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Ellis MJ, Lekka C, Holden KL, Tulmin H, Seedat F, O'Brien DP, Dhayal S, Zeissler ML, Knudsen JG, Kessler BM, Morgan NG, Todd JA, Richardson SJ, Stefana MI. Identification of high-performing antibodies for the reliable detection of Tau proteoforms by Western blotting and immunohistochemistry. Acta Neuropathol 2024; 147:87. [PMID: 38761203 PMCID: PMC11102361 DOI: 10.1007/s00401-024-02729-7] [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: 11/07/2023] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 05/20/2024]
Abstract
Antibodies are essential research tools whose performance directly impacts research conclusions and reproducibility. Owing to its central role in Alzheimer's disease and other dementias, hundreds of distinct antibody clones have been developed against the microtubule-associated protein Tau and its multiple proteoforms. Despite this breadth of offer, limited understanding of their performance and poor antibody selectivity have hindered research progress. Here, we validate a large panel of Tau antibodies by Western blot (79 reagents) and immunohistochemistry (35 reagents). We address the reagents' ability to detect the target proteoform, selectivity, the impact of protein phosphorylation on antibody binding and performance in human brain samples. While most antibodies detected Tau at high levels, many failed to detect it at lower, endogenous levels. By WB, non-selective binding to other proteins affected over half of the antibodies tested, with several cross-reacting with the related MAP2 protein, whereas the "oligomeric Tau" T22 antibody reacted with monomeric Tau by WB, thus calling into question its specificity to Tau oligomers. Despite the presumption that "total" Tau antibodies are agnostic to post-translational modifications, we found that phosphorylation partially inhibits binding for many such antibodies, including the popular Tau-5 clone. We further combine high-sensitivity reagents, mass-spectrometry proteomics and cDNA sequencing to demonstrate that presumptive Tau "knockout" human cells continue to express residual protein arising through exon skipping, providing evidence of previously unappreciated gene plasticity. Finally, probing of human brain samples with a large panel of antibodies revealed the presence of C-term-truncated versions of all main Tau brain isoforms in both control and tauopathy donors. Ultimately, we identify a validated panel of Tau antibodies that can be employed in Western blotting and/or immunohistochemistry to reliably detect even low levels of Tau expression with high selectivity. This work represents an extensive resource that will enable the re-interpretation of published data, improve reproducibility in Tau research, and overall accelerate scientific progress.
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Affiliation(s)
- Michael J Ellis
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Christiana Lekka
- Islet Biology Group, Department of Clinical & Biomedical Sciences, Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter, RILD Building, Exeter, UK
| | - Katie L Holden
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Hanna Tulmin
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Faheem Seedat
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Nuffield Department of Women's and Reproductive Health, Women's Centre, University of Oxford, John Radcliffe Hospital, Level 3, Oxford, UK
| | - Darragh P O'Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Shalinee Dhayal
- Islet Biology Group, Department of Clinical & Biomedical Sciences, Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter, RILD Building, Exeter, UK
| | - Marie-Louise Zeissler
- Islet Biology Group, Department of Clinical & Biomedical Sciences, Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter, RILD Building, Exeter, UK
| | - Jakob G Knudsen
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Department of Medicine, University of Oxford, Radcliffe, UK
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Noel G Morgan
- Islet Biology Group, Department of Clinical & Biomedical Sciences, Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter, RILD Building, Exeter, UK
| | - John A Todd
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Sarah J Richardson
- Islet Biology Group, Department of Clinical & Biomedical Sciences, Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter, RILD Building, Exeter, UK
| | - M Irina Stefana
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
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Ferguson MR, Mendez QM, Acca FE, Chapados CD, Driscoll HA, Jones KS, Mirando G, Weiner MP, Li X. Validation and the Determination of Antibody Bioactivity Using MILKSHAKE and Sundae Protocols. Methods Mol Biol 2023; 2702:451-465. [PMID: 37679635 PMCID: PMC10568615 DOI: 10.1007/978-1-0716-3381-6_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
To develop reproducible results, it is critical that all reagents used in an experiment be validated in an alternative or independent method. We present two such independent methods for determining the specificity of antibodies: (1) "MILKSHAKE," which can be used to validate the liability and specificity of antibodies directed against post-translationally-modified epitopes, and (2) "Sundae," which is a more complete alanine-like scanning method that can be used to better understand the binding and bioactivity of specific residues of a protein. We apply both of these methods to the interaction between an antibody and its antigen.
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An approach to identifying quality research antibodies. Biotechniques 2022; 73:167-170. [PMID: 36148881 DOI: 10.2144/btn-2022-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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The Anti-Glucocorticoid Receptor Antibody Clone 5E4: Raising Awareness of Unspecific Antibody Binding. Int J Mol Sci 2022; 23:ijms23095049. [PMID: 35563440 PMCID: PMC9104323 DOI: 10.3390/ijms23095049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
Unspecific antibody binding takes a significant toll on researchers in the form of both the economic burden and the disappointed hopes of promising new therapeutic targets. Despite recent initiatives promoting antibody validation, a uniform approach addressing this issue has not yet been developed. Here, we demonstrate that the anti-glucocorticoid receptor (GR) antibody clone 5E4 predominantly targets two different proteins of approximately the same size, namely AMP deaminase 2 (AMPD2) and transcription intermediary factor 1-beta (TRIM28). This paper is intended to generate awareness of unspecific binding of well-established reagents and advocate the use of more rigorous verification methods to improve antibody quality in the future.
