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Volpato V, Smith J, Sandor C, Ried JS, Baud A, Handel A, Newey SE, Wessely F, Attar M, Whiteley E, Chintawar S, Verheyen A, Barta T, Lako M, Armstrong L, Muschet C, Artati A, Cusulin C, Christensen K, Patsch C, Sharma E, Nicod J, Brownjohn P, Stubbs V, Heywood WE, Gissen P, De Filippis R, Janssen K, Reinhardt P, Adamski J, Royaux I, Peeters PJ, Terstappen GC, Graf M, Livesey FJ, Akerman CJ, Mills K, Bowden R, Nicholson G, Webber C, Cader MZ, Lakics V. Reproducibility of Molecular Phenotypes after Long-Term Differentiation to Human iPSC-Derived Neurons: A Multi-Site Omics Study. Stem Cell Reports 2018; 11:897-911. [PMID: 30245212 PMCID: PMC6178242 DOI: 10.1016/j.stemcr.2018.08.013] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 12/30/2022] Open
Abstract
Reproducibility in molecular and cellular studies is fundamental to scientific discovery. To establish the reproducibility of a well-defined long-term neuronal differentiation protocol, we repeated the cellular and molecular comparison of the same two iPSC lines across five distinct laboratories. Despite uncovering acceptable variability within individual laboratories, we detect poor cross-site reproducibility of the differential gene expression signature between these two lines. Factor analysis identifies the laboratory as the largest source of variation along with several variation-inflating confounders such as passaging effects and progenitor storage. Single-cell transcriptomics shows substantial cellular heterogeneity underlying inter-laboratory variability and being responsible for biases in differential gene expression inference. Factor analysis-based normalization of the combined dataset can remove the nuisance technical effects, enabling the execution of robust hypothesis-generating studies. Our study shows that multi-center collaborations can expose systematic biases and identify critical factors to be standardized when publishing novel protocols, contributing to increased cross-site reproducibility.
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Affiliation(s)
- Viola Volpato
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT UK
| | - James Smith
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Cynthia Sandor
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT UK
| | - Janina S Ried
- Neuroscience Discovery, Biology Department, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen, Germany
| | - Anna Baud
- Centre for Translational Omics, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Adam Handel
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT UK
| | - Sarah E Newey
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Frank Wessely
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT UK
| | - Moustafa Attar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Emma Whiteley
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Satyan Chintawar
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX3 9DU, UK
| | - An Verheyen
- Janssen Research and Development, Beerse 2340, Belgium
| | - Thomas Barta
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Lyle Armstrong
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Caroline Muschet
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg 85764, Germany
| | - Anna Artati
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg 85764, Germany
| | - Carlo Cusulin
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Klaus Christensen
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Christoph Patsch
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Eshita Sharma
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jerome Nicod
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Philip Brownjohn
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Victoria Stubbs
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Wendy E Heywood
- Centre for Translational Omics, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Paul Gissen
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Roberta De Filippis
- Neuroscience Discovery, Biology Department, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen, Germany
| | - Katharina Janssen
- Neuroscience Discovery, Biology Department, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen, Germany
| | - Peter Reinhardt
- Neuroscience Discovery, Biology Department, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen, Germany
| | - Jerzy Adamski
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg 85764, Germany
| | - Ines Royaux
- Janssen Research and Development, Beerse 2340, Belgium
| | | | - Georg C Terstappen
- Neuroscience Discovery, Biology Department, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen, Germany
| | - Martin Graf
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | | | - Colin J Akerman
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Kevin Mills
- Centre for Translational Omics, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - George Nicholson
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
| | - Caleb Webber
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT UK.
| | - M Zameel Cader
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX3 9DU, UK.
| | - Viktor Lakics
- Neuroscience Discovery, Biology Department, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen, Germany.
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