1
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Monteiro FL, Stepanauskaite L, Archer A, Williams C. Estrogen receptor beta expression and role in cancers. J Steroid Biochem Mol Biol 2024; 242:106526. [PMID: 38657699 DOI: 10.1016/j.jsbmb.2024.106526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/06/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Estrogen drives the growth of some cancers, such as breast cancer, via estrogen receptor alpha (ERα). Estrogen also activates ERβ, but whether ERβ is expressed and has a role in different cancers is debated. The use of nonspecific antibodies has contributed to the confusion, and this review delves into ERβ's controversial role in cancer and focuses on tumor expression that can be supported by non-antibody-dependent assays. We discuss its expression at the transcript level and focus on its potential role in lymphoma, granulosa cell tumors, testicular, and adrenal cancers, emphasizing recent findings and the complexities that necessitate further research.
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Affiliation(s)
- Fátima L Monteiro
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, Solna 171 21, Sweden; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 141 83, Sweden
| | - Lina Stepanauskaite
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, Solna 171 21, Sweden; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 141 83, Sweden
| | - Amena Archer
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, Solna 171 21, Sweden; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 141 83, Sweden
| | - Cecilia Williams
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, Solna 171 21, Sweden; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 141 83, Sweden.
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2
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Novotny J, Svobodova Z, Ilicova M, Hruskova D, Kostalova J, Bilkova Z, Foret F. Advantages of stereolithographic 3D printing in the fabrication of the Affiblot device for dot-blot assays. Mikrochim Acta 2024; 191:442. [PMID: 38954238 PMCID: PMC11219379 DOI: 10.1007/s00604-024-06512-z] [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: 04/15/2024] [Accepted: 06/15/2024] [Indexed: 07/04/2024]
Abstract
In stereolithographic (SLA) 3D printing, objects are constructed by exposing layers of photocurable resin to UV light. It is a highly user-friendly fabrication method that opens a possibility for technology sharing through CAD file online libraries. Here, we present a prototyping procedure of a microfluidics-enhanced dot-blot device (Affiblot) designed for simple and inexpensive screening of affinity molecule characteristics (antibodies, oligonucleotides, cell receptors, etc.). The incorporation of microfluidic features makes sample processing user-friendly, less time-consuming, and less laborious, all performed completely on-device, distinguishing it from other dot-blot devices. Initially, the Affiblot device was fabricated using CNC machining, which required significant investment in manual post-processing and resulted in low reproducibility. Utilization of SLA 3D printing reduced the amount of manual post-processing, which significantly streamlined the prototyping process. Moreover, it enabled the fabrication of previously impossible features, including internal fluidic channels. While 3D printing of sub-millimeter microchannels usually requires custom-built printers, we were able to fabricate microfluidic features on a readily available commercial printer. Open microchannels in the size range 200-300 μm could be fabricated with reliable repeatability and sealed with a replaceable foil. Economic aspects of device fabrication are also discussed.
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Affiliation(s)
- Jakub Novotny
- Institute of Analytical Chemistry of the CAS, v. v. i., Veveri 967/97, 60200, Brno, Czech Republic.
| | - Zuzana Svobodova
- Department of Biological and Medical Sciences, Faculty of Pharmacy in Hradec Kralove, Charles University, Pardubice, Czech Republic.
