My name is Joshua Welsh and I’m a postdoctoral research scientist currently conducting research in Jennifer Jones’ lab within the ‘Laboratory of Pathology‘ at the National Cancer Institute in Bethesda, Maryland.
My main research interest is on small lipid spheres released from cells, called extracellular vesicles (EVs). These small spheres contain proteins and genetic information from the cell they were released from. To date, I have investigated novel ways to detect and analyse EVs as well as their use as markers to diagnose and track the progression of disease. My current research focuses on utilizing EVs as a method for cancer diagnosis and predicting treatment prognosis..
Here you can find information on my research, interests, learning resources for analysis equipment, as well as links and information on software I have written.
Please feel free to contact me by email if you have any questions.
In the Translational Nanobiology Section I am developing a high-throughput, scalable, clinical pipeline for characterizing extracellular vesicles for their use as biomarkers. This work has required me to develop assays but also develop standalone software for the standardization of results, as well as perform multidimensional data analyses. I have led the planning, conducting, and analysis of experiments along with the writing of several manuscripts. I have also been the day-to-day supervisor of numerous postbaccalaureate and summer student’s lab members.
Following my PhD thesis, I was funded in-kind by Thermo Fisher Scientific to continue developing a high-sensitivity flow cytometry platform and standardization methods to characterize extracellular vesicles.
In this role I designed an 8-week course to teach to 2 classes of 14-15-year-old children at schools from underprivileged backgrounds. This initiative, organized by the Brilliant Club, is to help increase the variety of students in STEM fields at the top universities in the UK by having PhD students and postdoctoral researchers teach their specialty. The course that I delivered was on basics of flow cytometry and extracellular vesicles. One of my students was selected for having done outstanding work by peer-reviewed process and had their final project published in the organization’s journal.
In this position I taught groups of 30 students per week how to perform bacterial transformation and determine whether it was successful or not. I would then mark their experimental write-up of the lab data they produced. I chose to take this position to gain experience in disseminating knowledge to students as well as to gain experience teaching large groups.
Thesis title: Flow cytometer optimisation and standardisation for the study of extracellular vesicles as translational biomarkers.
Supervisors: Nicola Englyst, PhD; Judith Holloway, PhD; David Smith, BMBS, DM; James Wilkinson, PhD.
Biological Sciences: Physiology with Pharmacology
Currently organize, lead calls, and maintain website for the inter-societal working group of ~26 international researchers seeking to standardize extracellular vesicle analysis and reporting.
Regular attendee of CYTO meetings, and participant in the annual cytometry development workshops. Awarded Marylou Ingram Scholarship 2019-2023.
For contribution to patents and other intellectual property at NCI.
Awarded for our article: FCMPASS software aids extracellular vesicle light scatter standardisation having been one of the top downloaded articles in the Cytometry Part A journal.
Awarded by the International Society for Advancement of Cytometry, the ISAC Marylou Ingram Scholars Program is a five-year career development program designed to enhance the scientific and leadership experiences of research leaders in the field of cytometry. Being chosen as an ISAC Marylou Ingram Scholar is an indication that you are recognized for your scientific skills, research accomplishments, leadership potential and ability to achieve your career goals.
Nominated and following interviews of top 5 candidates was awarded the outstanding postdoctoral fellow by the Center for Cancer Research - Fellows and Young Investigator Colloquium (CCR-FYI).
Scholarship to attend the Keystone Single Cell Biology Meeting for abstract titled: The development of a scalable extracellular vesicle subset characterization pipeline. Chosen by Timm Schroeder PhD and Berthold Go ̈bgens DPhil.
Nominated for significantly contributing to the intellectual property of National Cancer Institute for the 4 patents I have submitted in the preceding year.
An award to cover the salary of a summer intern to work alongside me in the lab.
Awarded for my presentation titled: An Accessible Method of Flow Cytometer Scatter Standardisation for EV Analysis, given at the United Kingdom Society for Extracellular Vesicles (UKEV).
Awarded by the International Society for Advancement of Cytometry to allow me to attend the cytometry development workshop and present a talk titled: ‘Flow Cytometry SSC Collection Angle Can Be Deduced Using Acquisition of Reference Beads with Known Refractive Index’.
Faculty award to support travel to ISEV 2016 to present a talk titled: ‘Leukocyte microvesicle as fibrosis biomarkers in nonalcoholic fatty liver disease’.
