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Kahn RA, Virk H, Laflamme C, Houston DW, Polinski NK, Meijers R, Levey AI, Saper CB, Errington TM, Turn RE, Bandrowski A, Trimmer JS, Rego M, Freedman LP, Ferrara F, Bradbury ARM, Cable H, Longworth S. Antibody characterization is critical to enhance reproducibility in biomedical research. eLife 2024; 13:e100211. [PMID: 39140332 PMCID: PMC11324233 DOI: 10.7554/elife.100211] [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: 05/30/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024] Open
Abstract
Antibodies are used in many areas of biomedical and clinical research, but many of these antibodies have not been adequately characterized, which casts doubt on the results reported in many scientific papers. This problem is compounded by a lack of suitable control experiments in many studies. In this article we review the history of the 'antibody characterization crisis', and we document efforts and initiatives to address the problem, notably for antibodies that target human proteins. We also present recommendations for a range of stakeholders - researchers, universities, journals, antibody vendors and repositories, scientific societies and funders - to increase the reproducibility of studies that rely on antibodies.
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Affiliation(s)
- Richard A Kahn
- Department of Biochemistry, Emory University School of MedicineAtlantaUnited States
| | - Harvinder Virk
- Department of Respiratory Sciences, University of LeicesterLeicesterUnited Kingdom
| | - Carl Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Douglas W Houston
- The Development Studies Hybridoma Databank, University of IowaIowa CityUnited States
| | - Nicole K Polinski
- The Michael J Fox Foundation for Parkinson’s ResearchNew YorkUnited States
| | - Rob Meijers
- Institute for Protein InnovationBostonUnited States
| | - Allan I Levey
- Department of Neurology, Emory University School of MedicineAtlantaUnited States
| | - Clifford B Saper
- Department of Neurology and Program in Neuroscience, Harvard Medical School and Beth Israel Deaconess Medical CenterBostonUnited States
| | | | - Rachel E Turn
- Department of Microbiology and Immunology, Stanford University School of MedicineStanfordUnited States
| | - Anita Bandrowski
- Department of Neuroscience, University of California, San DiegoLa JollaUnited States
| | - James S Trimmer
- Department of Physiology and Membrane Biology, University of California, Davis School of MedicineDavisUnited States
| | | | | | | | | | - Hannah Cable
- Department of Research and Development, AbcamCambridgeUnited Kingdom
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Wang N, Zhang L, Ying Q, Song Z, Lu A, Treumann A, Liu Z, Sun T, Ding Z. A reverse phase protein array based phospho-antibody characterization approach and its applicability for clinical derived tissue specimens. Sci Rep 2022; 12:22373. [PMID: 36572710 PMCID: PMC9792559 DOI: 10.1038/s41598-022-26715-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 12/19/2022] [Indexed: 12/27/2022] Open
Abstract
Systematic quantification of phosphoprotein within cell signaling networks in solid tissues remains challenging and precise quantification in large scale samples has great potential for biomarker identification and validation. We developed a reverse phase protein array (RPPA) based phosphor-antibody characterization approach by taking advantage of the lysis buffer compatible with alkaline phosphatase (AP) treatment that differs from the conventional RPPA antibody validation procedure and applied it onto fresh frozen (FF) and formalin-fixed and paraffin-embedded tissue (FFPE) to test its applicability. By screening 106 phospho-antibodies using RPPA, we demonstrated that AP treatment could serve as an independent factor to be adopted for rapid phospho-antibody selection. We also showed desirable reproducibility and specificity in clincical specimens indicating its potential for tissue-based phospho-protein profiling. Of further clinical significance, using the same approach, based on melanoma and lung cancer FFPE samples, we showed great interexperimental reproducibility and significant correlation with pathological markers in both tissues generating meaningful data that match clinical features. Our findings set a benchmark of an efficient workflow for phospho-antibody characterization that is compatible with high-plex clinical proteomics in precison oncology.
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Affiliation(s)
- Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies, Floor 22, Overseas Chinese Innovation Zone, Gangxing 3rd Rd, High-Tech and Innovation Zone, Jinan, 250100 China
| | - Li Zhang
- grid.412474.00000 0001 0027 0586Department of Pathology, Beijing Cancer Hospital, No 52. Fucheng Rd, Haidian District, Beijing, 100142 China
| | - Qi Ying
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies, Floor 22, Overseas Chinese Innovation Zone, Gangxing 3rd Rd, High-Tech and Innovation Zone, Jinan, 250100 China
| | - Zhentao Song
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies, Floor 22, Overseas Chinese Innovation Zone, Gangxing 3rd Rd, High-Tech and Innovation Zone, Jinan, 250100 China
| | - Aiping Lu
- grid.412474.00000 0001 0027 0586Department of Pathology, Beijing Cancer Hospital, No 52. Fucheng Rd, Haidian District, Beijing, 100142 China
| | - Achim Treumann
- grid.1006.70000 0001 0462 7212Newcastle University Protein and Proteome Analysis, Newcastle University, Devonshire Building, Newcastle upon Tyne, NE1 7RU UK ,KBI Biopharma BV, Leuven, Flanders Belgium
| | - Zhaojian Liu
- grid.27255.370000 0004 1761 1174Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Tao Sun
- grid.27255.370000 0004 1761 1174Department of Haematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies, Floor 22, Overseas Chinese Innovation Zone, Gangxing 3rd Rd, High-Tech and Innovation Zone, Jinan, 250100 China
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3
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A systematic and sensitive method for critical reagent antibody evaluation with PCA technology. Bioanalysis 2022; 14:1479-1486. [PMID: 36799240 DOI: 10.4155/bio-2022-0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Background: Quality control of critical reagents is essential in basic research and in drug discovery and development. Protein conformational array (PCA) is an ELISA-based technology that has been successfully used for the development of novel and biosimilar biologics with excellent sensitivity and accuracy. Methodology & results: PCA ELISA is able to monitor higher order structure changes of mouse and rabbit antibodies under various stress and storage conditions. This study focused on the short- and long-term storage of antibodies and antiserum as well as the effect of multiple freeze-thaw cycles on the impact of antibody higher order structure. Conclusion: These results suggest that PCA ELISA can be used as a valuable method for quality testing of antibodies.
