Publications

Here you can find a list of the Translational Nanobiology Section publications and associated data:

2023

Arce J.E., Welsh J.A., Cook S., Tigges J., Ghiran I., Jones J.C., Jackson A., Roth M., Milosavljevic A. THe NanoFlow Repository., Bioinformatics, doi: 10.1093/bioinformatics/btad368 [website]

Welsh J.A., Arkesteijn G. J. A., Bremer M., Cimorelli M., Dignat-George F., Giebel B., Görgens A., Hendrix A., Kuiper M., Lacroix R., Lannigan J., van Leeuwen T. G., Lozano-Andrés E., Rao S., Robert S., de Rond L., Tang V.A., Tertel T., Yan X., Wauben M.H.M., Nolan J.P., Jones J.C., Nieuwland R., van der Pol E., A compendium of single extracellular vesicle flow cytometry., Journal of Extracellular Vesicles, doi: 10.1002/jev2.12299 [website]

2022

Nolan, J.P., Chiu D., Welsh J.A., Rigor and reproducibility: status and challenges for single vesicle analysis., Extracellular Vesicles and Circulating Nucleic Acids, doi: 10.20517/evcna.2022.28 [website]

Mateescu B., Jones J.C., Alexander R, An Ji, Asghari M, Boomgarden A, Alexander R, An JY, Asghari M, Boomgarden A, Bouchareychas L, Cayota A, Chang H, Charest A, Chiu DT, Coffey RJ, Das S, DeHoff P, D'Souza-Schorey C, Franklin J, Galas DJ, Gerstein MB, Ghiran IH, Go DB, Gould S, Higginbotham JN, Hladik F, Huang TJ, Huo X, Jeppesen DK, Jones J, Jovanovic-Talisman T, Junior GPDO, Keuren- Jensen KV, Kim BYS, Kim KM, Kim S, Kim Y, Kitchen RR, Knouse V, Laplante EL, Lebrilla CB, Lee LJ, Lennon KM, Li F, Li G, Li T, Liu T, Liu Z, Maniya N, Mateescu B, McCarthy K, Meechoovet B, Meng Y, Milosavljevic A, Min BH, Morey A, Ng M, Nolan J, Paulaitis ME, Phu TA, Raffai R, Raffai RL, Reategui E, Roth ME, Routenberg DA, Rozowsky J, Shachar S, Sharma H, Sood AK, Stavrakis S, Sturchler A, Tewari M, Tosar J, Tucker-Schwartz AK, Turchinovich A, Valkov N, Vickers KC, Vojtech L, Vreeland WN, Wang C, Wang K, Wang Z, Welsh JA, Witwer KW, Wong DT, Xie Y, Zaborowski MP, Zhang C, Zhang Q, Zivkovic AM, deMello A, Laurent LC, Phase 2 of Extracellular RNA Communication Consortium Charts Next-Generation Approaches for Extracellular RNA Research., iScience, doi: 10.1016/j.isci.2022.104653 [website]

Moles R, Sarkis S., Galli V.S., Omsland M, Artesi M, Bissa M, McKinnon K, Brown S, Hahaut V, Washington-Parks R, Welsh J.A., Venzon D.J., Gutowska A, Doster M, Breed M.W., Killoran K.E., Kramer J, Jones J, Moniuszko M, Van den Broeke A, Pise-Masison C.A., Franchini G., NK cells and Monocytes modulate primary HTLV-1 infection., PLoS Pathogens, doi: 10.1371/journal.ppat.1010416 [website]

Welsh J A, Killingsworth B, Kepley J, Traynor T, Cook S, Savage J, Marte J, Lee M, Maeng HM, Pleet ML, Magana S, Gorgens A, Maire CL, Lamszus K, Ricklefs FL, Merino MJ, Linehan WM, Greten T, Cooks T, Harris CC, Apolo A, Abdel-Mageed A, Ivanov AR, Trepel JB, Roth M, Tkach M, Milosavljevic A, Théry C, LeBlanc A, Berzofsky JA, Ruppin E, Aldape K, Camphausen K, Gulley JL, Ghiran I, Jacobson S, Jones J C, MPAPASS software enables stitched multiplex, multi-dimensional EV repertoire analysis, and a standard framework for reporting bead-based assays., Cell Reports Methods, doi: 10.1016/j.crmeth.2021.100136 [website]

van der Pol E, Welsh J A, Nieuwland R, Minimum information to report about a flow cytometry experiment on extracellular vesicles: communication from the ISTH SSC Subcommittee on Vascular Biology., Journal of Thrombosis & Haemostasis, doi: 10.1111/jth.15540 [website]

