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

• DOI: 10.1038/s41592-021-01291-4
• Publication Date: 2021-11-01T17:02:43Z
• Authors: Arne Peirsman; Eva Blondeel; Tasdiq Ahmed; Jasper Anckaert; Dominique Audenaert; Tom Boterberg; Krisztina Buzas; Neil Carragher; Gastone Castellani; Flávia Castro; Virginie Dangles-...; 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-Sch...; 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 Waeye...; Jo Vandesompele; Glenn Wagemans; Claudia Weindorfer; Nurten Yigit; Nina Zablowsky; Michele Zanoni; Phillip Blondeel; Olivier De Wever
• Keywords: Resource; Knowledge Bases; Cell Culture Techniques; METABOLISM; Biochemistry; CULTURE; 03 medical and health sciences; TUMOR SPHEROIDS; Neoplasms; Spheroids, Cellular; Medicine and Health Sciences; Biomarkers, Tumor; Tumor Cells, Cultured; Tumor Microenvironment; Humans; Biomarkers, Tumor; Cell Culture Techniques; Gene Expression Regulation, Neoplastic; Humans; Neoplasms; RNA-Seq; Reproducibility of Results; Spheroids, Cellular; Tumor Cells, Cultured; Cell Proliferation; Knowledge Bases; Software; Tumor Microenvironment; RNA-Seq; QH301 Biology / biológia; Molecular Biology; Cell Proliferation; 0303 health sciences; Reproducibility of Results; Cell Biology; [SDV] Life Sciences [q-bio]; Gene Expression Regulation, Neoplastic; HALLMARK; CELLS; Software; Biotechnology

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.