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Waury K, Willemse EAJ, Vanmechelen E, Zetterberg H, Teunissen CE, Abeln S. Bioinformatics tools and data resources for assay development of fluid protein biomarkers. Biomark Res 2022; 10:83. [DOI: 10.1186/s40364-022-00425-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
AbstractFluid protein biomarkers are important tools in clinical research and health care to support diagnosis and to monitor patients. Especially within the field of dementia, novel biomarkers could address the current challenges of providing an early diagnosis and of selecting trial participants. While the great potential of fluid biomarkers is recognized, their implementation in routine clinical use has been slow. One major obstacle is the often unsuccessful translation of biomarker candidates from explorative high-throughput techniques to sensitive antibody-based immunoassays. In this review, we propose the incorporation of bioinformatics into the workflow of novel immunoassay development to overcome this bottleneck and thus facilitate the development of novel biomarkers towards clinical laboratory practice. Due to the rapid progress within the field of bioinformatics many freely available and easy-to-use tools and data resources exist which can aid the researcher at various stages. Current prediction methods and databases can support the selection of suitable biomarker candidates, as well as the choice of appropriate commercial affinity reagents. Additionally, we examine methods that can determine or predict the epitope - an antibody’s binding region on its antigen - and can help to make an informed choice on the immunogenic peptide used for novel antibody production. Selected use cases for biomarker candidates help illustrate the application and interpretation of the introduced tools.
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Chiriboga L, Callis GM, Wang Y, Chlipala E. Guide for collecting and reporting metadata on protocol variables and parameters from slide-based histotechnology assays to enhance reproducibility. J Histotechnol 2022; 45:132-147. [DOI: 10.1080/01478885.2022.2134022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Luis Chiriboga
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- NYULH Center for Biospecimen Research and Development, New York, NY, USA
| | | | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas, MO, USA
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Abstract
Western blotting (WB), also known as immunoblotting, is a well-known molecular biology method that biologists often use to investigate many features of the protein, ranging from basic protein analysis to disease detection. WB is simple, unique, rapid, widely used routine tool with easy interpretation and definite results. It is being used in various fields of science, research and development, diagnostic labs and hospitals. The principle of WB is to accomplish the separation of proteins based on molecular weight and charge. This review addresses in detail the individual steps involved in the WB technique, its troubleshooting, internal loading controls, total protein staining and its diverse applications in scientific research and clinical settings, along with its future perspectives.
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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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MALDI-TOF-MS-Based Identification of Monoclonal Murine Anti-SARS-CoV-2 Antibodies within One Hour. Antibodies (Basel) 2022; 11:antib11020027. [PMID: 35466280 PMCID: PMC9036215 DOI: 10.3390/antib11020027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023] Open
Abstract
During the SARS-CoV-2 pandemic, many virus-binding monoclonal antibodies have been developed for clinical and diagnostic purposes. This underlines the importance of antibodies as universal bioanalytical reagents. However, little attention is given to the reproducibility crisis that scientific studies are still facing to date. In a recent study, not even half of all research antibodies mentioned in publications could be identified at all. This should spark more efforts in the search for practical solutions for the traceability of antibodies. For this purpose, we used 35 monoclonal antibodies against SARS-CoV-2 to demonstrate how sequence-independent antibody identification can be achieved by simple means applied to the protein. First, we examined the intact and light chain masses of the antibodies relative to the reference material NIST-mAb 8671. Already half of the antibodies could be identified based solely on these two parameters. In addition, we developed two complementary peptide mass fingerprinting methods with MALDI-TOF-MS that can be performed in 60 min and had a combined sequence coverage of over 80%. One method is based on the partial acidic hydrolysis of the protein by 5 mM of sulfuric acid at 99 °C. Furthermore, we established a fast way for a tryptic digest without an alkylation step. We were able to show that the distinction of clones is possible simply by a brief visual comparison of the mass spectra. In this work, two clones originating from the same immunization gave the same fingerprints. Later, a hybridoma sequencing confirmed the sequence identity of these sister clones. In order to automate the spectral comparison for larger libraries of antibodies, we developed the online software ABID 2.0. This open-source software determines the number of matching peptides in the fingerprint spectra. We propose that publications and other documents critically relying on monoclonal antibodies with unknown amino acid sequences should include at least one antibody fingerprint. By fingerprinting an antibody in question, its identity can be confirmed by comparison with a library spectrum at any time and context.
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9
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Collection of Monoclonal Antibodies Targeting SARS-CoV-2 Proteins. Viruses 2022; 14:v14020443. [PMID: 35216036 PMCID: PMC8875891 DOI: 10.3390/v14020443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/03/2022] [Accepted: 02/19/2022] [Indexed: 12/25/2022] Open
Abstract
In early 2020, the COVID-19 pandemic sparked a global crisis that continues to pose a serious threat to human health and the economy. Further advancement in research is necessary and requires the availability of quality molecular tools, including monoclonal antibodies. Here, we present the development and characterization of a collection of over 40 new monoclonal antibodies directed against different SARS-CoV-2 proteins. Recombinant SARS-CoV-2 proteins were expressed, purified, and used as immunogens. Upon development of specific hybridomas, the obtained monoclonal antibody (mAb) clones were tested for binding to recombinant proteins and infected cells. We generated mAbs against structural proteins, the Spike and Nucleocapsid protein, several non-structural proteins (nsp1, nsp7, nsp8, nsp9, nsp10, nsp16) and accessory factors (ORF3a, ORF9b) applicable in flow cytometry, immunofluorescence, or Western blot. Our collection of mAbs provides a set of novel, highly specific tools that will allow a comprehensive analysis of the viral proteome, which will allow further understanding of SARS-CoV-2 pathogenesis and the design of therapeutic strategies.
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10
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Rak M, Reiss K. Double Labeling Fluorescent Immunocytochemistry. Methods Mol Biol 2022; 2422:147-161. [PMID: 34859404 DOI: 10.1007/978-1-0716-1948-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fluorescent immunocytochemistry is a powerful technique based on detecting antigens. It leads to discoveries in cell composition and structure as well as its functioning by expanding knowledge on colocalization between its components. The potency of this method is based on findings in the areas of specific antibodies production, fluorescent labels, and microscopy. Since it merges different fields, it requires basic knowledge on all the steps that are needed in the procedure planning and implementation to be used properly and produce reliable results. Here we describe a protocol of LN-229 human glioblastoma cells double labeling of LC3 and IRS-1 proteins, highlighting the importance of some steps of the procedure and possible variables.
