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Biddle M, Stylianou P, Rekas M, Wright A, Sousa J, Ruddy D, Stefana MI, Kmiecik K, Bandrowski A, Kahn R, Laflamme C, Krockow EM, Virk H. Improving the integrity and reproducibility of research that uses antibodies: a technical, data sharing, behavioral and policy challenge. MAbs 2024; 16:2323706. [PMID: 38444344 PMCID: PMC10936606 DOI: 10.1080/19420862.2024.2323706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/22/2024] [Indexed: 03/07/2024] Open
Abstract
Antibodies are one of the most important reagents used in biomedical and fundamental research, used to identify, and quantify proteins, contribute to knowledge of disease mechanisms, and validate drug targets. Yet many antibodies used in research do not recognize their intended target, or recognize additional molecules, compromising the integrity of research findings and leading to waste of resources, lack of reproducibility, failure of research projects, and delays in drug development. Researchers frequently use antibodies without confirming that they perform as intended in their application of interest. Here we argue that the determinants of end-user antibody choice and use are critical, and under-addressed, behavioral drivers of this problem. This interacts with the batch-to-batch variability of these biological reagents, and the paucity of available characterization data for most antibodies, making it more difficult for researchers to choose high quality reagents and perform necessary validation experiments. The open-science company YCharOS works with major antibody manufacturers and knockout cell line producers to characterize antibodies, identifying high-performing renewable antibodies for many targets in neuroscience. This shows the progress that can be made by stakeholders working together. However, their work so far applies to only a tiny fraction of available antibodies. Where characterization data exists, end-users need help to find and use it appropriately. While progress has been made in the context of technical solutions and antibody characterization, we argue that initiatives to make best practice behaviors by researchers more feasible, easy, and rewarding are needed. Global cooperation and coordination between multiple partners and stakeholders will be crucial to address the technical, policy, behavioral, and open data sharing challenges. We offer potential solutions by describing our Only Good Antibodies initiative, a community of researchers and partner organizations working toward the necessary change. We conclude with an open invitation for stakeholders, including researchers, to join our cause.
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Affiliation(s)
- M. Biddle
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - P. Stylianou
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - M. Rekas
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - A. Wright
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - J. Sousa
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - D. Ruddy
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - M. I. Stefana
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - K. Kmiecik
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - A. Bandrowski
- Department of Neuroscience, UC San Diego, La Jolla, CA, USA
| | - R.A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, USA
| | - C. Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Canada
| | - E. M. Krockow
- School of Psychology and Vision Sciences, University of Leicester, Leicester, UK
| | - H.S. Virk
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
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Biddle MS, Virk HS. YCharOS open antibody characterisation data: Lessons learned and progress made. F1000Res 2023; 12:1344. [PMID: 37854875 PMCID: PMC10579855 DOI: 10.12688/f1000research.141719.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 10/20/2023] Open
Abstract
YCharOS is a collaborative initiative aimed at characterising antibodies against the entire human proteome. As of August 2023, they have presented comprehensive knockout characterisation data for 812 antibodies and 78 proteins using techniques such as Western blot, immunoprecipitation, and immunofluorescence. YCharOS consolidates its data into reports (one protein per report) available on Zenodo, a public repository controlled by CERN, to ensure open access. To enhance the visibility of their work, the group is progressively converting their Zenodo reports into F1000 articles, collected on the YCharOS Gateway, and indexed via PubMed. Their data is also accessible through searches on the Antibody Registry. The provided data is a valuable resource for researchers when selecting antibodies for specific applications, although certain limitations should be considered. The data accumulated thus far has illuminated the extent of the problem when poorly performing antibodies are employed in research. While the scientific community was already aware that this was likely a widespread issue, the establishment of a collaborative open science project with industry partners introduces an innovative solution that holds the potential to yield significant returns on investment in the public interest. This potential is substantiated by the number of antibodies that have either been withdrawn or had their recommended usage altered by the vendor. However, despite the discovery of high-performing renewable antibodies for most of the studied proteins, this accounts for a tiny fraction of the human proteome and the commercial antibody market. To realise the full potential of this work, end-users must adjust their antibody procurement and usage practises in line with the provided data. This editorial offers a guide on how individual scientists can utilise the YCharOS data, in addition to sharing the insights gained from the data thus far with the wider scientific community.