2021

Witwer, K.W., Goberdhan, D.C., O'Driscoll, L., Théry, C., Welsh J A, Blenkiron, C., Buzás, E.I., Di Vizio, D., Erdbrügger, U., Falcón-Pérez, J.M., Fu, Q.-L., Hill, A.F., Lenassi, M., Lötvall, J., Nieuwland, R., Ochiya, T., Rome, S., Sahoo, S. and Zheng, L., Updating MISEV: Evolving the minimal requirements for studies of extracellular vesicles., Journal of Extracellular Vesicles, doi: 10.1002/jev2.12182 [website]

Oliveira-Jr G P, Barbosa R H, Thompson L, Pinckney B, Murphy-Thornley M, Lu S, Jones J, Hansen C H, Tigges J, Wong W P, Ghiran I C, Electrophoretic mobility shift as a molecular beacon-based readout for miRNA detection., Biosensors & Bioelectronics, doi: 10.1039/D0NR07830A [website]

Killingswroth B, Welsh J A, Jones J C, EV Therapeutic Horizons as Viewed Across the Complex Landscape of Liquid Biopsies., Frontiers in Cell and Developmental Biology [In Press]

Welsh J A, Killingswroth B, Kepley J, Traynor T, McKinnon K, Savage J, Appel D, Aldape K, Camphausen K, Berzofsky J A, Ivanov A R, Ghiran I H, Jones J C, A simple, high-throughput method of protein and label removal from extracellular vesicle samples., Nanoscale, doi: 10.1039/D0NR07830A [website]

Marie A L, Ray S, Lu S, Jones J, Ghiran I, Ivanov A R. High-Sensitivity Glycan Profiling of Blood-Derived Immunoglobulin G, Plasma, and Extracellular Vesicle Isolates with Capillary Zone Electrophoresis-Mass Spectrometry., Anal Chem. 2021 Feb 2;93(4):1991-2002. doi: 10.1021/acs.analchem.0c03102 [website]

Maire C L, Fuh M M, Kaulich K, Fita K D, Stevic I, Heiland D H, Welsh J A, Jones J C, Görgens A, Ricklefs T, Dührsen L, Sauvigny T, Joosse S A, Reifenberger G, Pantel K, Glatzel M, Miklosi A G, Felce J H, Caselli M, Pereno V, Reimer R, Schlüter H, Westphal M, Schüller U, Lamszus K, Ricklefs F L, Genome-wide methylation profiling of glioblastoma cell-derived extracellular vesicle DNA allows tumor classification., Neuro-Oncology, doi: 10.1093/neuonc/noab012 [website]

2020

Welsh J A, Tang V A, van der Pol E, Görgens A, MIFlowCyt-EV: The next chapter in the reporting and reliability of single extracellular vesicle flow cytometry experiments., Cyometry Part A, doi: 10.1002/cyto.a.24268 [website]

Burnie J, Tang V A, Welsh J A, Persuad A T, Thaya L, Jones J C, Guzzo C, Flow virometry quantification of host proteins on the surface of HIV-1 pseudovirus particles., Viruses, doi: 10.3390/v12111296 [website]

Welsh J A, Jenkins L M, Kepley J., Lyons G C, Moore D M, Traynor T, Berzofsky J. Jones J.C., High-sensitivity protein gel electrophoresis label compatible with mass spectrometry., Biosensors, doi:10.3390/bios10110160 [Website]