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Considerations on Using Antibodies for Studying the Dynorphins/Kappa Opioid Receptor System. Handb Exp Pharmacol 2022; 271:23-38. [PMID: 34085120 PMCID: PMC9125580 DOI: 10.1007/164_2021_467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antibodies are important tools for protein and peptide research, including for the kappa opioid receptor (KOR) and dynorphins (Dyns). Well-characterized antibodies are essential for rigorous and reproducible research. However, lack of validation of antibody specificity has been thought to contribute significantly to the reproducibility crisis in biomedical research. Since 2003, many scientific journals have required documentation of validation of antibody specificity and use of knockout mouse tissues as a negative control is strongly recommended. Lack of specificity of antibodies against many G protein-coupled receptors (GPCRs) after extensive testing has been well-documented, but antibodies generated against partial sequences of the KOR have not been similarly investigated. For the dynorphins, differential processing has been described in distinct brain areas, resulting in controversial findings in immunohistochemistry (IHC) when different antibodies were used. In this chapter, we summarized accepted approaches for validation of antibody specificity. We discussed two KOR antibodies most commonly used in IHC and described generation and characterization of KOR antibodies and phospho-KOR specific antibodies in western blotting or immunoblotting (IB). In addition, applying antibodies targeting prodynorphin or mature dynorphin A illustrates the diversity of results obtained regarding the distribution of dynorphins in distinct brain areas.
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Svobodova Z, Novotny J, Ospalkova B, Slovakova M, Bilkova Z, Foret F. Affiblot: a dot blot-based screening device for selection of reliable antibodies. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3874-3884. [PMID: 34528947 DOI: 10.1039/d1ay00955a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The key factor in the development of antibody-based assays is to find an antibody that has an appropriate affinity, high specificity, and low cross-reactivity. However, this task is not easy to carry out since the research antibodies on the market may suffer from low specificity and reproducibility. Here, we report on a palm-sized dot blot-based device, called the affiblot, that has a specially designed lid that allows simultaneous semi-quantitative comparison of up to five antibodies from different suppliers regarding their affinity/avidity, cross-reactivity, and batch-to-batch reliability. The only required peripheral equipment is a vacuum pump, a camera, and densitometry software. The affiblot device was tested for its functionality and its measurements were compared against those obtained by standard dot blot and ELISA. The benefit over these methods, when various antibodies are evaluated, is in its simplicity. It allows easy antigen deposition, fast application and the discarding of the solutions, a compact undivided membrane, and therefore significant decrease of labor. The device was tested with specific anti-ApoE, anti-EpCAM, anti-Salmonella, anti-E. coli, and anti-Listeria antibodies from different suppliers. Their properties were compared for their ability to interact specifically with antigen and/or non-target structures and the best-suited antibody for the intended application was identified.
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Affiliation(s)
- Zuzana Svobodova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, Pardubice, Czech Republic.
- Department of Biological and Medical Sciences, Faculty of Pharmacy in Hradec Kralove, Charles University, Zborovska 2089, Czech Republic
| | - Jakub Novotny
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, Pardubice, Czech Republic.
- Institute of Analytical Chemistry of the CAS, v. v. i., Veveri 967/97, Brno, Czech Republic
| | - Barbora Ospalkova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, Pardubice, Czech Republic.
| | - Marcela Slovakova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, Pardubice, Czech Republic.
| | - Zuzana Bilkova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, Pardubice, Czech Republic.
| | - Frantisek Foret
- Institute of Analytical Chemistry of the CAS, v. v. i., Veveri 967/97, Brno, Czech Republic
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Normandeau F, Ng A, Beaugrand M, Juncker D. Spatial Bias in Antibody Microarrays May Be an Underappreciated Source of Variability. ACS Sens 2021; 6:1796-1806. [PMID: 33973474 DOI: 10.1021/acssensors.0c02613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibody microarrays enable multiplexed protein detection with minimal reagent consumption, but they continue to be plagued by lack of reproducibility. Chemically functionalized glass slides are used as substrates, yet antibody binding spatial inhomogeneity across the slide has not been analyzed in antibody microarrays. Here, we characterize spatial bias across five commercial slides patterned with nine overlapping dense arrays (by combining three buffers and three different antibodies), and we measure signal variation for both antibody immobilization and the assay signal, generating 270 heatmaps. Spatial bias varied across models, and the coefficient of variation ranged from 4.6 to 50%, which was unexpectedly large. Next, we evaluated three layouts of spot replicates-local, random, and structured random-for their capacity to predict assay variation. Local replicates are widely used but systematically underestimate the whole-slide variation by up to seven times; structured random replicates gave the most accurate estimation. Our results highlight the risk and consequences of using local replicates: the underappreciation of spatial bias as a source of variability, poor assay reproducibility, and possible overconfidence in assay results. We recommend the detailed characterization of spatial bias for antibody microarrays and the description and use of distributed positive replicates for research and clinical applications.
