additional, Davis, Jeremy L., additional, Gasmi, Billel, additional, Kleiner, David, additional, Steinberg, Seth M., additional, Jones, Jennifer C., additional, and Greten, Tim F., additional

Published
2021
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44. MPA PASS Enables Stitched Multiplex Multi-Dimensional EV Repertoire Analysis

Author

Welsh, Joshua, primary, Killingsworth, Bryce, additional, Kepley, Julia, additional, Traynor, Tim, additional, Cook, Sean, additional, Savage, Jason, additional, Marte, Jenn, additional, Lee, Min-Jung, additional, Maeng, Hoyoung, additional, Pleet, Michelle, additional, Magana, Setty, additional, Gorgens, Andre, additional, Maire, Cecile, additional, Lamszus, Katrin, additional, Ricklefs, Franz, additional, Merino, Maria J., additional, Linehan, W. Marston, additional, Greten, Tim, additional, Cooks, Tomer, additional, Harris, Curtis, additional, Apolo, Andrea, additional, Abdel-Mageed, Asim, additional, Ivanov, Alexander R., additional, Trepel, Jane, additional, Roth, Matthew, additional, Tkach, Mercedes, additional, Milosavljevic, Aleksandar, additional, Théry, Clotilde, additional, LeBlanc, Amy, additional, Berzofsky, Jay, additional, Ruppin, Eytan, additional, Aldape, Kenneth, additional, Camphausen, Kevin, additional, Gulley, James, additional, Ghiran, Ionita, additional, Jacobson, Steven, additional, and Jones, Jennifer C., additional

Published
2021
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45. A simple, high-throughput method of protein and label removal from extracellular vesicle samples

Author

Welsh, Joshua A., primary, Killingsworth, Bryce, additional, Kepley, Julia, additional, Traynor, Tim, additional, McKinnon, Kathy, additional, Savage, Jason, additional, Appel, Deven, additional, Aldape, Kenneth, additional, Camphausen, Kevin, additional, Berzofsky, Jay A., additional, Ivanov, Alexander R., additional, Ghiran, Ionita H., additional, and Jones, Jennifer C., additional

Published
2021
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50. Towards defining reference materials for measuring extracellular vesicle refractive index, epitope abundance, size and concentration

Author

Welsh, Joshua A., primary, Pol, Edwin, additional, Bettin, Britta A., additional, Carter, David R. F., additional, Hendrix, An, additional, Lenassi, Metka, additional, Langlois, Marc‐André, additional, Llorente, Alicia, additional, Nes, Arthur S., additional, Nieuwland, Rienk, additional, Tang, Vera, additional, Wang, Lili, additional, Witwer, Kenneth W., additional, and Jones, Jennifer C., additional

Published
2020
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