Apolo AB, Nadal R, Girardi DM, Niglio SA, Ley L, Cordes LM, Steinberg SM, Sierra Ortiz O, Cadena J, Diaz C, Mallek M, Davarpanah NN, Costello R, Trepel JB, Lee MJ, Merino MJ, Bagheri MH, Monk P, Figg WD, Gulley JL, Agarwal PK, Valera V, Chalfin HJ, Jones J, Streicher H, Wright JJ, Ning YM, Parnes HL, Dahut WL, Bottaro DP, Lara PN Jr, Saraiya B, Pal SK, Stein MN, Mortazavi A. Phase I Study of Cabozantinib and Nivolumab Alone or With Ipilimumab for Advanced or Metastatic Urothelial Carcinoma and Other Genitourinary Tumors., J Clin Oncol. 2020 Nov 1;38(31):3672-3684. doi: 10.1200/JCO.20.01652 [website]

Morales-Kastresana A*, Welsh J A*,Jones J C, Detection and Sorting of Extracellular Vesicles and Viruses using nanoFACS., Current Protocols in Cytometry, doi: [Website] [Protocols.io]

de Rond L, Coumans F A W, Welsh J A, Nieuwland R, Leeuwen T G., van der Pol E, Quantification of light scattering detection efficiency and background in flow cytometry., Cytometry Part A, doi: 10.1002/cyto.a.24243 [Website]

Welsh J A, Jones J C, Small Particle Fluorescence and Light Scatter Calibration Using FCMPASS Software, Current Protocols in Cytometry, 94, e79. doi: 10.1002/cpcy.79 [Website] [Protocols.io]

Welsh J A, van der Pol E, Bettin B A, Carter D R F, Hendrix A, Lenassi M, Langlois M, Llorente A, van de Nes A S, Nieuwland R, Tang V, Wang L, Witwer K W, Jones J C, Towards defining reference materials for extracellular vesicle refractive index, epitope abundance, size, and concentration., Journal of Extracellular Vesicles, doi: 10.1080/20013078.2020.1816641 [Website]

Nelson B C, Maragh S, Ghiran I C, Jones J C, DeRose P C, Elsheikh E, Vreeland W N, Wang L, Measurement and standardization challenges for extracellular vesicle therapeutic delivery vectors, Nanomedicine, doi: 10.2217/nnm-2020-0206 [Website]

Welsh J A, Jones J.C. Tang V A., Fluorescence and light scatter calibration allow comparisons of small particle data in standard units across different flow cytometry platforms and detector settings, Cytometry Part A, doi: 10.1002/cyto.a.24029. [website] [cytometry files - 720 MB]

Xie, C.; Duffy, A.; Brar, G.; Fioravanti, S.; Mabry-Hrones, D.; Walker, M.; Monge Bonilla, C.; Wood, B. J.; Citrin, D. E.; Gil Ramirez, E. M.; Escorcia, F. E.; Redd, B.; Hernandez, J. M.; Davis, J. L.; Gasmi, B.; Kleiner, D.; Steinberg, S. M.; Jones, J. C.; Greten, T. F., Immune checkpoint blockade in combination with stereotactic body radiotherapy in patients with metastatic pancreatic ductal adenocarcinoma. Clinical Cancer Research 2020, doi:10.1158/1078-0432.CCR-19-3624. [website]

Welsh J A, van der Pol E, Arkesteijn G, Bremer M, Brisson A, Coumans F, Dignat-George F, Duggan E, Ghiran I, Giebel B, Görgens A, Hendrix A, Lacroix R, Lannigan J, Libregts S, Lozano-Andrés E, Morales-Kastresana A, Robert S, de Rond L, Tertel T, Tigges J, de Wever O, Yan X, Nieuwland R, Wauben M, Nolan J, Jones, J C., MIFlowCyt-EV: a framework for standardized reporting of extracellular vesicle flow cytometry experiments, Journal of Extracellular Vesicles. doi: 10.1080/20013078.2020.1713526. [website]

Oliveira, G. P. d.; Zigon, E.; Rogers, G.; Davodian, D.; Lu, S.; Jovanovic-Talisman, T.; Jones, J.; Tigges, J.; Tyagi, S.; Ghiran, I. C., Detection of Extracellular Vesicle RNA Using Molecular Beacons. iScience 2020, 23 (1), doi:10.1016/j.isci.2019.100782. [website]