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Affiliation(s)
- Frédéric Normandeau
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Andy Ng
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Maiwenn Beaugrand
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - David Juncker
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 2B4, Canada
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8
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MacNeil T, Vathiotis IA, Martinez-Morilla S, Yaghoobi V, Zugazagoitia J, Liu Y, Rimm DL. Antibody validation for protein expression on tissue slides: a protocol for immunohistochemistry. Biotechniques 2020; 69:460-468. [PMID: 32852223 PMCID: PMC7807291 DOI: 10.2144/btn-2020-0095] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibodies play a crucial role in basic research and clinical decision-making. However, there are no standardized algorithms or guidelines to ensure their accuracy and validity. There have been efforts to generate consensus, but, with the exception of clinical labs, antibody validation remains variable in the literature and sometimes in clinical practice. Here we focus on immunohistochemistry, an example of a scientific and clinical tool where validation of antibodies is critical. We describe a protocol that we use to validate antibodies specifically for immunohistochemistry, including some of the pillars of antibody validation from Uhlen et al. 2016, as an example of a rigorous approach to build antibody-based tests for both basic and translational science labs and for the clinic.
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Affiliation(s)
- Tyler MacNeil
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | | | | | - Vesal Yaghoobi
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jon Zugazagoitia
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yuting Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
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Al-Khalili Szigyarto C. Duchenne Muscular Dystrophy: recent advances in protein biomarkers and the clinical application. Expert Rev Proteomics 2020; 17:365-375. [PMID: 32713262 DOI: 10.1080/14789450.2020.1773806] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Early biomarker discovery studies have praised the value of their emerging results, predicting an unprecedented impact on health care. Biomarkers are expected to provide tests with increased specificity and sensitivity compared to existing measures, improve the decision-making process, and accelerate the development of therapies. For rare disorders, like Duchenne Muscular Dystrophy (DMD) such biomarkers can assist the development of therapies, therefore also helping to find a cure for the disease. AREA COVERED State-of-the-art technologies have been used to identify blood biomarkers for DMD and efforts have been coordinated to develop and promote translation of biomarkers for clinical practice. Biomarker translation to clinical practice is however, adjoined by challenges related to the complexity of the disease, involving numerous biological processes, and the limited sample resources. This review highlights the current progress on the development of biomarkers, describing the proteomics technologies used, the most promising findings and the challenges encountered. EXPERT OPINION Strategies for effective use of samples combined with orthogonal proteomics methods for protein quantification are essential for translating biomarkers to the patient's bed side. Progress is achieved only if strong evidence is provided that the biomarker constitutes a reliable indicator of the patient's health status for a specific context of use.
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Affiliation(s)
- Cristina Al-Khalili Szigyarto
- Science for Life Laboratory, KTH - Royal Institute of Technology , Solna, Sweden.,School of Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology , Stockholm, Sweden
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10
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Pillai-Kastoori L, Schutz-Geschwender AR, Harford JA. A systematic approach to quantitative Western blot analysis. Anal Biochem 2020; 593:113608. [PMID: 32007473 DOI: 10.1016/j.ab.2020.113608] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/16/2019] [Accepted: 01/27/2020] [Indexed: 12/19/2022]
Abstract
Attaining true quantitative data from WB requires that all the players involved in the procedure are quality controlled including the user. Appropriate protein extraction method, electrophoresis, and transfer of proteins, immunodetection of blotted protein by antibodies, and the ultimate step of imaging and analyzing the data is nothing short of a symphony. Like with any other technology in life-sciences research, Western blotting can produce erroneous and irreproducible data. We provide a systematic approach to generate quantitative data from Western blot experiments that incorporates critical validation steps to identify and minimize sources of error and variability throughout the Western blot process.
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Affiliation(s)
| | | | - Jeff A Harford
- LI-COR Biosciences, 4647 Superior Street, Lincoln, NE, 68504, USA
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Pillai-Kastoori L, Heaton S, Shiflett SD, Roberts AC, Solache A, Schutz-Geschwender AR. Antibody validation for Western blot: By the user, for the user. J Biol Chem 2019; 295:926-939. [PMID: 31819006 PMCID: PMC6983856 DOI: 10.1074/jbc.ra119.010472] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
Well-characterized antibody reagents play a key role in the reproducibility of research findings, and inconsistent antibody performance leads to variability in Western blotting and other immunoassays. The current lack of clear, accepted standards for antibody validation and reporting of experimental details contributes to this problem. Because the performance of primary antibodies is strongly influenced by assay context, recommendations for validation and usage are unique to each type of immunoassay. Practical strategies are proposed for the validation of primary antibody specificity, selectivity, and reproducibility using Western blot analysis. The antibody should produce reproducible results within and between Western blotting experiments and the observed effect confirmed with a complementary or orthogonal method. Routine implementation of standardized antibody validation and reporting in immunoassays such as Western blotting may promote improved reproducibility across the global life sciences community.
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Affiliation(s)
| | - Sam Heaton
- Abcam Plc, Discovery Drive, Cambridge Biomedical Campus, Cambridge CB2 0AX, United Kingdom
| | | | - Annabelle C Roberts
- Abcam Plc, Discovery Drive, Cambridge Biomedical Campus, Cambridge CB2 0AX, United Kingdom
| | - Alejandra Solache
- Abcam Plc, Discovery Drive, Cambridge Biomedical Campus, Cambridge CB2 0AX, United Kingdom
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Validation of anti-glucocerebrosidase antibodies for western blot analysis on protein lysates of murine and human cells. Biochem J 2019; 476:261-274. [DOI: 10.1042/bcj20180708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 02/01/2023]
Abstract
Abstract
Gaucher disease (GD) is a rare lysosomal storage disorder caused by mutations in the GBA1 gene, encoding the lysosome-resident glucocerebrosidase enzyme involved in the hydrolysis of glucosylceramide. The discovery of an association between mutations in GBA1 and the development of synucleinopathies, including Parkinson disease, has directed attention to glucocerebrosidase as a potential therapeutic target for different synucleinopathies. These findings initiated an exponential growth in research and publications regarding the glucocerebrosidase enzyme. The use of various commercial and custom-made glucocerebrosidase antibodies has been reported, but standardized in-depth validation is still not available for many of these antibodies. This work details the evaluation of several previously reported glucocerebrosidase antibodies for western blot analysis, tested on protein lysates of murine gba+/+ and gba−/− immortalized neurons and primary human wild-type and type 2 GD fibroblasts.