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Affiliation(s)
- Monika Rak
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Kraków, Poland.
- Departments of Medicine & Neurological Cancer Research, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA.
| | - Krzysztof Reiss
- Departments of Medicine & Neurological Cancer Research, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
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Stähler T, Danquah W, Demeules M, Gondé H, Hardet R, Haag F, Adriouch S, Koch-Nolte F, Menzel S. Development of Antibody and Nanobody Tools for P2X7. Methods Mol Biol 2022; 2510:99-127. [PMID: 35776322 DOI: 10.1007/978-1-0716-2384-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antibodies that recognize the ATP-gated P2X7 ion channel are etablished research tools. Nanobodies correspond to the antigen-binding variable immunoglobulin domain (VHH) of heavy chain antibodies that naturally occur in camelids. Nanobodies display better solubility than the variable domains (VH) of conventional antibodies. Therefore, it is much easier to construct bivalent and multivalent fusion proteins with nanobodies than with VH domains or with paired VH-VL domains. Moreover, nanobodies can bind functional crevices that are poorly accessbile to conventional VH-VL domains. This makes nanobodies particulary well suited as functional modulators. Here we provide protocols to raise antibodies and nanobodies against mouse and human P2X7 using cDNA-immunization. This approach evokes antibodies and nanobodies that recognize the P2X7 ion channel in native confirmation, some of which inhibit or potentiate gating of P2X7 by extracellular ATP. Furthermore, we developed protocols for producing P2X7-specific nanobodies and antibodies in vivo using rAAV vectors (AAVnano). This approach can be used either to durably inhibit or potentiate P2X7 function in vivo, or to deplete P2X7-expressing cells.
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Affiliation(s)
- Tobias Stähler
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Welbeck Danquah
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Melanie Demeules
- UNIROUEN, INSERM, U1234, Pathophysiology, Autoimmunity, aNd immunoTHERapies (PANTHER), Normandie University, 76000 Rouen, France
| | - Henri Gondé
- UNIROUEN, INSERM, U1234, Pathophysiology, Autoimmunity, aNd immunoTHERapies (PANTHER), Normandie University, 76000 Rouen, France
| | - Romain Hardet
- UNIROUEN, INSERM, U1234, Pathophysiology, Autoimmunity, aNd immunoTHERapies (PANTHER), Normandie University, 76000 Rouen, France
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sahil Adriouch
- UNIROUEN, INSERM, U1234, Pathophysiology, Autoimmunity, aNd immunoTHERapies (PANTHER), Normandie University, 76000 Rouen, France
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Stephan Menzel
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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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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13
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Regan B, O'Kennedy R, Collins D. Advances in point-of-care testing for cardiovascular diseases. Adv Clin Chem 2021; 104:1-70. [PMID: 34462053 DOI: 10.1016/bs.acc.2020.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Point-of-care testing (POCT) is a specific format of diagnostic testing that is conducted without accompanying infrastructure or sophisticated instrumentation. Traditionally, such rapid sample-to-answer assays provide inferior analytical performances to their laboratory counterparts when measuring cardiac biomarkers. Hence, their potentially broad applicability is somewhat bound by their inability to detect clinically relevant concentrations of cardiac troponin (cTn) in the early stages of myocardial injury. However, the continuous refinement of biorecognition elements, the optimization of detection techniques, and the fabrication of tailored fluid handling systems to manage the sensing process has stimulated the production of commercial assays that can support accelerated diagnostic pathways. This review will present the latest commercial POC assays and examine their impact on clinical decision-making. The individual elements that constitute POC assays will be explored, with an emphasis on aspects that contribute to economically feasible and highly sensitive assays. Furthermore, the prospect of POCT imparting a greater influence on early interventions for medium to high-risk individuals and the potential to re-shape the paradigm of cardiovascular risk assessments will be discussed.
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Affiliation(s)
- Brian Regan
- School of Biotechnology, Dublin City University, Dublin, Ireland.
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland; Research Complex, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - David Collins
- School of Biotechnology, Dublin City University, Dublin, Ireland
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14
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Avidin-Biotin ELISA-Based Detection of 5hmC. Methods Mol Biol 2021. [PMID: 34009609 DOI: 10.1007/978-1-0716-1294-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The enzyme-linked immunosorbent assay (ELISA) technique has been developed half a century ago, and yet its role in molecular biology remains significant. Among the most sensitive of immunoassays, it offers high throughput, combined with affordability and ease of use. This chapter provides the procedure of a highly reproducible indirect sandwich ELISA protocol, which can be applied to a variety of semi-quantitative assays for the investigation of the molecular biology of 5-hydroxymethylcytosine (5hmC) or TET enzymes. Three variations of this protocol are described: assessment and validation of 5hmC-binding proteins, screening and validation of anti-5hmC antibodies, or a readout of TET catalytic activity in in vitro experiments. The assay principle is based on the use of a high affinity avidin-biotin system for efficient immobilization of DNA fragments for further detection by high specificity antibodies. A colorimetric enzymatic reaction is ultimately developed with intensity correlating with the amount of attached antigen.
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15
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Rodent Models of Congenital Cytomegalovirus Infection. Methods Mol Biol 2021. [PMID: 33555596 DOI: 10.1007/978-1-0716-1111-1_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Human cytomegalovirus (HCMV) is a leading viral cause of congenital infections in the central nervous system (CNS) and may result in severe long-term sequelae. High rates of sequelae following congenital HCMV infection and insufficient antiviral therapy in the perinatal period makes the development of an HCMV-specific vaccine a high priority of modern medicine. Due to the species specificity of HCMV, animal models are frequently used to study CMV pathogenesis. Studies of murine cytomegalovirus (MCMV) infections of adult mice have played a significant role as a model of CMV biology and pathogenesis, while MCMV infection of newborn mice has been successfully used as a model of perinatal CMV infection. Newborn mice infected with MCMV have high levels of viremia during which the virus establishes a productive infection in most organs, coupled with a robust inflammatory response. Productive infection in the brain parenchyma during early postnatal period leads to an extensive nonnecrotizing multifocal widespread encephalitis characterized by infiltration of components of both innate and adaptive immunity. As a result, impairment in postnatal development of mouse cerebellum leads to long-term motor and sensor disabilities. This chapter summarizes current findings of rodent models of perinatal CMV infection and describes methods for analysis of perinatal MCMV infection in newborn mice.