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Affiliation(s)
- Michael S. Biddle
- NIHR BRC-Respiratory, University of Leicester, Leicester, England, UK
| | - Harvinder S. Virk
- NIHR BRC-Respiratory, University of Leicester, Leicester, England, UK
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Ayoubi R, Ryan J, Biddle MS, Alshafie W, Fotouhi M, Bolivar SG, Moleon VR, Eckmann P, Worrall D, McDowell I, Southern K, Reintsch W, Durcan TM, Brown CM, Bandrowski A, Virk HS, Edwards AM, McPherson PS, Laflamme C. Scaling of an antibody validation procedure enables quantification of antibody performance in major research applications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543292. [PMID: 37398479 PMCID: PMC10312534 DOI: 10.1101/2023.06.01.543292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Antibodies are critical reagents to detect and characterize proteins. It is commonly understood that many commercial antibodies do not recognize their intended targets, but information on the scope of the problem remains largely anecdotal, and as such, feasibility of the goal of at least one potent and specific antibody targeting each protein in a proteome cannot be assessed. Focusing on antibodies for human proteins, we have scaled a standardized characterization approach using parental and knockout cell lines (Laflamme et al., 2019) to assess the performance of 614 commercial antibodies for 65 neuroscience-related proteins. Side-by-side comparisons of all antibodies against each target, obtained from multiple commercial partners, demonstrates that: i) more than 50% of all antibodies failed in one or more tests, ii) yet, ~50-75% of the protein set was covered by at least one high-performing antibody, depending on application, suggesting that coverage of human proteins by commercial antibodies is significant; and iii) recombinant antibodies performed better than monoclonal or polyclonal antibodies. The hundreds of underperforming antibodies identified in this study were found to have been used in a large number of published articles, which should raise alarm. Encouragingly, more than half of the underperforming commercial antibodies were reassessed by the manufacturers, and many had alterations to their recommended usage or were removed from the market. This first such study helps demonstrate the scale of the antibody specificity problem but also suggests an efficient strategy toward achieving coverage of the human proteome; mine the existing commercial antibody repertoire, and use the data to focus new renewable antibody generation efforts.
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Affiliation(s)
- Riham Ayoubi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Joel Ryan
- Advanced BioImaging Facility (ABIF), McGill University, Montreal, Canada
| | - Michael S Biddle
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Walaa Alshafie
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Maryam Fotouhi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Sara Gonzalez Bolivar
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Vera Ruiz Moleon
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Peter Eckmann
- Department of Neuroscience, UC San Diego, La Jolla, CA, United States of America
| | - Donovan Worrall
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Ian McDowell
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Kathleen Southern
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Wolfgang Reintsch
- The Neuro’s Early Drug Discovery Unit (EDDU), Structural Genomics Consortium, McGill University, Montreal, Quebec, Canada
| | - Thomas M Durcan
- The Neuro’s Early Drug Discovery Unit (EDDU), Structural Genomics Consortium, McGill University, Montreal, Quebec, Canada
| | - Claire M Brown
- Advanced BioImaging Facility (ABIF), McGill University, Montreal, Canada
| | - Anita Bandrowski
- Department of Neuroscience, UC San Diego, La Jolla, CA, United States of America
| | - Harvinder S Virk
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Aled M Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Peter S McPherson
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Carl Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
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Andres-Alonso M, Grochowska KM, Gundelfinger ED, Karpova A, Kreutz MR. Protein transport from pre- and postsynapse to the nucleus: Mechanisms and functional implications. Mol Cell Neurosci 2023; 125:103854. [PMID: 37084990 DOI: 10.1016/j.mcn.2023.103854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 04/23/2023] Open
Abstract
The extreme length of neuronal processes poses a challenge for synapse-to-nucleus communication. In response to this challenge several different mechanisms have evolved in neurons to couple synaptic activity to the regulation of gene expression. One of these mechanisms concerns the long-distance transport of proteins from pre- and postsynaptic sites to the nucleus. In this review we summarize current evidence on mechanisms of transport and consequences of nuclear import of these proteins for gene transcription. In addition, we discuss how information from pre- and postsynaptic sites might be relayed to the nucleus by this type of long-distance signaling. When applicable, we highlight how long-distance protein transport from synapse-to-nucleus can provide insight into the pathophysiology of disease or reveal new opportunities for therapeutic intervention.
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Affiliation(s)
- Maria Andres-Alonso
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany; Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Katarzyna M Grochowska
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany; Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Eckart D Gundelfinger
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany; Center for Behavioral Brain Sciences, Otto von Guericke University, 39120 Magdeburg, Germany; Institute of Pharmacology and Toxicology, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Anna Karpova
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany; Center for Behavioral Brain Sciences, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Michael R Kreutz
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany; Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; Center for Behavioral Brain Sciences, Otto von Guericke University, 39120 Magdeburg, Germany; German Center for Neurodegenerative Diseases (DZNE), 39120 Magdeburg, Germany.