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Enhanced validation of antibodies for research applications. Nat Commun 2018; 9:4130. [PMID: 30297845 PMCID: PMC6175901 DOI: 10.1038/s41467-018-06642-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/04/2018] [Indexed: 01/24/2023] Open
Abstract
There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies, and capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.
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Abstract
Validation of antibodies and other protein binders is a subject of pressing concern for the research community and one which is uppermost in the minds of all who use antibodies as research and diagnostic reagents. Assessing an antibody's fitness for purpose includes accurate ascertainment of its target specificity and suitability for the envisaged task. Moreover, standardised procedures are essential to guarantee sample quality in testing procedures. The problem of defining precise standards for antibody validation has engendered much debate in recent publications and meetings, but gradually a consensus is emerging. At the 8th Alpbach Affinity Proteomics workshop (March 2017), a panel of leaders in the antibody field discussed suggestions which could bring this complex but essential issue a step nearer to a resolution. 'Alpbach recommendations' for best practice include tailoring binder validation processes according to the intended applications and promoting greater transparency in publications and in the information available from commercial antibody developers/providers. A single approach will not fit all applications and end users must ensure that the reported validation holds for their specific requirements, highlighting the need for adequate training in the fundamentals of antibody characterisation and validation across the user community.
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Affiliation(s)
- Michael J Taussig
- Cambridge Protein Arrays Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Cláudia Fonseca
- Cambridge Protein Arrays Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - James S Trimmer
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA, 95616, USA; Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA, 95616, USA.
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Koch RJ, Barrette AM, Stern AD, Hu B, Bouhaddou M, Azeloglu EU, Iyengar R, Birtwistle MR. Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array. Sci Rep 2018; 8:11329. [PMID: 30054510 PMCID: PMC6063895 DOI: 10.1038/s41598-018-29436-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/10/2018] [Indexed: 01/11/2023] Open
Abstract
Fluorescence-based western blots are quantitative in principal, but require determining linear range for each antibody. Here, we use microwestern array to rapidly evaluate suitable conditions for quantitative western blotting, with up to 192 antibody/dilution/replicate combinations on a single standard size gel with a seven-point, two-fold lysate dilution series (~100-fold range). Pilot experiments demonstrate a high proportion of investigated antibodies (17/24) are suitable for quantitative use; however this sample of antibodies is not yet comprehensive across companies, molecular weights, and other important antibody properties, so the ubiquity of this property cannot yet be determined. In some cases microwestern struggled with higher molecular weight membrane proteins, so the technique may not be uniformly applicable to all validation tasks. Linear range for all validated antibodies is at least 8-fold, and up to two orders of magnitude. Phospho-specific and total antibodies do not have discernable trend differences in linear range or limit of detection. Total antibodies generally required higher working concentrations, but more comprehensive antibody panels are required to better establish whether this trend is general or not. Importantly, we demonstrate that results from microwestern analyses scale to normal "macro" western for a subset of antibodies.
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Affiliation(s)
- Rick J Koch
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anne Marie Barrette
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alan D Stern
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Hu
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mehdi Bouhaddou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Evren U Azeloglu
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ravi Iyengar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Marc R Birtwistle
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA.
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Krishnan VV, Selvan SR, Parameswaran N, Venkateswaran N, Luciw PA, Venkateswaran KS. Proteomic profiles by multiplex microsphere suspension array. J Immunol Methods 2018; 461:1-14. [PMID: 30003895 DOI: 10.1016/j.jim.2018.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 02/08/2023]
Abstract
Advances in high-throughput proteomic approaches have provided substantial momentum to novel disease-biomarker discovery research and have augmented the quality of clinical studies. Applications based on multiplexed microsphere suspension array technology are making strong in-roads into the clinical diagnostic/prognostic practice. Conventional proteomic approaches are designed to discover a broad set of proteins that are associated with a specific medical condition. In comparison, multiplex microsphere immunoassays use quantitative measurements of selected set(s) of specific/particular molecular markers such as cytokines, chemokines, pathway signaling or disease-specific markers for detection, metabolic disorders, cancer, and infectious agents causing human, plant and animal diseases. This article provides a foundation to the multiplexed microsphere suspension array technology, with an emphasis on the improvements in the technology, data analysis approaches, and applications to translational and clinical research with implications for personalized and precision medicine.