Miyahira, A. K.; Sharp, A.; Ellis, L.; Jones, J.; Kaochar, S.; Larman, H. B.; Quigley, D. A.; Ye, H.; Simons, J. W.; Pienta, K. J.; Soule, H. R., Prostate cancer research: The next generation; report from the 2019 Coffey-Holden Prostate Cancer Academy Meeting. The Prostate 2020, 80 (2), 113-132. doi:10.1002/pros.23934. [website]

2019

Jones, J., Glioblastoma single extracellular vesicle analysis profiles: wading into new oceans of tumor data. Neuro-Oncology 2019, 21 (5), 562-564. doi:10.1093/neuonc/noz045. [website]

Czechowska K., Lannigan J., Aghaeepour N., Back J.B., Begum J., Behbehani G., Bispo C., Bitoun D., Fernández A.B., Boova S.T., Brinkman R.R., Ciccolella C.O., Cotleur B., Davies D., Dela Cruz G.V., Del Rio‐Guerra R., Des Lauriers‐Cox A.M., Douagi I., Dumrese C., Bonilla Escobar D.L., Estevam J., Ewald C., Fossum A., Gaudillière B., Green C., Groves C., Hall C., Haque Y., Hedrick M.N., Hogg K., Hsieh E.W., Irish J., Lederer J., Leipold M., Lewis‐Tuffin L.J., Litwin V., Lopez, P., Nasdala, I., Nedbal, J., Ohlsson‐Wilhelm, B.M., Price, K.M., Rahman A.H., Rayanki R., Rieger A.M., Robinson J.P., Shapiro H., Sun Y.S., Tang V.A., Tesfa L., Telford W.G., Walker R., Welsh J.A., Wheeler P. and Tárnok A. (2019), Cyt‐Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2019 Conference Workshops , Cytometry Part A, 95: 1236-1274. doi:10.1002/cyto.a.23941. [website]

Clayton A, Boilard E, Buzas E I, Cheng L, Falcón-Perez J M, Gardiner C, Gustafson D, Gualerzi A, Hendrix A, Hoffman A, Jones J, Lässer C, Lawson C, Lenassi M, Nazarenko I, O’Driscoll L, Pink R, Siljander P R-M, Soekmadji C, Wauben M, Welsh J A, Witwer K, Zheng L, Nieuwland R, Considerations towards a roadmap for collection, handling and storage of blood extracellular vesicles , Journal of Extracellular Vesicles, 8:1, dos: 10.1080/20013078.2019.1647027. [website]

Tang V.A., Fritzsche A.K., Renner T.M., Burger D., van der Pol E., Lannigan J.A., Brittain G.C., Welsh J.A., Jones J.C., Langlois M., Engineered Retroviruses as Fluorescent Biological Reference Particles for Small Particle Flow Cytometry , BioRXiv, doi: 10.1101/614461. [website]

Welsh J A, Horak P, Wilkinson J S, Ford V, Jones J C, Smith D C, Holloway J A, Englyst N A, FCMPASS software aids extracellular vesicle light scatter standardisation , Cytometry Part A, doi: 10.1002/cyto.a.23782. [website]

Morales-Kastresana A*, Musich T*, Welsh J A*, Telford W, Demberg T, Wood J C S, Felton E J, Bigos M, Ross C D, Kachynski A, Dean A, Dyke J V, Tigges J, Toxavidis V, Parks D R, Overton W R, Kesarwala A P, Freeman G J, Rosner A, Perfetto S P, Pasquet L, Terabe M, McKinnon K, Kapoor V, Trepel J B, Puri A, Kobayashi H, Yung B, Chen X, Guion P, Choyke P, Knox S J, Ghiran I, Robert-Guroff M, Berzofsky J A, Jones J C, High Fidelity Detection and Sorting of Nanoscale Vesicles in Viral Disease and Cancer , Journal of Extracellular Vesicles, doi: 10.1080/20013078.2019.1597603. [website]

