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

Journal: Nature methods
PMID:

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.

Authors

  • Arne Peirsman
    Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Eva Blondeel
    Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Tasdiq Ahmed
    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, USA.
  • Jasper Anckaert
    OncoRNALab, Cancer Research Institute, Ghent, Belgium.
  • Dominique Audenaert
    VIB Screening Core and Ghent University Expertise Centre for Bioassay Development and Screening (C-BIOS-VIB), Ghent University, Ghent, Belgium.
  • Tom Boterberg
    Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium.
  • Krisztina Buzas
    Department of Immunology, University of Szeged, Faculty of Medicine-Faculty of Science and Informatics, Szeged, Hungary.
  • Neil Carragher
    Institute of Genetics and Cancer, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK.
  • Gastone Castellani
    Department of Specialised, Diagnostic and Experimental Medicine, University of Bologna, 40126, Bologna, BO, Italy.
  • Flávia Castro
    i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.
  • Virginie Dangles-Marie
    Translational Research Department, Institut Curie, PSL Research University, and Faculty of Pharmacy, Paris, France.
  • John Dawson
    Institute of Genetics and Cancer, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK.
  • Pascal De Tullio
    Center for Interdisciplinary Research on Medicines (CIRM), Metabolomics Group, Université de Liège, Liège, Belgium.
  • Elly De Vlieghere
    Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Sándor Dedeyne
    Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Herman Depypere
    Menopause and Breast Clinic, Ghent University Hospital, Ghent, Belgium.
  • Akos Diosdi
    Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Biological Research Center (BRC), Szeged, Hungary.
  • Ruslan I Dmitriev
    Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
  • Helmut Dolznig
    Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria.
  • Suzanne Fischer
    Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Christian Gespach
    INSERM U938 Hospital Saint-Antoine Research Center CRSA, Team Céline Prunier, TGFbeta Signaling in Cellular Plasticity and Cancer, Sorbonne University, Paris, France.
  • Vera Goossens
    VIB Screening Core and Ghent University Expertise Centre for Bioassay Development and Screening (C-BIOS-VIB), Ghent University, Ghent, Belgium.
  • Jyrki Heino
    Department of Life Technologies, University of Turku, Turku, Finland.
  • An Hendrix
    Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Péter Horváth
    Department of Pulmonology, Semmelweis University, Budapest, Hungary.
  • Leoni A Kunz-Schughart
    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.
  • Sebastiaan Maes
    Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium.
  • Christophe Mangodt
    Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Pieter Mestdagh
    OncoRNALab, Cancer Research Institute, Ghent, Belgium.
  • Soňa Michlíková
    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.
  • Maria José Oliveira
    i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.
  • Francesco Pampaloni
    Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany.
  • Filippo Piccinini
    Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy.
  • Cláudio Pinheiro
    Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Jennifer Rahn
    Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
  • Stephen M Robbins
    Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
  • Elina Siljamäki
    Department of Life Technologies, University of Turku, Turku, Finland.
  • Patrick Steigemann
    Lead Discovery, Nuvisan ICB, Berlin, Germany.
  • Gwen Sys
    Department of Orthopedics and Traumatology, Ghent University Hospital, Ghent University, Ghent, Belgium.
  • Shuichi Takayama
  • Anna Tesei
    IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy.
  • Joeri Tulkens
    Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Michiel Van Waeyenberge
    Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium.
  • Jo Vandesompele
    OncoRNALab, Cancer Research Institute, Ghent, Belgium.
  • Glenn Wagemans
    Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Claudia Weindorfer
    Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria.
  • Nurten Yigit
    OncoRNALab, Cancer Research Institute, Ghent, Belgium.
  • Nina Zablowsky
    Lead Discovery, Nuvisan ICB, Berlin, Germany.
  • Michele Zanoni
    IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy.
  • Phillip Blondeel
    Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium.
  • Olivier De Wever
    Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium. olivier.dewever@ugent.be.