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Affiliation(s)
- Viswanathan V Krishnan
- Department of Chemistry, California State University, Fresno, CA 93750, United States; Department of Medical Pathology and Laboratory Medicine, University of California School of Medicine, Sacramento, CA 95817, United States.
| | | | | | | | - Paul A Luciw
- Center for Comparative Medicine, University of California Davis, Davis, CA 95616, United States; Department of Medical Pathology and Laboratory Medicine, University of California School of Medicine, Sacramento, CA 95817, United States
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Uhlen M, Bandrowski A, Carr S, Edwards A, Ellenberg J, Lundberg E, Rimm DL, Rodriguez H, Hiltke T, Snyder M, Yamamoto T. A proposal for validation of antibodies. Nat Methods 2016; 13:823-7. [PMID: 27595404 DOI: 10.1038/nmeth.3995] [Citation(s) in RCA: 404] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Mathias Uhlen
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anita Bandrowski
- Center for Research in Biological Systems, University of California at San Diego, San Diego, California, USA
| | - Steven Carr
- Proteomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Aled Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Emma Lundberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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19
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Bradbury AR, Plückthun A. Getting to reproducible antibodies: the rationale for sequenced recombinant characterized reagents. Protein Eng Des Sel 2015; 28:303-5. [DOI: 10.1093/protein/gzv051] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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20
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Chiarella P, Carbonari D, Iavicoli S. Utility of checklist to describe experimental methods for investigating molecular biomarkers. Biomark Med 2015; 9:989-95. [DOI: 10.2217/bmm.15.82] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Introduction: In research articles, detailed description of experimental methods and reagents is fundamental for correct reproducibility of the published data. This becomes even more important when such data contribute to identify molecular targets and toxicity biomarkers whose role is crucial in the physiology and pathology of human health. Methods & Objectives: To achieve good reproducibility of data we took advantage of others’ experiences and analyzed molecular biology and immunodetection techniques in 32 journal articles investigating the human NRF2 and Keap1 genes involved in the cell response to oxidative stress. Results & Conclusions: In conclusion of the analysis, we assessed deficiency of information in the published methods, making it difficult to select appropriate protocols. Underlining the importance of assay reproducibility, this paper proposes the utility of a minimum information checklist of methods for biomarker detection.
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Affiliation(s)
- Pieranna Chiarella
- Department of Occupational & Environmental Medicine, Epidemiology & Hygiene, INAIL Italian Workers’ Compensation Authority, Via Fontana Candida 1, 00040 Monteporzio Catone, Rome, Italy
| | - Damiano Carbonari
- Department of Occupational & Environmental Medicine, Epidemiology & Hygiene, INAIL Italian Workers’ Compensation Authority, Via Fontana Candida 1, 00040 Monteporzio Catone, Rome, Italy
| | - Sergio Iavicoli
- Department of Occupational & Environmental Medicine, Epidemiology & Hygiene, INAIL Italian Workers’ Compensation Authority, Via Fontana Candida 1, 00040 Monteporzio Catone, Rome, Italy
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Abstract
Antibody use is ubiquitous in the biomedical sciences. However, determining best research practices has not been trivial. Many commercially available antibodies and antibody-conjugates are poorly characterized and lack proper validation. Uncritical application of such useless tools has contributed to the reproducibility crisis in biomedical research. Despite early initiatives such as MIAPAR or PSI-PAR, a best practice guideline for antibody characterization is still not in prospect. Here, we analyze 24 antibody-related databases and compare their content with regard to validation aspects and coverage. We also provide a flowchart for end-users with all necessary steps to facilitate finding and choosing specific and sensitive antibodies for their experiments. Based on a growing demand for better and standardized validation procedures and characterization guidelines for antibody molecules we have summarized our findings in a five-point plan. We intend to keep the discussion alive and hope that properly used antibodies will remain as central to biomedicine as they are today.
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Affiliation(s)
- Diana Pauly
- Department of Ophthalmology, University Hospital Regensburg, Regensburg, 93053, Germany
| | - Katja Hanack
- Department of Immunotechnology, University of Potsdam, Potsdam, 14476, Germany
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22
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Marschall ALJ, Dübel S, Böldicke T. Specific in vivo knockdown of protein function by intrabodies. MAbs 2015; 7:1010-35. [PMID: 26252565 PMCID: PMC4966517 DOI: 10.1080/19420862.2015.1076601] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 01/02/2023] Open
Abstract
Intracellular antibodies (intrabodies) are recombinant antibody fragments that bind to target proteins expressed inside of the same living cell producing the antibodies. The molecules are commonly used to study the function of the target proteins (i.e., their antigens). The intrabody technology is an attractive alternative to the generation of gene-targeted knockout animals, and complements knockdown techniques such as RNAi, miRNA and small molecule inhibitors, by-passing various limitations and disadvantages of these methods. The advantages of intrabodies include very high specificity for the target, the possibility to knock down several protein isoforms by one intrabody and targeting of specific splice variants or even post-translational modifications. Different types of intrabodies must be designed to target proteins at different locations, typically either in the cytoplasm, in the nucleus or in the endoplasmic reticulum (ER). Most straightforward is the use of intrabodies retained in the ER (ER intrabodies) to knock down the function of proteins passing the ER, which disturbs the function of members of the membrane or plasma proteomes. More effort is needed to functionally knock down cytoplasmic or nuclear proteins because in this case antibodies need to provide an inhibitory effect and must be able to fold in the reducing milieu of the cytoplasm. In this review, we present a broad overview of intrabody technology, as well as applications both of ER and cytoplasmic intrabodies, which have yielded valuable insights in the biology of many targets relevant for drug development, including α-synuclein, TAU, BCR-ABL, ErbB-2, EGFR, HIV gp120, CCR5, IL-2, IL-6, β-amyloid protein and p75NTR. Strategies for the generation of intrabodies and various designs of their applications are also reviewed.