Murillo O D, Thistlethwaite W, Rozowsky J, Subramanian S L, Lucero R, Shah N, Jackson A R, Srinivasan S, Chung A, Laurent C D, Kitchen R R, Galeev T, Warrell J, Diao J A, Welsh J A, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah R, Yeri A, Jenkins L M, Ahsen M E, Dogra N, Gifford S M, Smith J T, Stolovitzky G, Tewari A K, Wunsch B H, Yadav K K, Alexander R P, Wang L, Wu C, Wong D, Galas D J, Keuren-Jensen K, Patel T, Jones J C, Das S, Cheung K, Pico A, Su A I, Raffai R L, Laurent L C, Roth M E, Gerstein M B, Milosavljevic A, ExRNA Atlas analysis reveals distinct extracellular RNA cargo types present across human biofluids , Cell, doi: 10.1016/j.cell.2019.02.018. [website]

Görgens A., Bremer M., Ferrer-Tur R., Murke F., Tertel T., Horn P.A., Thalmann S., Welsh J.A., Probst C, Guerin C., Boulanger C.M., Jones J.C., Hanenberg H., Erdbrügger U., Lannigan J., Ricklefs F.L., Andaloussi S., Giebel B., Optimisation of Imaging Flow Cytometry for the Analysis of Single Extracellular Vesicles by Using Fluorescence-tagged Vesicles as Biological Reference Material , Journal of Extracellular Vesicles, doi: 10.1080/20013078.2019.1587567. [website]

Bloom, A. C.; Bender, L. H.; Tiwary, S.; Pasquet, L.; Clark, K.; Jiang, T.; Xia, Z.; Morales-Kastresana, A.; Jones, J. C.; Walters, I.; Terabe, M.; Berzofsky, J. A., Intratumorally delivered formulation, INT230-6, containing potent anticancer agents induces protective T cell immunity and memory. OncoImmunology 2019, 8 (10), e1625687. doi:10.1080/2162402X.2019.1625687. [website]

Pinto, D. O.; DeMarino, C.; Pleet, M. L.; Cowen, M.; Branscome, H.; Al Sharif, S.; Jones, J.; Dutartre, H.; Lepene, B.; Liotta, L. A.; Mahieux, R.; Kashanchi, F., HTLV-1 Extracellular Vesicles Promote Cell-to-Cell Contact. Frontiers in Microbiology 2019, 10 (2147).

2018

Théry C., Witwer K., et al., 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 , Journal of Extracellular Vesicles, 8:1, 1535750, doi: 10.1080/20013078.2018.1535750. [website]

Welsh J.A, Kepley J., Rosner A., Horak P., Berzofsky J. Jones J.C., Prospective use of high-refractive index materials for single molecule detection in flow cytometry. , Sensors, doi:10.3390/s18082461. [website]

Wiklander OPB, Bostancioglu RB, Welsh JA, Zickler AM, Murke F, Corso G, Felldin U, Hagey DW, Evertsson B, Liang X-M, Gustafsson MO, Mohammad DK, Wiek C, Hanenberg H, Bremer M, Gupta D, Björnstedt M, Giebel B, Nordin JZ, Jones JC, EL Andaloussi S and Görgens A., Systematic methodological evaluation of a multiplex bead-based flow cytometry assay for detection of extracellular vesicle surface signatures , Front. Immunol., doi: 10.3389/fimmu.2018.01326. [website]

Watson, D. C.; Yung, B. C.; Bergamaschi, C.; Chowdhury, B.; Bear, J.; Stellas, D.; Morales-Kastresana, A.; Jones, J. C.; Felber, B. K.; Chen, X.; Pavlakis, G. N., Scalable, cGMP-compatible purification of extracellular vesicles carrying bioactive human heterodimeric IL-15/lactadherin complexes. Journal of Extracellular Vesicles 2018, 7 (1), 1442088. doi: 10.1080/20013078.2018.1442088. [website]

Anderson, M. R.; Pleet, M. L.; Enose-Akahata, Y.; Erickson, J.; Monaco, M. C.; Akpamagbo, Y.; Velluci, A.; Tanaka, Y.; Azodi, S.; Lepene, B.; Jones, J.; Kashanchi, F.; Jacobson, S., Viral antigens detectable in CSF exosomes from patients with retrovirus associated neurologic disease: functional role of exosomes. Clinical and Translational Medicine 2018, 7 (1), 24. doi: 10.1186/s40169-018-0204-7. [website]