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16
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Frohner IE, Mudrak I, Schüchner S, Anrather D, Hartl M, Sontag JM, Sontag E, Wadzinski BE, Preglej T, Ellmeier W, Ogris E. PP2A C Phospho-Tyr 307 Antibodies Are Not Specific for this Modification but Are Sensitive to Other PP2A C Modifications Including Leu 309 Methylation. Cell Rep 2021; 30:3171-3182.e6. [PMID: 32130916 DOI: 10.1016/j.celrep.2020.02.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/03/2019] [Accepted: 02/07/2020] [Indexed: 02/06/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is an important regulator of signal transduction pathways and a tumor suppressor. Phosphorylation of the PP2A catalytic subunit (PP2AC) at tyrosine 307 has been claimed to inactivate PP2A and was examined in more than 180 studies using commercial antibodies, but this modification was never identified using mass spectrometry. Here we show that the most cited pTyr307 monoclonal antibodies, E155 and F-8, are not specific for phosphorylated Tyr307 but instead are hampered by PP2AC methylation at leucine 309 or phosphorylation at threonine 304. Other pTyr307 antibodies are sensitive to PP2AC methylation as well, and some cross-react with pTyr residues in general, including phosphorylated hemagglutinin tags. We identify pTyr307 using targeted mass spectrometry after transient overexpression of PP2AC and Src kinase. Yet under such conditions, none of the tested antibodies show exclusive pTyr307 specificity. Thus, data generated using these antibodies need to be revisited, and the mechanism of PP2A inactivation needs to be redefined.
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Affiliation(s)
- Ingrid E Frohner
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Ingrid Mudrak
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Stefan Schüchner
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Dorothea Anrather
- Mass Spectrometry Facility, Max Perutz Labs, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max Perutz Labs, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Jean-Marie Sontag
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Estelle Sontag
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Brian E Wadzinski
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Teresa Preglej
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Wilfried Ellmeier
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Egon Ogris
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
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17
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Hernández R, Rodríguez FM, Gareis NC, Rey F, Barbeito CG, Diessler ME. Abundance of insulin-like growth factors 1 and 2, and type 1 insulin-like growth factor receptor in placentas of dogs. Anim Reprod Sci 2020; 221:106554. [PMID: 32861116 DOI: 10.1016/j.anireprosci.2020.106554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 10/23/2022]
Abstract
Insulin-like growth factors (IGFs) are among the primary compounds regulating placental development. In bitches, relative abundance of IGF1, IGF2 and IGFR1 mRNA transcripts have been studied in the pre-implantation uterus and early endotheliochorial placentas. The IGF2 and IGFR1 distribution has also been previously described in the uterus before embryo implantation. The aim of this study was to detect, characterize, and localize the presence of IGF1, IGF2, and IGFR1 in early-developing and mature placentas of dogs. Placentas of 15 bitches were analyzed using immunohistochemistry. The IGFs were located in endometrial epithelium and glands, with the staining pattern and intensity being less in mature placentas. Cytotrophoblast cells (CTB) and syncytiotrophoblast (STB) cells contained both IGFs; the labeling was greater in CTB of the early-developing than mature placentas. The maternal endothelium was positively stained for both IGFs, while the vascular endothelium of the chorioallantoic membrane were only stained for IGF2. The IGFR1 was detected in all cell populations evaluated. Results regarding trophoblastic IGF are quite consistent with those reported in human placentas. Spatiotemporal IGFs/IGFR1 pattern might reflect the occurrence of autocrine and paracrine signaling during placentation in bitches, and the involvement in early placental developmental processes. Furthermore, it is hypothesized that, besides hemotrophic actions of plasma IGFs, endometrial secreted IGFs may promote early placental development through histotrophic signaling.
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Affiliation(s)
- Rocío Hernández
- Laboratorio de Histología y Embriología Descriptiva, Experimental y Comparada (LHYEDEC), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata (FCV, UNLP), Avda. 60 y 118, 1900, La Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), FCV, UNLP, La Plata, Argentina.
| | - Fernanda M Rodríguez
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) / Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina; Facultad de Ciencias Veterinarias del Litoral, Universidad Nacional del Litoral (UNL), Esperanza, Santa Fe, Argentina.
| | - Natalia C Gareis
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) / Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina; Facultad de Ciencias Veterinarias del Litoral, Universidad Nacional del Litoral (UNL), Esperanza, Santa Fe, Argentina.
| | - Florencia Rey
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) / Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina; Facultad de Ciencias Veterinarias del Litoral, Universidad Nacional del Litoral (UNL), Esperanza, Santa Fe, Argentina.
| | - Claudio G Barbeito
- Laboratorio de Histología y Embriología Descriptiva, Experimental y Comparada (LHYEDEC), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata (FCV, UNLP), Avda. 60 y 118, 1900, La Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), FCV, UNLP, La Plata, Argentina.
| | - Mónica E Diessler
- Laboratorio de Histología y Embriología Descriptiva, Experimental y Comparada (LHYEDEC), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata (FCV, UNLP), Avda. 60 y 118, 1900, La Plata, Argentina.
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18
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Schwarz N, Junge M, Haag F, Koch-Nolte F. Flow Cytometry of Membrane Purinoreceptors. Methods Mol Biol 2020; 2041:117-136. [PMID: 31646484 DOI: 10.1007/978-1-4939-9717-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mammalian purinoreceptors respond to extracellular nucleotides and their metabolites, for example, following the release of ATP or NAD+ from cells and their hydrolysis by ectonucleotidases. Membrane purinoreceptors are expressed as ionotropic ligand-gated ion channels designated P2X receptors, or as metabotropic G-protein coupled receptors designated P1 or P2Y receptors, on the cell surface of different cell types. In this chapter, we provide protocols to monitor the expression and activity of purinoreceptors on the cell membrane of living cells by flow cytometry.