| | - Marie Ilicova
- Department of Biological and Medical Sciences, Faculty of Pharmacy in Hradec Kralove, Charles University, Pardubice, Czech Republic
| | - Dominika Hruskova
- Department of Economy and Management of Chemical and Foodstuff Industry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Jana Kostalova
- Department of Economy and Management of Chemical and Foodstuff Industry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Zuzana Bilkova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Frantisek Foret
- Institute of Analytical Chemistry of the CAS, v. v. i., Veveri 967/97, 60200, Brno, Czech Republic
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3
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Biddle M, Stylianou P, Rekas M, Wright A, Sousa J, Ruddy D, Stefana MI, Kmiecik K, Bandrowski A, Kahn R, Laflamme C, Krockow EM, Virk H. Improving the integrity and reproducibility of research that uses antibodies: a technical, data sharing, behavioral and policy challenge. MAbs 2024; 16:2323706. [PMID: 38444344 PMCID: PMC10936606 DOI: 10.1080/19420862.2024.2323706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/22/2024] [Indexed: 03/07/2024] Open
Abstract
Antibodies are one of the most important reagents used in biomedical and fundamental research, used to identify, and quantify proteins, contribute to knowledge of disease mechanisms, and validate drug targets. Yet many antibodies used in research do not recognize their intended target, or recognize additional molecules, compromising the integrity of research findings and leading to waste of resources, lack of reproducibility, failure of research projects, and delays in drug development. Researchers frequently use antibodies without confirming that they perform as intended in their application of interest. Here we argue that the determinants of end-user antibody choice and use are critical, and under-addressed, behavioral drivers of this problem. This interacts with the batch-to-batch variability of these biological reagents, and the paucity of available characterization data for most antibodies, making it more difficult for researchers to choose high quality reagents and perform necessary validation experiments. The open-science company YCharOS works with major antibody manufacturers and knockout cell line producers to characterize antibodies, identifying high-performing renewable antibodies for many targets in neuroscience. This shows the progress that can be made by stakeholders working together. However, their work so far applies to only a tiny fraction of available antibodies. Where characterization data exists, end-users need help to find and use it appropriately. While progress has been made in the context of technical solutions and antibody characterization, we argue that initiatives to make best practice behaviors by researchers more feasible, easy, and rewarding are needed. Global cooperation and coordination between multiple partners and stakeholders will be crucial to address the technical, policy, behavioral, and open data sharing challenges. We offer potential solutions by describing our Only Good Antibodies initiative, a community of researchers and partner organizations working toward the necessary change. We conclude with an open invitation for stakeholders, including researchers, to join our cause.
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Affiliation(s)
- M. Biddle
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - P. Stylianou
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - M. Rekas
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - A. Wright
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - J. Sousa
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - D. Ruddy
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - M. I. Stefana
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - K. Kmiecik
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - A. Bandrowski
- Department of Neuroscience, UC San Diego, La Jolla, CA, USA
| | - R.A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, USA
| | - C. Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Canada
| | - E. M. Krockow
- School of Psychology and Vision Sciences, University of Leicester, Leicester, UK
| | - H.S. Virk
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of Leicester, Leicester, UK
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4
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Biddle MS, Virk HS. YCharOS open antibody characterisation data: Lessons learned and progress made. F1000Res 2023; 12:1344. [PMID: 37854875 PMCID: PMC10579855 DOI: 10.12688/f1000research.141719.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 10/20/2023] Open
Abstract
YCharOS is a collaborative initiative aimed at characterising antibodies against the entire human proteome. As of August 2023, they have presented comprehensive knockout characterisation data for 812 antibodies and 78 proteins using techniques such as Western blot, immunoprecipitation, and immunofluorescence. YCharOS consolidates its data into reports (one protein per report) available on Zenodo, a public repository controlled by CERN, to ensure open access. To enhance the visibility of their work, the group is progressively converting their Zenodo reports into F1000 articles, collected on the YCharOS Gateway, and indexed via PubMed. Their data is also accessible through searches on the Antibody Registry. The provided data is a valuable resource for researchers when selecting antibodies for specific applications, although certain limitations should be considered. The data accumulated thus far has illuminated the extent of the problem when poorly performing antibodies are employed in research. While the scientific community was already aware that this was likely a widespread issue, the establishment of a collaborative open science project with industry partners introduces an innovative solution that holds the potential to yield significant returns on investment in the public interest. This potential is substantiated by the number of antibodies that have either been withdrawn or had their recommended usage altered by the vendor. However, despite the discovery of high-performing renewable antibodies for most of the studied proteins, this accounts for a tiny fraction of the human proteome and the commercial antibody market. To realise the full potential of this work, end-users must adjust their antibody procurement and usage practises in line with the provided data. This editorial offers a guide on how individual scientists can utilise the YCharOS data, in addition to sharing the insights gained from the data thus far with the wider scientific community.
