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

Arne Peirsman; Eva Blondeel; Tasdiq Ahmed; Jasper Anckaert; Dominique Audenaert; Tom Boterberg; Krisztina Buzas; Neil Carragher; Gastone Castellani; Flávia Castro; Virginie Dangles-marie; John Dawson; Pascal De Tullio; Elly De Vlieghere; Sándor Dedeyne; Herman Depypere; Akos Diosdi; Ruslan I. Dmitriev; Helmut Dolznig; Suzanne Fischer; Christian Gespach; Vera Goossens; Jyrki Heino; An Hendrix; Peter Horvath; Leoni A. Kunz-schughart; Sebastiaan Maes; Christophe Mangodt; Pieter Mestdagh; Soňa Michlíková; Maria José Oliveira; Francesco Pampaloni; Filippo Piccinini; Cláudio Pinheiro; Jennifer Rahn; Stephen M. Robbins; Elina Siljamäki; Patrick Steigemann; Gwen Sys; Shuichi Takayama; Anna Tesei; Joeri Tulkens; Michiel Van Waeyenberge; Jo Vandesompele; Glenn Wagemans; Claudia Weindorfer; Nurten Yigit; Nina Zablowsky; Michele Zanoni; Phillip Blondeel; Olivier De Wever

doi:10.1038/s41592-021-01291-4

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

Arne Peirsman, Eva Blondeel, Tasdiq Ahmed, Jasper Anckaert, Dominique Audenaert, Tom Boterberg, Krisztina Buzas, Neil Carragher, Gastone Castellani, Flávia Castro, Virginie Dangles-marie, John Dawson, Pascal De Tullio, Elly De Vlieghere, Sándor Dedeyne, Herman Depypere, Akos Diosdi, Ruslan I. Dmitriev, Helmut Dolznig, Suzanne FischerChristian Gespach, Vera Goossens, Jyrki Heino, An Hendrix, Peter Horvath, Leoni A. Kunz-schughart, Sebastiaan Maes, Christophe Mangodt, Pieter Mestdagh, Soňa Michlíková, Maria José Oliveira, Francesco Pampaloni, Filippo Piccinini, Cláudio Pinheiro, Jennifer Rahn, Stephen M. Robbins, Elina Siljamäki, Patrick Steigemann, Gwen Sys, Shuichi Takayama, Anna Tesei, Joeri Tulkens, Michiel Van Waeyenberge, Jo Vandesompele, Glenn Wagemans, Claudia Weindorfer, Nurten Yigit, Nina Zablowsky, Michele Zanoni, Phillip Blondeel, Olivier De Wever

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English
Pages (from-to)	1294-1303
Journal	Nature Methods
Volume	18
Issue number	11
Early online date	1 Nov 2021
DOIs	https://doi.org/10.1038/s41592-021-01291-4
Publication status	E-pub ahead of print - 1 Nov 2021

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Spheroids are three-dimensional cellular models with widespread basic and translational application across academia and industryFinal published version, 10.6 MB

https://www.nature.com/articles/s41592-021-01291-4

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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., ... De Wever, O. (2021). MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity. Nature Methods, 18(11), 1294-1303. Advance online publication. https://doi.org/10.1038/s41592-021-01291-4

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abstract = "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.",

author = "Arne Peirsman and Eva Blondeel and Tasdiq Ahmed and Jasper Anckaert and Dominique Audenaert and Tom Boterberg and Krisztina Buzas and Neil Carragher and Gastone Castellani and Fl{\'a}via Castro and Virginie Dangles-marie and John Dawson and \{De Tullio\}, Pascal and \{De Vlieghere\}, Elly and S{\'a}ndor Dedeyne and Herman Depypere and Akos Diosdi and Dmitriev, \{Ruslan I.\} and Helmut Dolznig and Suzanne Fischer and Christian Gespach and Vera Goossens and Jyrki Heino and An Hendrix and Peter Horvath and Kunz-schughart, \{Leoni A.\} and Sebastiaan Maes and Christophe Mangodt and Pieter Mestdagh and So{\v n}a Michl{\'i}kov{\'a} and Oliveira, \{Maria Jos{\'e}\} and Francesco Pampaloni and Filippo Piccinini and Cl{\'a}udio Pinheiro and Jennifer Rahn and Robbins, \{Stephen M.\} and Elina Siljam{\"a}ki and Patrick Steigemann and Gwen Sys and Shuichi Takayama and Anna Tesei and Joeri Tulkens and \{Van Waeyenberge\}, Michiel and Jo Vandesompele and Glenn Wagemans and Claudia Weindorfer and Nurten Yigit and Nina Zablowsky and Michele Zanoni and Phillip Blondeel and \{De Wever\}, Olivier",

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doi = "10.1038/s41592-021-01291-4",

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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, RI, Dolznig, H, Fischer, S, Gespach, C, Goossens, V, Heino, J, Hendrix, A, Horvath, P, Kunz-schughart, LA, Maes, S, Mangodt, C, Mestdagh, P, Michlíková, S, Oliveira, MJ, Pampaloni, F, Piccinini, F, Pinheiro, C, Rahn, J, Robbins, SM, Siljamäki, 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 2021, 'MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity', Nature Methods, vol. 18, no. 11, pp. 1294-1303. https://doi.org/10.1038/s41592-021-01291-4

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AU - Peirsman, Arne

AU - Blondeel, Eva

AU - Ahmed, Tasdiq

AU - Anckaert, Jasper

AU - Audenaert, Dominique

AU - Boterberg, Tom

AU - Buzas, Krisztina

AU - Carragher, Neil

AU - Castellani, Gastone

AU - Castro, Flávia

AU - Dangles-marie, Virginie

AU - Dawson, John

AU - De Tullio, Pascal

AU - De Vlieghere, Elly

AU - Dedeyne, Sándor

AU - Depypere, Herman

AU - Diosdi, Akos

AU - Dmitriev, Ruslan I.

AU - Dolznig, Helmut

AU - Fischer, Suzanne

AU - Gespach, Christian

AU - Goossens, Vera

AU - Heino, Jyrki

AU - Hendrix, An

AU - Horvath, Peter

AU - Kunz-schughart, Leoni A.

AU - Maes, Sebastiaan

AU - Mangodt, Christophe

AU - Mestdagh, Pieter

AU - Michlíková, Soňa

AU - Oliveira, Maria José

AU - Pampaloni, Francesco

AU - Piccinini, Filippo

AU - Pinheiro, Cláudio

AU - Rahn, Jennifer

AU - Robbins, Stephen M.

AU - Siljamäki, Elina

AU - Steigemann, Patrick

AU - Sys, Gwen

AU - Takayama, Shuichi

AU - Tesei, Anna

AU - Tulkens, Joeri

AU - Van Waeyenberge, Michiel

AU - Vandesompele, Jo

AU - Wagemans, Glenn

AU - Weindorfer, Claudia

AU - Yigit, Nurten

AU - Zablowsky, Nina

AU - Zanoni, Michele

AU - Blondeel, Phillip

AU - De Wever, Olivier

PY - 2021/11/1

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AB - 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.

U2 - 10.1038/s41592-021-01291-4

DO - 10.1038/s41592-021-01291-4

M3 - Article

SN - 1548-7091

VL - 18

SP - 1294

EP - 1303

JO - Nature Methods

JF - Nature Methods

IS - 11

ER -

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

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