Clayton A, Buschmann D, Byrd J B, Carter D R F, Cheng L, Compton C, Daaboul G, Devitt A, Falcon-Perez J M, Gardiner C, Gustafson D, Harrison P, Helmbrecht C, Hendrix A, Hill A, Hoffman A, Jones J C, Kalluri R, Kang J Y, Kirchner B, Lässer C, Lawson C, Lenassi M, Levin C, Llorente A, Martens-Uzunova E S, Möller A, Musante L, Ochiya T, Pink R C, Tahara H, Wauben M H M, Webber J P, Welsh J A, Witwer K W, Yin H, Nieuwland R, (2018) Summary of the ISEV workshop on extracellular vesicles as disease biomarkers, held in Birmingham, UK, during December 2017 , Journal of Extracellular Vesicles, 7:1, 1473707, doi: 10.1080/20013078.2018.1473707. [website]

2017

Datta, A.; Kim, H.; Lal, M.; McGee, L.; Johnson, A.; Moustafa, A. A.; Jones, J. C.; Mondal, D.; Ferrer, M.; Abdel-Mageed, A. B., Manumycin A suppresses exosome biogenesis and secretion via targeted inhibition of Ras/Raf/ERK1/2 signaling and hnRNP H1 in castration-resistant prostate cancer cells. Cancer Letters 2017, 408, 73-81. doi: 10.1016/j.canlet.2017.08.020. [website]

Musich, T.; Jones, J. C.; Keele, B. F.; Jenkins, L. M. M.; Demberg, T.; Uldrick, T. S.; Yarchoan, R.; Robert-Guroff, M., Flow virometric sorting and analysis of HIV quasispecies from plasma. JCI Insight 2017, 2 (4). doi: 10.1172/jci.insight.90626. [website]

Nolan, J. P.; Jones, J. C., Detection of platelet vesicles by flow cytometry. Platelets 2017, 28 (3), 256-262. doi: 10.1080/09537104.2017.1280602. [website]

Morales-Kastresana, A.; Jones, J. C., Flow Cytometric Analysis of Extracellular Vesicles. In Exosomes and Microvesicles: Methods and Protocols, Hill, A. F., Ed. Springer New York: New York, NY, 2017; pp 215-225. doi: 10.1007/978-1-4939-6728-5_16. [website]

Morales-Kastresana, A.; Telford, B.; Musich, T. A.; McKinnon, K.; Clayborne, C.; Braig, Z.; Rosner, A.; Demberg, T.; Watson, D. C.; Karpova, T. S.; Freeman, G. J.; DeKruyff, R. H.; Pavlakis, G. N.; Terabe, M.; Robert-Guroff, M.; Berzofsky, J. A.; Jones, J. C., Labeling Extracellular Vesicles for Nanoscale Flow Cytometry. Sci Rep 2017, 7 (1), 1878. doi: 10.1038/s41598-017-01731-2. [website]

Mateescu, B.; Kowal, E. J.; van Balkom, B. W.; Bartel, S.; Bhattacharyya, S. N.; Buzas, E. I.; Buck, A. H.; de Candia, P.; Chow, F. W.; Das, S.; Driedonks, T. A.; Fernandez-Messina, L.; Haderk, F.; Hill, A. F.; Jones, J. C.; Van Keuren-Jensen, K. R.; Lai, C. P.; Lasser, C.; Liegro, I. D.; Lunavat, T. R.; Lorenowicz, M. J.; Maas, S. L.; Mager, I.; Mittelbrunn, M.; Momma, S.; Mukherjee, K.; Nawaz, M.; Pegtel, D. M.; Pfaffl, M. W.; Schiffelers, R. M.; Tahara, H.; Thery, C.; Tosar, J. P.; Wauben, M. H.; Witwer, K. W.; Nolte-'t Hoen, E. N., Obstacles and opportunities in the functional analysis of extracellular vesicle RNA - an ISEV position paper. J Extracell Vesicles 2017, 6 (1), doi: 10.1080/20013078.2017.1286095. [website]