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Affiliation(s)
- Michael S. Biddle
- NIHR BRC-Respiratory, University of Leicester, Leicester, England, UK
| | - Harvinder S. Virk
- NIHR BRC-Respiratory, University of Leicester, Leicester, England, UK
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5
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Qin Y, Zhang X, Song Y, Zhong B, Liu L, Wang D, Zhang Y, Lu W, Zhao X, Jia Z, Li M, Zhang L, Qing G. A highly sensitive nanochannel device for the detection of SUMO1 peptides. Chem Sci 2023; 14:8360-8368. [PMID: 37564410 PMCID: PMC10411628 DOI: 10.1039/d3sc02140h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/13/2023] [Indexed: 08/12/2023] Open
Abstract
SUMOylation is an important and highly dynamic post-translational modification (PTM) process of protein, and its disequilibrium may cause various diseases, such as cancers and neurodegenerative disorders. SUMO proteins must be accurately detected to understand disease states and develop effective drugs. Reliable antibodies against SUMO2/3 are commercially available; however, efficient detectors are yet to be developed for SUMO1, which has only 50% homology with SUMO2 and SUMO3. Here, using phage display technology, we identified two cyclic peptide (CP) sequences that could specifically bind to the terminal dodecapeptide sequence of SUMO1. Then we combined the CPs and polyethylene terephthalate conical nanochannel films to fabricate a nanochannel device highly sensitive towards the SUMO1 terminal peptide and protein; sensitivity was achieved by ensuring marked variations in both transmembrane ionic current and Faraday current. The satisfactory SUMO1-sensing ability of this device makes it a promising tool for the time-point monitoring of the SENP1 enzyme-catalyzed de-SUMOylation reaction and cellular imaging. This study not only solves the challenge of SUMO1 precise recognition that could promote SUMO1 proteomics analysis, but also demonstrates the good potential of the nanochannel device in monitoring of enzymes and discovery of effective drugs.
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Affiliation(s)
- Yue Qin
- College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology No. 11 Street, Economic and Technological Development Zone Shenyang 110142 P. R. China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Xiaoyu Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Yanling Song
- College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology No. 11 Street, Economic and Technological Development Zone Shenyang 110142 P. R. China
| | - Bowen Zhong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Lu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Dongdong Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Yahui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Wenqi Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Xinjia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Zhiqi Jia
- College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology No. 11 Street, Economic and Technological Development Zone Shenyang 110142 P. R. China
| | - Minmin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
- College of Chemistry and Chemical Engineering, Wuhan Textile University 1 Sunshine Road Wuhan 430200 P. R. China
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6
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Zou R, Guo Y, Wang Y, Lu X, Ma Z, Shou L, Liu Y, Zhu G, Guo Y. Insights into the Binding Profile of Anti-chlorpyrifos Recombinant Antibodies: From Computational Simulation to Immunoassay Validation. Anal Chem 2023; 95:11287-11295. [PMID: 37459591 DOI: 10.1021/acs.analchem.3c01355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
A novel virtual screening strategy was proposed for the profiling and discovery of active variable regions (VRs) that encode hapten-specific recombinant antibodies (rAbs). Chlorpyrifos, a hazardous organophosphorus pesticide, was selected as the target. First, a VR model-14G4 from anti-chlorpyrifos hybridoma was built via homology modeling. Its binding pattern toward seven organophosphorus analogues was assessed through virtual screening by performing molecular docking. Based on energy scoring, visual examination, and molecular interaction analysis, chlorpyrifos-methyl was also inferred as the high-affinity target for model-14G4 and was then confirmed via a non-competitive surface plasmon resonance (SPR) assay. Subsequently, we attempted to discover hapten-specific VRs by creating a collection of VR models for anonymous testing. Chlorpyrifos and model-14G4 were employed as the known hit and active VRs, respectively. After molecular docking, a novel anti-chlorpyrifos VR (model-1) was identified due to its satisfactory energy scoring and a similar binding pattern to the reference model-14G4. Expressed by HEK293(F) mammalian cells, the newly prepared full-length rAb-model-1 and rAb-14G4 exhibited high sensitivities for detecting chlorpyrifos by the indirect competitive enzyme-linked immunosorbent assay (ic-ELISA), with IC50 of 3.01 ng/mL and 42.82 ng/mL, respectively. They recognized chlorpyrifos-methyl with a cross-reactivity (CR) of 2.5-17.3%. Moreover, the binding properties of rAb-model-1 for recognizing chlorpyrifos and chlorpyrifos-methyl were confirmed via a non-competitive microscale thermophoresis (MST) method. Thus, the experimental results showed good agreement with computational outputs on antibody profiling. Furthermore, the recognition diversity of rAb-model-1 for chlorpyrifos and chlorpyrifos-methyl was studied via molecular dynamics simulation. Overall, the proposed study provides a versatile and economical strategy for antibody characterization and promotes the in vitro production of rAbs for pesticide monitoring.