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Affiliation(s)
- Nicole Schwarz
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marten Junge
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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19
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Metabolic reprogramming and disease progression in cancer patients. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165721. [PMID: 32057942 DOI: 10.1016/j.bbadis.2020.165721] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/22/2020] [Accepted: 02/09/2020] [Indexed: 12/19/2022]
Abstract
Genomics has contributed to the treatment of a fraction of cancer patients. However, there is a need to profile the proteins that define the phenotype of cancer and its pathogenesis. The reprogramming of metabolism is a major trait of the cancer phenotype with great potential for prognosis and targeted therapy. This review overviews the major changes reported in the steady-state levels of proteins of metabolism in primary carcinomas, paying attention to those enzymes that correlate with patients' survival. The upregulation of enzymes of glycolysis, pentose phosphate pathway, lipogenesis, glutaminolysis and the antioxidant defense is concurrent with the downregulation of mitochondrial proteins involved in oxidative phosphorylation, emphasizing the potential of mitochondrial metabolism as a promising therapeutic target in cancer. We stress that high-throughput quantitative expression profiling of differentially expressed proteins in large cohorts of carcinomas paired with normal tissues will accelerate translation of metabolism to a successful personalized medicine in cancer.
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20
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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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21
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Voskuil JL, Bandrowski A, Begley CG, Bradbury AR, Chalmers AD, Gomes AV, Hardcastle T, Lund-Johansen F, Plückthun A, Roncador G, Solache A, Taussig MJ, Trimmer JS, Williams C, Goodman SL. The Antibody Society's antibody validation webinar series. MAbs 2020; 12:1794421. [PMID: 32748696 PMCID: PMC7531563 DOI: 10.1080/19420862.2020.1794421] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 01/09/2023] Open
Abstract
In the wake of the reproducibility crisis and numerous discussions on how commercially available antibodies as research tool contribute to it, The Antibody Society developed a series of 10 webinars to address the issues involved. The webinars were delivered by speakers with both academic and commercial backgrounds. This report highlights the problems, and offers solutions to help the scientific community appropriately identify the right antibodies and to validate them for their research and development projects. Despite the various solutions proposed here, they must be applied on a case-by-case basis. Each antibody must be verified based on the content of the product sheet, and subsequently through experimentation to confirm integrity, specificity and selectivity. Verification needs to focus on the precise application and tissue/cell type for which the antibody will be used, and all verification data must be reported openly. The various approaches discussed here all have caveats, so a combination of solutions must be considered.
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Affiliation(s)
| | - Anita Bandrowski
- Center for Research in Biological Systems, University of California, La Jolla, CA, USA
| | | | | | - Andrew D. Chalmers
- Department of Biology and Biochemistry, University of Bath, Bath, UK
- CiteAb, Bath, UK
| | - Aldrin V. Gomes
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, CA, USA
| | | | | | - Andreas Plückthun
- Department. of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Giovanna Roncador
- Monoclonal Antibody Unit, Spanish National Cancer Research Center, Madrid, Spain
| | - Alejandra Solache
- Abcam Plc, Discovery Drive, Cambridge Biomedical Campus, Cambridge, UK
| | | | - James S. Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA, USA
| | - Cecilia Williams
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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22
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Carter RJ, Milani M, Butterworth M, Alotibi A, Harper N, Yedida G, Greaves G, Al-Zebeeby A, Jorgensen AL, Schache AG, Risk JM, Shaw RJ, Jones TM, Sacco JJ, Hurlstone A, Cohen GM, Varadarajan S. Exploring the potential of BH3 mimetic therapy in squamous cell carcinoma of the head and neck. Cell Death Dis 2019; 10:912. [PMID: 31801952 PMCID: PMC6892862 DOI: 10.1038/s41419-019-2150-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Accepted: 10/31/2019] [Indexed: 01/14/2023]
Abstract
Squamous cell carcinoma of the head and neck (SCCHN) is the sixth most common cancer worldwide, with overall survival of less than 50%. Current therapeutic strategies involving a combination of surgery, radiation, and/or chemotherapy are associated with debilitating side effects, highlighting the need for more specific and efficacious therapies. Inhibitors of BCL-2 family proteins (BH3 mimetics) are under investigation or in clinical practice for several hematological malignancies and show promise in solid tumors. In order to explore the therapeutic potential of BH3 mimetics in the treatment of SCCHN, we assessed the expression levels of BCL-2, BCL-XL, and MCL-1 via Western blots and immunohistochemistry, in cell lines, primary cells derived from SCCHN patients and in tissue microarrays containing tumor tissue from a cohort of 191 SCCHN patients. All preclinical models exhibited moderate to high levels of BCL-XL and MCL-1, with little or no BCL-2. Although expression levels of BCL-XL and MCL-1 did not correlate with patient outcome, a combination of BH3 mimetics to target these proteins resulted in decreased clonogenic potential and enhanced apoptosis in all preclinical models, including tumor tissue resected from patients, as well as a reduction of tumor volume in a zebrafish xenograft model of SCCHN. Our results show that SCCHN is dependent on both BCL-XL and MCL-1 for apoptosis evasion and combination therapy targeting both proteins may offer significant therapeutic benefits in this disease.
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Affiliation(s)
- Rachel J Carter
- Liverpool Head and Neck Centre, Liverpool, L69 3GE, UK.,Department of Molecular and Clinical Cancer Medicine, Liverpool, L69 3GE, UK
| | - Mateus Milani
- Department of Molecular and Clinical Cancer Medicine, Liverpool, L69 3GE, UK
| | - Michael Butterworth
- Department of Molecular and Clinical Cancer Medicine, Liverpool, L69 3GE, UK
| | - Ahoud Alotibi
- Department of Molecular and Clinical Cancer Medicine, Liverpool, L69 3GE, UK
| | - Nicholas Harper
- Department of Molecular and Clinical Pharmacology, Liverpool, L69 3GE, UK
| | - Govindaraju Yedida
- Department of Molecular and Clinical Cancer Medicine, Liverpool, L69 3GE, UK
| | - Georgia Greaves
- Department of Molecular and Clinical Cancer Medicine, Liverpool, L69 3GE, UK
| | - Aoula Al-Zebeeby
- Department of Molecular and Clinical Cancer Medicine, Liverpool, L69 3GE, UK
| | - Andrea L Jorgensen
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GE, UK
| | | | - Janet M Risk
- Liverpool Head and Neck Centre, Liverpool, L69 3GE, UK
| | | | - Terry M Jones
- Liverpool Head and Neck Centre, Liverpool, L69 3GE, UK
| | | | - Adam Hurlstone
- Faculty of Biology, Medicine and Health, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, M13 9PT, UK
| | - Gerald M Cohen
- Liverpool Head and Neck Centre, Liverpool, L69 3GE, UK.,Department of Molecular and Clinical Cancer Medicine, Liverpool, L69 3GE, UK.,Department of Molecular and Clinical Pharmacology, Liverpool, L69 3GE, UK
| | - Shankar Varadarajan
- Liverpool Head and Neck Centre, Liverpool, L69 3GE, UK. .,Department of Molecular and Clinical Cancer Medicine, Liverpool, L69 3GE, UK. .,Department of Molecular and Clinical Pharmacology, Liverpool, L69 3GE, UK.