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Affiliation(s)
- Andrea LJ Marschall
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics; Braunschweig, Germany
| | - Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics; Braunschweig, Germany
| | - Thomas Böldicke
- Helmholtz Centre for Infection Research, Recombinant Protein Expression/Intrabody Unit, Helmholtz Centre for Infection Research; Braunschweig, Germany
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23
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Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H. Development of data representation standards by the human proteome organization proteomics standards initiative. J Am Med Inform Assoc 2015; 22:495-506. [PMID: 25726569 PMCID: PMC4457114 DOI: 10.1093/jamia/ocv001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/29/2014] [Accepted: 01/05/2015] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To describe the goals of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization, the methods that the PSI has employed to create data standards, the resulting output of the PSI, lessons learned from the PSI's evolution, and future directions and synergies for the group. MATERIALS AND METHODS The PSI has 5 categories of deliverables that have guided the group. These are minimum information guidelines, data formats, controlled vocabularies, resources and software tools, and dissemination activities. These deliverables are produced via the leadership and working group organization of the initiative, driven by frequent workshops and ongoing communication within the working groups. Official standards are subjected to a rigorous document process that includes several levels of peer review prior to release. RESULTS We have produced and published minimum information guidelines describing what information should be provided when making data public, either via public repositories or other means. The PSI has produced a series of standard formats covering mass spectrometer input, mass spectrometer output, results of informatics analysis (both qualitative and quantitative analyses), reports of molecular interaction data, and gel electrophoresis analyses. We have produced controlled vocabularies that ensure that concepts are uniformly annotated in the formats and engaged in extensive software development and dissemination efforts so that the standards can efficiently be used by the community.Conclusion In its first dozen years of operation, the PSI has produced many standards that have accelerated the field of proteomics by facilitating data exchange and deposition to data repositories. We look to the future to continue developing standards for new proteomics technologies and workflows and mechanisms for integration with other omics data types. Our products facilitate the translation of genomics and proteomics findings to clinical and biological phenotypes. The PSI website can be accessed at http://www.psidev.info.
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Affiliation(s)
| | - Juan Pablo Albar
- Died July 18, 2014 Proteomics Facility, Centro Nacional de Biotecnología - CSIC, Madrid, Spain ProteoRed Consortium, Spanish National Institute of Proteomics, Madrid, Spain
| | - Pierre-Alain Binz
- CHUV Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Martin Eisenacher
- Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, Bochum, Germany
| | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gerhard Mayer
- Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, Bochum, Germany
| | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, USA Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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24
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Uhlen M. Integrating omics to study human biology and disease. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.1723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Vempati UD, Chung C, Mader C, Koleti A, Datar N, Vidović D, Wrobel D, Erickson S, Muhlich JL, Berriz G, Benes CH, Subramanian A, Pillai A, Shamu CE, Schürer SC. Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS). JOURNAL OF BIOMOLECULAR SCREENING 2014; 19:803-16. [PMID: 24518066 PMCID: PMC7723305 DOI: 10.1177/1087057114522514] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/13/2014] [Indexed: 01/15/2023]
Abstract
The National Institutes of Health Library of Integrated Network-based Cellular Signatures (LINCS) program is generating extensive multidimensional data sets, including biochemical, genome-wide transcriptional, and phenotypic cellular response signatures to a variety of small-molecule and genetic perturbations with the goal of creating a sustainable, widely applicable, and readily accessible systems biology knowledge resource. Integration and analysis of diverse LINCS data sets depend on the availability of sufficient metadata to describe the assays and screening results and on their syntactic, structural, and semantic consistency. Here we report metadata specifications for the most important molecular and cellular components and recommend them for adoption beyond the LINCS project. We focus on the minimum required information to model LINCS assays and results based on a number of use cases, and we recommend controlled terminologies and ontologies to annotate assays with syntactic consistency and semantic integrity. We also report specifications for a simple annotation format (SAF) to describe assays and screening results based on our metadata specifications with explicit controlled vocabularies. SAF specifically serves to programmatically access and exchange LINCS data as a prerequisite for a distributed information management infrastructure. We applied the metadata specifications to annotate large numbers of LINCS cell lines, proteins, and small molecules. The resources generated and presented here are freely available.