Award to support travel costs and allow me to attend the UK-Brazil Extracellular Vesicle and Neglected Tropical Diseases Workshop.
Awarded by the International Society for Advancement of Cytometry to allow me to attend CYTO 2015 and present a talk titled: A Comparison of Extracellular Vesicle Probe Effectiveness Using Simultaneous Labeling.
Faculty award to support travel to ISEV 2015 to present a talk titled: ‘A New Fluorescent Probe for Identi- fying Microvesicles’.
Award to support travel costs and allow me to attend the UK–Russia Researcher Links Workshop: extra- cellular vesicles – mechanisms of biogenesis and roles in disease pathogenesis.
National competition to identify individuals who have significantly contributed to innovation in STEM projects.
Awarded for my final year project titled: Do endogenous human platelet-delivered microparticles contain intracellular Ca2+ stores?
Awarded for exceeding the academic entry requirements of the course.
The importance of orthogonal measurement techniques for EV quantification. Invited by Jean-Luc Fraikin, PhD
Towards evaluating the prognostic potential of extracellular vesicles. Invited by Clotilde Théry, PhD
Towards evaluating the prognostic potential of extracellular vesicles. Invited by Rosandra Kaplan, MD
Extracellular Vesicle Flow Cytometry: A multiplex to single EV analysis (MtSEA) pipeline. Invited by William Telford PhD
Extracellular Vesicle Flow Cytometry, Invited by Randy Carney PhD
FCMPASS utilizes MIFlowCyt-EV framework criteria and extracts flow cytometry setting information to allow transparent reporting irrespective of file sharing repository. Invited by: Workshop Committee
FCMPASS provides light scatter and fluorescence calibration tools for reporting small particle data in standard units. Invited by: Workshop Committee. Invited by: Joanne Lannigan MS
EV standardization. Invited by: John Nolan PhD
Next Generation Extracellular Vesicles Studies for Cancer Research. Invited by: DSFCM Committee
Next Generation Extracellular Vesicles Studies for Cancer Research. Invited by: CCR-FYI Committee
Tools for extracellular vesicles analysis using flow cytometry. Invited by: Aleksander Keselman, PhD
Tools for extracellular vesicles analysis using flow cytometry. Invited by: Mehrnoosh Abshari, MSc
Development of hyperplexed EV phenotyping assays and software. Invited by: John Nolan, PhD
Developing tools for a multiplex-to-single EV analysis pipeline. Invited by: Vera Tang, PhD & Marc-André Langlois, PhD
Scatter-based reference materials. Invited by: Marca Wauben, PhD
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., BioRxiv, doi:10.1101/2020.08.20.260307 [website]
Welsh J A, Jones J C, Small particle fluorescence and light scatter calibration using FCMPASS software., Current Protocols in Cytometry, [In Press]
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 size, concentration, refractive index and epitope abundance, arXiv, arXiv:2004.09428v1. [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]
Butement J.T., Holloway P.M., Welsh J.A., Holloway J.A, Englyst N.A., Horak P, West J, Wilkinson J.S., Monolithically-integrated cytometer for measuring particle diameter in the extracellular vesicle size range using multi-angle scattering, Lab on a Chip, 2020, doi: 10.1039/C9LC01182J [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]
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]
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]
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]
Ramirez M I, Amorim M G, Gadelha C, Milic I, Welsh J A, Freitas V M, Nawaz M, Akbar N, Couch Y, Makin L, Cooke F, Vettore A L, Batista P C, Freezor R A, Pezuk, J A, Rosa-Fernandes L, Carreira A C O, Devitt A, Jacobs L, Silva I T, Coakley G, Nunes D N, Carter D, Palmisano G, Dias-Neto E., Technical challenges of working with extracellular vesicles. , Nanoscale, 2017, 00, 1–26. doi: 10.1039/c7nr08360b [website]
Welsh J A, Holloway JA, Wilkinson JS and Englyst NA, Extracellular Vesicle Flow Cytometry Analysis and Standardization. , Front. Cell Dev. Biol., 2017, 5:78. doi: 10.3389/fcell.2017.00078 [website]
Welsh J A, Holloway JA, Englyst NA, Microvesicles as Biomarkers in Diabetes, Obesity and Non-Alcoholic Fatty Liver Disease: Current Knowledge and Future Directions. , Intern Med, S6:009, 2014. doi: 10.4172/2165-8048.S6-009 [website]