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23
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Bergmann P, Garcia de Paco E, Rissiek B, Menzel S, Dubberke G, Hua J, Rassendren F, Ulmann L, Koch-Nolte F. Generation and Characterization of Specific Monoclonal Antibodies and Nanobodies Directed Against the ATP-Gated Channel P2X4. Front Cell Neurosci 2019; 13:498. [PMID: 31798414 PMCID: PMC6861843 DOI: 10.3389/fncel.2019.00498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/21/2019] [Indexed: 12/19/2022] Open
Abstract
The P2X4 channel is involved in different physiological and pathological conditions and functions in the nervous system. Despite the existence of several mouse models for which the expression of the gene was manipulated, there is still little information on the expression of the protein at the cellular level. In particular, supposedly specific available antibodies have often proved to recognize unrelated proteins in P2X4-deficient mice. Here, we used an in vivo DNA vaccine approach to generate a series of monoclonal antibodies and nanobodies specific for human, mouse, and rat P2X4 channels. We further characterized these antibodies and show that they solely recognize the native form of the proteins both in biochemical and cytometric applications. Some of these antibodies prove to specifically recognize P2X4 channels by immunostaining in brain or sensory ganglia slices, as well as at the cellular and subcellular levels. Due to their clonality, these different antibodies should represent versatile tools for further characterizing the cellular functions of P2X4 in the nervous system as well as at the periphery.
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Affiliation(s)
- Philine Bergmann
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elvira Garcia de Paco
- Institut de Génomique Fonctionnelle (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France.,Laboratoire d'Excellence Canaux Ioniques d'Intérêt Thérapeutique (LabEx ICST), Montpellier, France
| | - Björn Rissiek
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Menzel
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gudrun Dubberke
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jennifer Hua
- Institut de Génomique Fonctionnelle (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France.,Laboratoire d'Excellence Canaux Ioniques d'Intérêt Thérapeutique (LabEx ICST), Montpellier, France
| | - François Rassendren
- Institut de Génomique Fonctionnelle (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France.,Laboratoire d'Excellence Canaux Ioniques d'Intérêt Thérapeutique (LabEx ICST), Montpellier, France
| | - Lauriane Ulmann
- Institut de Génomique Fonctionnelle (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France.,Laboratoire d'Excellence Canaux Ioniques d'Intérêt Thérapeutique (LabEx ICST), Montpellier, France
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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24
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Kalina T, Lundsten K, Engel P. Relevance of Antibody Validation for Flow Cytometry. Cytometry A 2019; 97:126-136. [DOI: 10.1002/cyto.a.23895] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/10/2019] [Accepted: 08/22/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Tomas Kalina
- CLIP‐Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Medical SchoolCharles University and University Hospital Motol Prague Czech Republic
| | | | - Pablo Engel
- Department of Biomedical SciencesFaculty of Medicine and Health Sciences, University of Barcelona Barcelona Spain
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25
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Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Nat Protoc 2019; 14:2900-2930. [PMID: 31534232 DOI: 10.1038/s41596-019-0206-y] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/03/2019] [Indexed: 12/27/2022]
Abstract
Multiplexed tissue imaging enables precise, spatially resolved enumeration and characterization of cell types and states in human resection specimens. A growing number of methods applicable to formalin-fixed, paraffin-embedded (FFPE) tissue sections have been described, the majority of which rely on antibodies for antigen detection and mapping. This protocol provides step-by-step procedures for confirming the selectivity and specificity of antibodies used in fluorescence-based tissue imaging and for the construction and validation of antibody panels. Although the protocol is implemented using tissue-based cyclic immunofluorescence (t-CyCIF) as an imaging platform, these antibody-testing methods are broadly applicable. We demonstrate assembly of a 16-antibody panel for enumerating and localizing T cells and B cells, macrophages, and cells expressing immune checkpoint regulators. The protocol is accessible to individuals with experience in microscopy and immunofluorescence; some experience in computation is required for data analysis. A typical 30-antibody dataset for 20 FFPE slides can be generated within 2 weeks.
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26
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Abstract
The International Antibody Validation meetings offer a welcome British forum for discussing this important topic, which is existentially crucial for the biological sciences community. Now in its 6th year, the biennial meeting is organized by Andrew Chalmers (University of Bath; CiteAb), this year with Carly Dix (Astra Zeneca). The organizers gathered some 100 members of industry and academia, producers and users, for a day and a half to describe their efforts to ensure that their antibodies have the desired specificity and selectively for well-defined molecular targets. The meeting is largely available as WebCasts (
http://www.antibodyvalidation.co.uk/past-events/2018).
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27
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Fricker SP, Sprott K, Spyra M, Uhlig P, Lange N, David K, Wang Y. Characterization and Validation of Antibodies for Immunohistochemical Staining of the Chemokine CXCL12. J Histochem Cytochem 2018; 67:257-266. [PMID: 30562126 DOI: 10.1369/0022155418818788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Chemokines and their receptors have been implicated in cancer biology. The CXCL12/CXCR4 axis is essential for the homing and retention of hematopoietic stem cells in bone marrow niches, and has a significant role in neonatal development. It is also implicated in multiple facets of cancer biology including metastasis, angiogenesis/neo-vasculogenesis, and immune cell trafficking at the tumor microenvironment (TME). Immunohistochemistry (IHC) is an ideal method for investigating involvement of CXCL12 in the TME. Three antibodies were evaluated here for their suitability to stain CXCL12. Both D8G6H and K15C gave apparent specific staining in both lymphoid and tumor tissue, but with converse staining patterns. D8G6H stained cells in the parafollicular zone whereas K15C showed staining of lymphoid cells in the interfollicular zone of tonsil tissue. Using a cell line with high CXCL12 expression, TOV21G, as a positive control, it was found that D8G6H gave strong staining of TOV21G cells whereas no staining was observed with K15C indicating that D8G6H specifically stains CXCL12. Significant staining of CXCL12 in the ovarian TME using tissue microarray was observed using D8G6H. These data demonstrate the importance of antibody characterization for IHC applications, and provide further evidence for the involvement of CXCL12 in ovarian cancer biology.