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Alshafie W, Fotouhi M, Shlaifer I, Ayoubi R, Edwards AM, Durcan TM, McPherson PS, Laflamme C. Identification of highly specific antibodies for Serine/threonine-protein kinase TBK1 for use in immunoblot, immunoprecipitation and immunofluorescence. F1000Res 2022; 11:977. [PMID: 36415206 PMCID: PMC9647147 DOI: 10.12688/f1000research.124632.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
TBK1 is a serine-threonine protein kinase that has been linked to a number of diseases including amyotrophic lateral sclerosis and frontotemporal dementia. Reproducible research on TBK1 has been hampered by the lack of well characterized antibodies. In this study, we characterized 11 commercial antibodies for TBK1 for use in immunoblot, immunofluorescence and immunoprecipitation, using an isogeneic knock-out cell line as a control. We identify antibodies that appear specific for all three applications but invite the readers to interpret the present findings based on their own scientific expertise and use this report as a guide to select the most appropriate antibody for their specific needs.
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Affiliation(s)
- Walaa Alshafie
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Maryam Fotouhi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Irina Shlaifer
- The Neuro's Early Drug Discovery Unit (EDDU), Structural Genomics Consortium, McGill University, Montreal, Quebec, Canada
| | - Riham Ayoubi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Aled M. Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Thomas M. Durcan
- The Neuro's Early Drug Discovery Unit (EDDU), Structural Genomics Consortium, McGill University, Montreal, Quebec, Canada
| | - Peter S. McPherson
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Carl Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada,
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Alshafie W, Fotouhi M, Shlaifer I, Ayoubi R, Edwards AM, Durcan TM, McPherson PS, Laflamme C. Identification of highly specific antibodies for Serine/threonine-protein kinase TBK1 for use in immunoblot, immunoprecipitation and immunofluorescence. F1000Res 2022; 11:977. [PMID: 36415206 PMCID: PMC9647147 DOI: 10.12688/f1000research.124632.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 08/08/2023] Open
Abstract
TBK1 is a serine-threonine protein kinase that has been linked to a number of diseases including amyotrophic lateral sclerosis and frontotemporal dementia. Reproducible research on TBK1 has been hampered by the lack of well characterized antibodies. In this study, we characterized 11 commercial antibodies for TBK1 for use in immunoblot, immunofluorescence and immunoprecipitation, using an isogeneic knock-out cell line as a control. We identify antibodies that appear specific for all three applications but invite the readers to interpret the present findings based on their own scientific expertise and use this report as a guide to select the most appropriate antibody for their specific needs.
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Affiliation(s)
- Walaa Alshafie
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Maryam Fotouhi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Irina Shlaifer
- The Neuro's Early Drug Discovery Unit (EDDU), Structural Genomics Consortium, McGill University, Montreal, Quebec, Canada
| | - Riham Ayoubi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Aled M. Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Thomas M. Durcan
- The Neuro's Early Drug Discovery Unit (EDDU), Structural Genomics Consortium, McGill University, Montreal, Quebec, Canada
| | - Peter S. McPherson
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Carl Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
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Opportunities and challenges of alpha-synuclein as a potential biomarker for Parkinson's disease and other synucleinopathies. NPJ Parkinsons Dis 2022; 8:93. [PMID: 35869066 PMCID: PMC9307631 DOI: 10.1038/s41531-022-00357-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/24/2022] [Indexed: 02/07/2023] Open
Abstract
Parkinson’s disease (PD), the second most common progressive neurodegenerative disease, develops and progresses for 10–15 years before the clinical diagnostic symptoms of the disease are manifested. Furthermore, several aspects of PD pathology overlap with other neurodegenerative diseases (NDDs) linked to alpha-synuclein (aSyn) aggregation, also called synucleinopathies. Therefore, there is an urgent need to discover and validate early diagnostic and prognostic markers that reflect disease pathophysiology, progression, severity, and potential differences in disease mechanisms between PD and other NDDs. The close association between aSyn and the development of pathology in synucleinopathies, along with the identification of aSyn species in biological fluids, has led to increasing interest in aSyn species as potential biomarkers for early diagnosis of PD and differentiate it from other synucleinopathies. In this review, we (1) provide an overview of the progress toward mapping the distribution of aSyn species in the brain, peripheral tissues, and biological fluids; (2) present comparative and critical analysis of previous studies that measured total aSyn as well as other species such as modified and aggregated forms of aSyn in different biological fluids; and (3) highlight conceptual and technical gaps and challenges that could hinder the development and validation of reliable aSyn biomarkers; and (4) outline a series of recommendations to address these challenges. Finally, we propose a combined biomarker approach based on integrating biochemical, aggregation and structure features of aSyn, in addition to other biomarkers of neurodegeneration. We believe that capturing the diversity of aSyn species is essential to develop robust assays and diagnostics for early detection, patient stratification, monitoring of disease progression, and differentiation between synucleinopathies. This could transform clinical trial design and implementation, accelerate the development of new therapies, and improve clinical decisions and treatment strategies.
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