Article (Scientific journals)
MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity
Peirsman, A.; Blondeel, E.; Ahmed, T. et al.
2021In Nature Methods, 18 (11), p. 1294-1303
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Keywords :
Biomarkers, Tumor; Cell Culture Techniques; Cell Proliferation; Gene Expression Regulation, Neoplastic; Humans; Knowledge Bases; Neoplasms; Reproducibility of Results; RNA-Seq; Software; Spheroids, Cellular; Tumor Cells, Cultured; Tumor Microenvironment
Abstract :
[en] 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).
Disciplines :
Human health sciences: Multidisciplinary, general & others
Author, co-author :
Peirsman, A.;  Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium, Department of Human Structure and Repair, Ghent University, Ghent, Belgium, Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium
Blondeel, E.;  Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
Ahmed, T.;  Wallace H Coulter Department of Biomedical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, United States
Anckaert, J.;  OncoRNALab, Cancer Research Institute, Ghent, Belgium, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
Audenaert, D.;  VIB Screening Core and Ghent University Expertise Centre for Bioassay Development and Screening (C-BIOS-VIB), Ghent University, Ghent, Belgium
Boterberg, T.;  Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium
Buzas, K.;  Department of Immunology, University of Szeged, Faculty of Medicine-Faculty of Science and Informatics, Szeged, Hungary
Carragher, N.;  Institute of Genetics and Cancer, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, United Kingdom
Castellani, G.;  Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
Castro, F.;  i3S – Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
Dangles-Marie, V.;  Translational Research Department, Institut Curie, PSL Research University, and Faculty of Pharmacy, Paris, France, Faculty of Pharmacy, Université Paris Descartes, Paris, France
Dawson, J.;  Institute of Genetics and Cancer, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, United Kingdom
De Tullio, Pascal ;  Université de Liège - ULiège > Département de pharmacie > Chimie pharmaceutique
De Vlieghere, E.;  Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
Dedeyne, S.;  Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
Depypere, H.;  Menopause and Breast Clinic, Ghent University Hospital, Ghent, Belgium
Diosdi, A.;  Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Biological Research Center (BRC), Szeged, Hungary
Dmitriev, R. I.;  Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
Dolznig, H.;  Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
Fischer, S.;  Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
Gespach, C.;  INSERM U938 Hospital Saint-Antoine Research Center CRSA, Team Céline Prunier, TGFbeta Signaling in Cellular Plasticity and Cancer, Sorbonne University, Paris, France
Goossens, V.;  VIB Screening Core and Ghent University Expertise Centre for Bioassay Development and Screening (C-BIOS-VIB), Ghent University, Ghent, Belgium
Heino, J.;  Department of Life Technologies, University of Turku, Turku, Finland
Hendrix, A.;  Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
Horvath, P.;  Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Biological Research Center (BRC), Szeged, Hungary
Kunz-Schughart, L. A.;  OncoRay – National Center for Radiation Research in Oncology, University Hospital Carl Gustav Carus Dresden, Carl Gustav Carus Faculty of Medicine at TU Dresden, and Helmholtz-Zentrum Dresden–Rossendorf, Dresden, Germany
Maes, S.;  Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium
Mangodt, C.;  Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
Mestdagh, P.;  OncoRNALab, Cancer Research Institute, Ghent, Belgium, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
Michlíková, S.;  OncoRay – National Center for Radiation Research in Oncology, University Hospital Carl Gustav Carus Dresden, Carl Gustav Carus Faculty of Medicine at TU Dresden, and Helmholtz-Zentrum Dresden–Rossendorf, Dresden, Germany
Oliveira, M. J.;  i3S – Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
Pampaloni, F.;  Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
Piccinini, F.;  IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) ‘Dino Amadori’, Meldola, Italy
Pinheiro, C.;  Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
Rahn, J.;  Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
Robbins, S. M.;  Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
Siljamäki, E.;  Department of Life Technologies, University of Turku, Turku, Finland
Steigemann, P.;  Lead Discovery, Nuvisan ICB, Berlin, Germany
Sys, G.;  Department of Orthopedics and Traumatology, Ghent University Hospital, Ghent University, Ghent, Belgium
Takayama, S.;  Wallace H Coulter Department of Biomedical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, United States
Tesei, A.;  IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) ‘Dino Amadori’, Meldola, Italy
Tulkens, J.;  Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
Van Waeyenberge, M.;  Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium
Vandesompele, J.;  OncoRNALab, Cancer Research Institute, Ghent, Belgium, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
Wagemans, G.;  Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
Weindorfer, C.;  Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
Yigit, N.;  OncoRNALab, Cancer Research Institute, Ghent, Belgium, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
Zablowsky, N.;  Lead Discovery, Nuvisan ICB, Berlin, Germany
Zanoni, M.;  IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) ‘Dino Amadori’, Meldola, Italy
Blondeel, P.;  Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium
De Wever, O.;  Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
More authors (41 more) Less
Language :
English
Title :
MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity
Publication date :
2021
Journal title :
Nature Methods
ISSN :
1548-7091
eISSN :
1548-7105
Publisher :
Nature Research
Volume :
18
Issue :
11
Pages :
1294-1303
Peer reviewed :
Peer Reviewed verified by ORBi
Funding text :
1198121N; National Institutes of Health, NIH: R01 CA196018, R21 AG061687; Foundation for the National Institutes of Health, FNIH; Horizon 2020 Framework Programme, H2020: 668350-2; Canadian Institutes of Health Research, CIHR; fr:IRSC: 147081; Cancer Research UK, CRUK: A28596, A29368; European External Action Service, EEAS: 828931; ZonMw; Brain Tumour Charity: GN-000676; Bundesministerium für Bildung und Forschung, BMBF: 03Z1N512, 114027003, 13N11115; Universiteit Gent: 01G02221; Stichting Tegen Kanker: 2020-073; Sigrid Juséliuksen Säätiö; Syöpäjärjestöt, CSF; Kom op tegen Kanker
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