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Affiliation(s)
| | - Kam Sprott
- X4 Pharmaceuticals, Cambridge, Massachusetts
| | | | | | | | | | - Yan Wang
- X4 Pharmaceuticals, Cambridge, Massachusetts
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28
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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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29
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Abstract
Many results reported in the biomedical research literature cannot be independently reproduced, undermining the basic foundations of science. This overview is intended for researchers who are committed to improving the quality and integrity of biomedical science by raising awareness of both the sources of irreproducibility, and activities specifically targeted to address the issue. The irreproducibility of biomedical research is due to a variety of factors, known and unknown, that markedly influence experimental outcomes. Among the known factors are inadequate training or mentoring, or experimenter incompetence. These may result in flawed experimental design and execution that reflect a lack of planning, leading to an underpowering of a study, an absence of appropriate controls, selective data analysis, inappropriate statistical analysis, and/or investigator bias or fraud. Another frequently overlooked source of irreproducibility is failure to ensure that the equipment used is performing up to manufacturer specifications. Failure to validate/authenticate the experimental reagents is another source of irreproducibility. These include compounds, cell lines, antibodies, and the animal models used in a study. This overview discusses how a lack of validation of research reagents negatively impact experimental reproducibility, and provides guidelines to avoid these pitfalls. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Michael Williams
- Department of Biological Chemistry and Pharmacology, College of Medicine, Ohio State University, Columbus, Ohio
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30
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Goodman SL. The path to VICTORy - a beginner's guide to success using commercial research antibodies. J Cell Sci 2018; 131:131/10/jcs216416. [PMID: 29764917 DOI: 10.1242/jcs.216416] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Commercial research antibodies are crucial tools in modern cell biology and biochemistry. In the USA some $2 billion a year are spent on them, but many are apparently not fit-for-purpose, and this may contribute to the 'reproducibility crisis' in biological sciences. Inadequate antibody validation and characterization, lack of user awareness, and occasional incompetence amongst suppliers have had immense scientific and personal costs. In this Opinion, I suggest some paths to make the use of these vital tools more successful. I have attempted to summarize and extend expert views from the literature to suggest that sustained routine efforts should made in: (1) the validation of antibodies, (2) their identification, (3) communication and controls, (4) the training of potential users, (5) the transparency of original equipment manufacturer (OEM) marketing agreements, and (5) in a more widespread use of recombinant antibodies (together denoted the 'VICTOR' approach).
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31
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Antibodies and methods for immunohistochemistry of extracellular matrix proteins. Matrix Biol 2018; 71-72:10-27. [PMID: 29730502 DOI: 10.1016/j.matbio.2018.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 01/12/2023]
Abstract
The diversity of extracellular matrix (ECM) proteins encoded in mammalian genomes and detected by proteomic analyses generates a need for well validated antibodies against these proteins. We present characterization of a large number of antibodies against ECM proteins, from both commercial and academic sources, together with discussion of methods and strategies for their effective use in immunohistochemistry and illustrations of their efficacy. These data should be of value to investigators seeking well validated antibodies to ECM proteins of interest and save significant time and money tracking down effective reagents.
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32
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Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron Kain D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Khambadkone SG, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Montelione GT, Anderson S, Myers RM, Boeke JD, Fenyö D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, Blackshaw S. A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Nat Methods 2018; 15:330-338. [PMID: 29638227 PMCID: PMC6063793 DOI: 10.1038/nmeth.4632] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 01/25/2018] [Indexed: 01/08/2023]
Abstract
A key component of efforts to address the reproducibility crisis in biomedical research is the development of rigorously validated and renewable protein-affinity reagents. As part of the US National Institutes of Health (NIH) Protein Capture Reagents Program (PCRP), we have generated a collection of 1,406 highly validated immunoprecipitation- and/or immunoblotting-grade mouse monoclonal antibodies (mAbs) to 737 human transcription factors, using an integrated production and validation pipeline. We used HuProt human protein microarrays as a primary validation tool to identify mAbs with high specificity for their cognate targets. We further validated PCRP mAbs by means of multiple experimental applications, including immunoprecipitation, immunoblotting, chromatin immunoprecipitation followed by sequencing (ChIP-seq), and immunohistochemistry. We also conducted a meta-analysis that identified critical variables that contribute to the generation of high-quality mAbs. All validation data, protocols, and links to PCRP mAb suppliers are available at http://proteincapture.org.
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Affiliation(s)
- Anand Venkataraman
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kun Yang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Paolo Mita
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zheng Kuang
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Lin Xue
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Devlina Ghosh
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shuang Liu
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | - Sarah Keegan
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Richard Saul
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Simona Colantonio
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Hongyan Zhang
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Guang Song
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jessica McDade
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brian S Clark
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sooyeon Yoo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Seva G Khambadkone
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jimmy de Melo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Milanka Stevanovic
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lizhi Jiang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yana Li
- Eukaryotic Tissue Culture Facility, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Atul Tandon
- NeoBiotechnologies, Inc., Union City, California, USA
| | - Elliot Campbell
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Stephen Anderson
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Jef D Boeke
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David Fenyö
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Gordon Whiteley
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Heng Zhu
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Weller MG. Ten Basic Rules of Antibody Validation. ANALYTICAL CHEMISTRY INSIGHTS 2018; 13:1177390118757462. [PMID: 29467569 PMCID: PMC5813849 DOI: 10.1177/1177390118757462] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/07/2018] [Indexed: 12/24/2022]
Abstract
The quality of research antibodies is an issue for decades. Although several papers have been published to improve the situation, their impact seems to be limited. This publication makes the effort to simplify the description of validation criteria in a way that the occasional antibody user is able to assess the validation level of an immunochemical reagent. A simple, 1-page checklist is supplied for the practical application of these criteria.