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Affiliation(s)
- Uma D Vempati
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Caty Chung
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Chris Mader
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Amar Koleti
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Nakul Datar
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Dušica Vidović
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - David Wrobel
- ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, USA
| | - Sean Erickson
- ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, USA
| | - Jeremy L Muhlich
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gabriel Berriz
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Cyril H Benes
- Center for Molecular Therapeutics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Ajay Pillai
- National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Caroline E Shamu
- ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, USA Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephan C Schürer
- Center for Computational Science, University of Miami, Miami, FL, USA Department of Molecular and Cellular Pharmacology, University of Miami, Miami, Florida, USA
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26
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Taussig MJ, Schmidt R, Cook EA, Stoevesandt O. Development of proteome-wide binding reagents for research and diagnostics. Proteomics Clin Appl 2014; 7:756-66. [PMID: 24178846 DOI: 10.1002/prca.201300060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/11/2023]
Abstract
Alongside MS, antibodies and other specific protein-binding molecules have a special place in proteomics as affinity reagents in a toolbox of applications for determining protein location, quantitative distribution and function (affinity proteomics). The realisation that the range of research antibodies available, while apparently vast is nevertheless still very incomplete and frequently of uncertain quality, has stimulated projects with an objective of raising comprehensive, proteome-wide sets of protein binders. With progress in automation and throughput, a remarkable number of recent publications refer to the practical possibility of selecting binders to every protein encoded in the genome. Here we review the requirements of a pipeline of production of protein binders for the human proteome, including target prioritisation, antigen design, 'next generation' methods, databases and the approaches taken by ongoing projects in Europe and the USA. While the task of generating affinity reagents for all human proteins is complex and demanding, the benefits of well-characterised and quality-controlled pan-proteome binder resources for biomedical research, industry and life sciences in general would be enormous and justify the effort. Given the technical, personnel and financial resources needed to fulfil this aim, expansion of current efforts may best be addressed through large-scale international collaboration.
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Affiliation(s)
- Michael J Taussig
- Protein Technology Group, The Babraham Institute, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK
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27
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Stoevesandt O, Taussig MJ. Affinity proteomics: the role of specific binding reagents in human proteome analysis. Expert Rev Proteomics 2014; 9:401-14. [DOI: 10.1586/epr.12.34] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Martínez-Bartolomé S, Binz PA, Albar JP. The Minimal Information about a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative. Methods Mol Biol 2014; 1072:765-80. [PMID: 24136562 DOI: 10.1007/978-1-62703-631-3_53] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During the last 10 years, the Proteomics Standards Initiative from the Human Proteome Organization (HUPO-PSI) has worked on defining standards for proteomics data representation as well as guidelines that state the minimum information that should be included when reporting a proteomics experiment (MIAPE). Such minimum information must describe the complete experiment, including both experimental protocols and data processing methods, allowing a critical evaluation of the whole process and the potential recreation of the work. In this chapter we describe the standardization work performed by the HUPO-PSI, and then we concentrate on the MIAPE guidelines, highlighting its importance when publishing proteomics experiments particularly in specialized proteomics journals. Finally, we describe existing bioinformatics resources that generate MIAPE compliant reports or that check proteomics data files for MIAPE compliance.
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29
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Gu Q, Yu LR. Proteomics quality and standard: from a regulatory perspective. J Proteomics 2013; 96:353-9. [PMID: 24316359 DOI: 10.1016/j.jprot.2013.11.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 11/07/2013] [Accepted: 11/22/2013] [Indexed: 12/30/2022]
Abstract
Proteomics has emerged as a rapidly expanding field dealing with large-scale protein analyses. It is anticipated that proteomics data will be increasingly submitted to the U.S. Food and Drug Administration (FDA) for biomarker qualification or in conjunction with applications for the approval of drugs, medical devices, and other FDA-regulated consumer products. To date, however, no established guideline has been available regarding the generation, submission and assessment of the quality of proteomics data that will be reviewed by regulatory agencies for decision making. Therefore, this commentary is aimed at provoking some thoughts and debates towards developing a framework which can guide future proteomics data submission. The ultimate goal is to establish quality control standards for proteomics data generation and evaluation, and to prepare government agencies such as the FDA to meet future obligations utilizing proteomics data to support regulatory decision.
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Affiliation(s)
- Qiang Gu
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, USA
| | - Li-Rong Yu
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, USA.
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30
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Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA. On the reproducibility of science: unique identification of research resources in the biomedical literature. PeerJ 2013; 1:e148. [PMID: 24032093 PMCID: PMC3771067 DOI: 10.7717/peerj.148] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 08/12/2013] [Indexed: 12/24/2022] Open
Abstract
Scientific reproducibility has been at the forefront of many news stories and there exist numerous initiatives to help address this problem. We posit that a contributor is simply a lack of specificity that is required to enable adequate research reproducibility. In particular, the inability to uniquely identify research resources, such as antibodies and model organisms, makes it difficult or impossible to reproduce experiments even where the science is otherwise sound. In order to better understand the magnitude of this problem, we designed an experiment to ascertain the “identifiability” of research resources in the biomedical literature. We evaluated recent journal articles in the fields of Neuroscience, Developmental Biology, Immunology, Cell and Molecular Biology and General Biology, selected randomly based on a diversity of impact factors for the journals, publishers, and experimental method reporting guidelines. We attempted to uniquely identify model organisms (mouse, rat, zebrafish, worm, fly and yeast), antibodies, knockdown reagents (morpholinos or RNAi), constructs, and cell lines. Specific criteria were developed to determine if a resource was uniquely identifiable, and included examining relevant repositories (such as model organism databases, and the Antibody Registry), as well as vendor sites. The results of this experiment show that 54% of resources are not uniquely identifiable in publications, regardless of domain, journal impact factor, or reporting requirements. For example, in many cases the organism strain in which the experiment was performed or antibody that was used could not be identified. Our results show that identifiability is a serious problem for reproducibility. Based on these results, we provide recommendations to authors, reviewers, journal editors, vendors, and publishers. Scientific efficiency and reproducibility depend upon a research-wide improvement of this substantial problem in science today.
