MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity

Spheroids are three-dimensional cellular models with widespread basic and translational application across academia and industry. However, methodological transparency and guidelines for spheroid research have not yet been established. The MISpheroID Consortium developed a crowdsourcing knowledgebase that assembles the experimental parameters of 3,058 published spheroid-related experiments. Interrogation of this knowledgebase identified heterogeneity in the methodological setup of spheroids. Empirical evaluation and interlaboratory validation of selected variations in spheroid methodology revealed diverse impacts on spheroid metrics. To facilitate interpretation, stimulate transparency and increase awareness, the Consortium defines the MISpheroID string, a minimum set of experimental parameters required to report spheroid research. Thus, MISpheroID combines a valuable resource and a tool for three-dimensional cellular models to mine experimental parameters and to improve reproducibility. © 2021, The Author(s)

Robust sequential biophysical fractionation of blood plasma to study variations in the biomolecular landscape of systemically circulating extracellular vesicles across clinical conditions

Abstract Separating extracellular vesicles (EV) from blood plasma is challenging and complicates their biological understanding and biomarker development. In this study, we fractionate blood plasma by combining size-exclusion chromatography (SEC) and OptiPrep density gradient centrifugation to study clinical context-dependent and time-dependent variations in the biomolecular landscape of systemically circulating EV. Using pooled blood plasma samples from breast cancer patients, we first demonstrate the technical repeatability of blood plasma fractionation. Using serial blood plasma samples from HIV and ovarian cancer patients (n = 10) we next show that EV carry a clinical context-dependent and/or time-dependent protein and small RNA composition, including miRNA and tRNA. In addition, differential analysis of blood plasma fractions provides a catalogue of putative proteins not associated with systemically circulating EV. In conclusion, the implementation of blood plasma fractionation allows to advance the biological understanding and biomarker development of systemically circulating EV

MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity

none51siSpheroids are three-dimensional cellular models with widespread basic and translational application across academia and industry. However, methodological transparency and guidelines for spheroid research have not yet been established. The MISpheroID Consortium developed a crowdsourcing knowledgebase that assembles the experimental parameters of 3,058 published spheroid-related experiments. Interrogation of this knowledgebase identified heterogeneity in the methodological setup of spheroids. Empirical evaluation and interlaboratory validation of selected variations in spheroid methodology revealed diverse impacts on spheroid metrics. To facilitate interpretation, stimulate transparency and increase awareness, the Consortium defines the MISpheroID string, a minimum set of experimental parameters required to report spheroid research. Thus, MISpheroID combines a valuable resource and a tool for three-dimensional cellular models to mine experimental parameters and to improve reproducibility.openPeirsman A.; Blondeel E.; Ahmed T.; Anckaert J.; Audenaert D.; Boterberg T.; Buzas K.; Carragher N.; Castellani G.; Castro F.; Dangles-Marie V.; Dawson J.; De Tullio P.; De Vlieghere E.; Dedeyne S.; Depypere H.; Diosdi A.; Dmitriev R.I.; Dolznig H.; Fischer S.; Gespach C.; Goossens V.; Heino J.; Hendrix A.; Horvath P.; Kunz-Schughart L.A.; Maes S.; Mangodt C.; Mestdagh P.; Michlikova S.; Oliveira M.J.; Pampaloni F.; Piccinini F.; Pinheiro C.; Rahn J.; Robbins S.M.; Siljamaki E.; Steigemann P.; Sys G.; Takayama S.; Tesei A.; Tulkens J.; Van Waeyenberge M.; Vandesompele J.; Wagemans G.; Weindorfer C.; Yigit N.; Zablowsky N.; Zanoni M.; Blondeel P.; De Wever O.Peirsman A.; Blondeel E.; Ahmed T.; Anckaert J.; Audenaert D.; Boterberg T.; Buzas K.; Carragher N.; Castellani G.; Castro F.; Dangles-Marie V.; Dawson J.; De Tullio P.; De Vlieghere E.; Dedeyne S.; Depypere H.; Diosdi A.; Dmitriev R.I.; Dolznig H.; Fischer S.; Gespach C.; Goossens V.; Heino J.; Hendrix A.; Horvath P.; Kunz-Schughart L.A.; Maes S.; Mangodt C.; Mestdagh P.; Michlikova S.; Oliveira M.J.; Pampaloni F.; Piccinini F.; Pinheiro C.; Rahn J.; Robbins S.M.; Siljamaki E.; Steigemann P.; Sys G.; Takayama S.; Tesei A.; Tulkens J.; Van Waeyenberge M.; Vandesompele J.; Wagemans G.; Weindorfer C.; Yigit N.; Zablowsky N.; Zanoni M.; Blondeel P.; De Wever O