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Affiliation(s)
- Michael G Weller
- Division 1.5 Protein Analysis, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
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34
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The antibody horror show: an introductory guide for the perplexed. N Biotechnol 2018; 45:9-13. [PMID: 29355666 DOI: 10.1016/j.nbt.2018.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/03/2018] [Accepted: 01/16/2018] [Indexed: 01/21/2023]
Abstract
The biological literature reverberates with the inadequacies of commercial research-tool antibodies. The scientific community spends some $2 billion per year on such reagents. Excellent accessible scientific platforms exist for reliably making, validating and using antibodies, yet the laboratory end-user reality is somehow depressing - because they often "don't work". This experience is due to a bizarre and variegated spectrum of causes including: inadequately identified antibodies; inappropriate user and supplier validation; poor user training; and overloaded publishers. Colourful as this may appear, the outcomes for the community are uniformly grim, including badly damaged scientific careers, wasted public funding, and contaminated literature. As antibodies are amongst the most important of everyday reagents in cell biology and biochemistry, I have tried here to gently suggest a few possible solutions, including: a move towards using recombinant antibodies; obligatory unique identification of antibodies, their immunogens, and their producers; centralized international banking of standard antibodies and their ligands; routine, accessible open-source documentation of user experience with antibodies; and antibody-user certification.
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35
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Challenges in Developing a Biochip for Intact Histamine Using Commercial Antibodies. CHEMOSENSORS 2017. [DOI: 10.3390/chemosensors5040033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This study describes the development and the challenges in the development of an on-chip immunoassay for histamine using commercially available antibodies. Histamine can be used as an indicator of food freshness and quality, but it is also a relevant marker in clinical diagnostics. Due to its low molecular weight, simple structure and thus low immunogenicity production of high specificity and affinity antibodies is difficult. From six commercial anti-histamine antibodies tested, only two bound the histamine free in the solution. A fluorescent on-chip immunoassay for histamine was established with a dynamic range of 8–111 µg/mL using polyclonal anti-histamine antibody H7403 from Sigma (Mendota Heights, MN, USA). The anti-histamine antibodies described and used in published literature are thoroughly reviewed and the quality of commercial antibodies and their traceability and quality issues are highlighted and extensively discussed.
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36
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Blagg J, Workman P. Choose and Use Your Chemical Probe Wisely to Explore Cancer Biology. Cancer Cell 2017; 32:9-25. [PMID: 28697345 PMCID: PMC5511331 DOI: 10.1016/j.ccell.2017.06.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/31/2017] [Accepted: 06/09/2017] [Indexed: 01/15/2023]
Abstract
Small-molecule chemical probes or tools have become progressively more important in recent years as valuable reagents to investigate fundamental biological mechanisms and processes causing disease, including cancer. Chemical probes have also achieved greater prominence alongside complementary biological reagents for target validation in drug discovery. However, there is evidence of widespread continuing misuse and promulgation of poor-quality and insufficiently selective chemical probes, perpetuating a worrisome and misleading pollution of the scientific literature. We discuss current challenges with the selection and use of chemical probes, and suggest how biologists can and should be more discriminating in the probes they employ.
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Affiliation(s)
- Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK.
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK.
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37
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Abstract
This article further discusses the reproducibility crisis in biomedical science and how poor conduct of commercial antibodies contribute to this. In addition, the way quality data are presented on product sheets by antibody vendors is scrutinized. The article proposes that there is a distinction between testing data and validation data, and special attention is asked for consistency between batches and aliquots. Moreover, the article separates the specifics, such as formulation, antigen and price, from the specifics on performance. Finally, a two-tier approach is discussed, enabling scientists to anticipate how an antibody is likely to perform when repeated purchases are required.
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38
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Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis. Sci Rep 2016; 6:39774. [PMID: 28008969 PMCID: PMC5180089 DOI: 10.1038/srep39774] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/28/2016] [Indexed: 12/19/2022] Open
Abstract
High-quality immunoreagents enhance the performance and reproducibility of immunoassays and, in turn, the quality of both biological and clinical measurements. High quality recombinant immunoreagents are generated using antibody-phage display. One metric of antibody quality – the binding affinity – is quantified through the dissociation constant (KD) of each recombinant antibody and the target antigen. To characterize the KD of recombinant antibodies and target antigen, we introduce affinity electrophoretic mobility shift assays (EMSAs) in a high-throughput format suitable for small volume samples. A microfluidic card comprised of free-standing polyacrylamide gel (fsPAG) separation lanes supports 384 concurrent EMSAs in 30 s using a single power source. Sample is dispensed onto the microfluidic EMSA card by acoustic droplet ejection (ADE), which reduces EMSA variability compared to sample dispensing using manual or pin tools. The KD for each of a six-member fragment antigen-binding fragment library is reported using ~25-fold less sample mass and ~5-fold less time than conventional heterogeneous assays. Given the form factor and performance of this micro- and mesofluidic workflow, we have developed a sample-sparing, high-throughput, solution-phase alternative for biomolecular affinity characterization.
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39
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Determining antigen specificity of a monoclonal antibody using genome-scale CRISPR-Cas9 knockout library. J Immunol Methods 2016; 439:8-14. [DOI: 10.1016/j.jim.2016.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 09/16/2016] [Accepted: 09/20/2016] [Indexed: 12/26/2022]
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40
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[Letter to the Editor] The need for improved education and training in research antibody usage and validation practices. Biotechniques 2016; 61:16-8. [PMID: 27401669 DOI: 10.2144/000114431] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/08/2016] [Indexed: 11/23/2022] Open
Abstract
Address correspondence to Leonard P. Freedman, Global Biological Standards Institute, 1020 19th Street, NW, Suite 550, Washington, DC, 20036. E-mail: lfreedman@gbsi.org.
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41
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Polyclonal Antibody Production for Membrane Proteins via Genetic Immunization. Sci Rep 2016; 6:21925. [PMID: 26908053 PMCID: PMC4764931 DOI: 10.1038/srep21925] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/02/2016] [Indexed: 01/08/2023] Open
Abstract
Antibodies are essential for structural determinations and functional studies of membrane proteins, but antibody generation is limited by the availability of properly-folded and purified antigen. We describe the first application of genetic immunization to a structurally diverse set of membrane proteins to show that immunization of mice with DNA alone produced antibodies against 71% (n = 17) of the bacterial and viral targets. Antibody production correlated with prior reports of target immunogenicity in host organisms, underscoring the efficiency of this DNA-gold micronanoplex approach. To generate each antigen for antibody characterization, we also developed a simple in vitro membrane protein expression and capture method. Antibody specificity was demonstrated upon identifying, for the first time, membrane-directed heterologous expression of the native sequences of the FopA and FTT1525 virulence determinants from the select agent Francisella tularensis SCHU S4. These approaches will accelerate future structural and functional investigations of therapeutically-relevant membrane proteins.
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