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EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research

Abstract

We argue that the field of extracellular vesicle (EV) biology needs more transparent reporting to facilitate interpretation and replication of experiments. To achieve this, we describe EV-TRACK, a crowdsourcing knowledgebase (http://evtrack.org) that centralizes EV biology and methodology with the goal of stimulating authors, reviewers, editors and funders to put experimental guidelines into practice.

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Figure 1
Figure 2: Implementation of the EV-TRACK knowledgebase.
Figure 3: Using the EV-METRIC to evaluate transparent reporting in EV research.

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Acknowledgements

This work was supported by the Fund for Scientific Spearheads of the Ghent University Hospital, Concerted Research Actions from Ghent University, Stichting tegen Kanker, Kom Op Tegen Kanker, H2020/COST ME-HaD, PhD (J.V.D.) and postdoctoral (A.H., P.M.) positions from Fund for Scientific Research Flanders (FWO) and Krediet aan Navorsers (A.H.) from FWO. This manuscript does not necessarily represent the views of organizations of which authors may be members.

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Contributions

J.V.D., P.M., O.D.W., J.V. and A.H. designed the study and analyzed and interpreted the data. J.V.D., P.M., P.A., G.B., J.G., B.G., A.F.H., S.M., E.N.M.N.-'t.H., L.O., M.W.P., S.S., J.V.S., C.T., G.V.N., M.W., K.W.W., O.D.W., J.V. and A.H. discussed and prepared the manuscript. J.V.D., P.M., J.A., O.D.W., J.V. and A.H. developed the online tool. All authors annotated data and approved of the final manuscript.

Corresponding author

Correspondence to An Hendrix.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Evolution of the study aim of EV research publications from 2010-2014 as recorded by EV-TRACK.

Supplementary Figure 2 Creation of the EV-TRACK knowledgebase.

Supplementary Figure 3 Mapping the reporting landscape in EV research.

Binary heatmap showing the reported experimental parameters (rows of the heatmap, selection of 79 out of 115 parameters for binarity and relevance to experimental results) for each experiment (columns of the heatmap, total n=1742). The heatmap is divided horizontally into three sections of parameters (“Isolation method”, “Protein analysis” and “Particle analysis”; indicated in green, blue and purple and including 41, 22 and 16 parameters, respectively), and vertically in five blocks according to sample type (cell culture supernatant (n=1047), blood plasma (n=146), serum (n=136), urine (n=131), mammalian-other (n=198) and nonmammalian (n=84)). For each section, rows (parameters) and columns (experiments) are sorted according to descending total number of reported experimental parameters. Parameters that were not reported in an experiment appear as a white space in its corresponding column. Abbreviations: AB: antibody; AFM: atomic force microscopy; DG: density gradient; DLS: dynamic light scattering; dUC: differential ultracentrifugation; EM: electron microscopy; IEM: immuno-EM; NTA: nanoparticle tracking analysis; SEM: scanning EM; TEM: transmission EM; TRPS: tunable resistive pulse sensing.

Supplementary Figure 4 Ratio of adjusted k-factor to pelleting time for dUC protocols.

The adjusted k-factor is a measure of the pelleting efficiency of a rotor that is run below its maximum velocity (see Online Methods). The ratio of adjusted k-factor to pelleting time should be similar in order to pellet objects with similar sedimentation coefficients (Cvjetkovic et al., 2014). Experiments on cell culture supernatant and including title word “exosome(s)” that specified a rotor type and pelleting time were included. Experiments that included a combination of dUC with a density gradient, density cushion and/or immunoaffinity capture and studies investigating the influence of centrifugation parameters on exosome pelleting were excluded from this figure. Dots were jittered horizontally to reduce overlap.

Reference: Cvjetkovic, A., Lotvall, J. & Lasser, C. The influence of rotor type and centrifugation time on the yield and purity of extracellular vesicles. Journal of extracellular vesicles 3, doi:10.3402/jev.v3.23111 (2014).

Supplementary Figure 5 Use of EV isolation methods between 2010 and 2014.

(a) Evolution of the use of EV isolation methods between 2010 and 2014. Experiments with combined methods were excluded. (b) Overview of the most commonly used commercial methods to obtain EVs.

Supplementary Figure 6 Commonly analyzed EV-enriched proteins.

Tree maps showing the most used EV-enriched proteins, subdivided for biofluid and isolation method. Methods of EV-enriched protein analysis include Western blot, flow cytometry, ELISA and immuno-electron microscopy. Only experiments evaluating the presence of at least one protein are included in the figure. Gene symbols are generally used to denote proteins, with the exception of MHC2 (all proteins of major histocompatibility class II), TUB (both tubulin alpha and beta), HSP70 (all members of heat shock protein family A) and HSP90 (HSP90AA1 and HSP90AB1).

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6, Supplementary Tables 1–5 and Supplementary Methods (PDF 3526 kb)

Supplementary Table 6

Calculation of the EV-METRIC for all EV-TRACK experiments. (XLSX 90 kb)

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EV-TRACK Consortium., Van Deun, J., Mestdagh, P. et al. EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research. Nat Methods 14, 228–232 (2017). https://doi.org/10.1038/nmeth.4185

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