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Affiliation(s)
- Nicole A Vasilevsky
- Ontology Development Group, Library, Oregon Health & Science University , Portland, OR , USA
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31
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Fields C, O'Connell D, Xiao S, Lee GU, Billiald P, Muzard J. Creation of recombinant antigen-binding molecules derived from hybridomas secreting specific antibodies. Nat Protoc 2013; 8:1125-48. [DOI: 10.1038/nprot.2013.057] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Uhlen M. A Human Protein Atlas to study human biology and disease. N Biotechnol 2012. [DOI: 10.1016/j.nbt.2012.08.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Exploring the Human Protein Atlas in the field of toxicology. Toxicol Lett 2012. [DOI: 10.1016/j.toxlet.2012.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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34
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Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolomé S, Vizcaíno JA, Hermjakob H. From Proteomics Data Representation to Public Data Flow: A Report on the HUPO-PSI Workshop September 2011, Geneva, Switzerland. Proteomics 2012; 12:351-5. [DOI: 10.1002/pmic.201290016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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35
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Pla-Roca M, Leulmi RF, Tourekhanova S, Bergeron S, Laforte V, Moreau E, Gosline SJC, Bertos N, Hallett M, Park M, Juncker D. Antibody colocalization microarray: a scalable technology for multiplex protein analysis in complex samples. Mol Cell Proteomics 2011; 11:M111.011460. [PMID: 22171321 PMCID: PMC3322566 DOI: 10.1074/mcp.m111.011460] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
DNA microarrays were rapidly scaled up from 256 to 6.5 million targets, and although antibody microarrays were proposed earlier, sensitive multiplex sandwich assays have only been scaled up to a few tens of targets. Cross-reactivity, arising because detection antibodies are mixed, is a known weakness of multiplex sandwich assays that is mitigated by lengthy optimization. Here, we introduce (1) vulnerability as a metric for assays. The vulnerability of multiplex sandwich assays to cross-reactivity increases quadratically with the number of targets, and together with experimental results, substantiates that scaling up of multiplex sandwich assays is unfeasible. We propose (2) a novel concept for multiplexing without mixing named antibody colocalization microarray (ACM). In ACMs, both capture and detection antibodies are physically colocalized by spotting to the same two-dimensional coordinate. Following spotting of the capture antibodies, the chip is removed from the arrayer, incubated with the sample, placed back onto the arrayer and then spotted with the detection antibodies. ACMs with up to 50 targets were produced, along with a binding curve for each protein. The ACM was validated by comparing it to ELISA and to a small-scale, conventional multiplex sandwich assay (MSA). Using ACMs, proteins in the serum of breast cancer patients and healthy controls were quantified, and six candidate biomarkers identified. Our results indicate that ACMs are sensitive, robust, and scalable.
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Affiliation(s)
- M Pla-Roca
- Biomedical Engineering Department, McGill University, Montreal, Quebec, Canada
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36
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On the trail to therapeutic antibodies. N Biotechnol 2011; 28:431-3. [DOI: 10.1016/j.nbt.2011.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Orchard S, Al-Lazikani B, Bryant S, Clark D, Calder E, Dix I, Engkvist O, Forster M, Gaulton A, Gilson M, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, Larminie C, Lynch N, Mann RK, Murray-Rust P, Lo Piparo E, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J. Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov 2011; 10:661-9. [DOI: 10.1038/nrd3503] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Affiliation(s)
- Mathias Uhlen
- Albanova University Center and Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, Sweden
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39
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Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL. Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Stand Genomic Sci 2010; 3:259-66. [PMID: 21304730 PMCID: PMC3035314 DOI: 10.4056/sigs.147362] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://mibbi.org/.
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Affiliation(s)
| | - Dawn Field
- Centre for Ecology & Hydrology, Oxfordshire UK
| | | | - Chris Taylor
- The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jan Aerts
- Faculty of Engineering - ESAT/SCD, Leuven University, Leuven-Heverlee, Belgium
| | - Nigel Binns
- Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, UK
| | - Andrew Blake
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, UK
| | - Cedrik M. Britten
- Medical Department, University Medical Center, Johannes Gutenberg University-Mainz, Mainz, DE
| | - Ario de Marco
- Consortium for Genomic Technology, Milano, Italy
- University of Nova Gorica, Nova Gorica, Slovenia
| | | | | | - Alejandra González-Beltrán
- Computational and Systems Medicine and Department of Computer Science, University College London, London, UK
| | - Nigel Hardy
- Department of Computer Science, Aberystwyth University, Aberystwyth, UK
| | - Jan Hellemans
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Henning Hermjakob
- The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Nick Juty
- The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, U.S.A
| | - Eamonn Maguire
- University of Oxford, Oxford e-Research Centre, Oxfordshire, UK
| | - Steffen Neumann
- Department of Stress- and Developmental Biology, Institute for Plant Biochemistry, Halle, DE
| | - Sandra Orchard
- The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Helen Parkinson
- The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - William Piel
- Peabody Museum of Natural History, Yale University, New Haven, CT, U.S.A
| | - Shoba Ranganathan
- Macquarie University, Sydney NSW, Australia
- National University of Singapore, Singapore
| | | | - Annapaola Santarsiero
- The Mario Negri Institute for Pharmacological Research, Cancer Pharmacology, 20156 Milan, Italy
| | - David Shotton
- Image Bioinformatics Research Group, Department of Zoology, University of Oxford, Oxford, UK
| | - Peter Sterk
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Andreas Untergasser
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Patricia L. Whetzel
- The National Center for Biomedical Ontology / Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, U.S.A
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