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Affiliation(s)
- Rubing Zou
- Institute of Pesticide and Environmental Toxicology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Yuanhao Guo
- Institute of Pesticide and Environmental Toxicology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
- Quality and Safety Engineering Institute of Food and Drug, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Yan Wang
- Institute of Pesticide and Environmental Toxicology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Xinying Lu
- Institute of Pesticide and Environmental Toxicology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Zhongjie Ma
- Institute of Pesticide and Environmental Toxicology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Linfei Shou
- Zhejiang Provincial Plant Protection Quarantine and Pesticide Management Institute, Hangzhou 310004, China
| | - Yihua Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Guonian Zhu
- Institute of Pesticide and Environmental Toxicology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Yirong Guo
- Institute of Pesticide and Environmental Toxicology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
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Upadhya SR, Ryan CJ. Antibody reliability influences observed mRNA-protein correlations in tumour samples. Life Sci Alliance 2023; 6:e202201885. [PMID: 37169592 PMCID: PMC10176110 DOI: 10.26508/lsa.202201885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
Reverse phase protein arrays (RPPA) have been used to quantify the abundance of hundreds of proteins across thousands of tumour samples in the Cancer Genome Atlas. By number of samples, this is the largest tumour proteomic dataset available and it provides an opportunity to systematically assess the correlation between mRNA and protein abundances. However, the RPPA approach is highly dependent on antibody reliability and approximately one-quarter of the antibodies used in the the Cancer Genome Atlas are deemed to be somewhat less reliable. Here, we assess the impact of antibody reliability on observed mRNA-protein correlations. We find that, in general, proteins measured with less reliable antibodies have lower observed mRNA-protein correlations. This is not true of the same proteins when measured using mass spectrometry. Furthermore, in cell lines, we find that when the same protein is quantified by both mass spectrometry and RPPA, the overall correlation between the two measurements is lower for proteins measured with less reliable antibodies. Overall our results reinforce the need for caution in using RPPA measurements from less reliable antibodies.
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Affiliation(s)
- Swathi Ramachandra Upadhya
- School of Computer Science, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Colm J Ryan
- School of Computer Science, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
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8
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Loyez M, Adolphson M, Liao J, Yang L. From Whispering Gallery Mode Resonators to Biochemical Sensors. ACS Sens 2023. [PMID: 37390481 DOI: 10.1021/acssensors.2c02876] [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: 07/02/2023]
Abstract
Optical biosensors are frontrunners for the rapid and real-time detection of analytes, particularly for low concentrations. Among them, whispering gallery mode (WGM) resonators have recently attracted a growing focus due to their robust optomechanical features and high sensitivity, measuring down to single binding events in small volumes. In this review, we provide a broad overview of WGM sensors along with critical advice and additional "tips and tricks" to make them more accessible to both biochemical and optical communities. Their structures, fabrication methods, materials, and surface functionalization chemistries are discussed. We propose this reflection under a pedagogical approach to describe and explain these biochemical sensors with a particular focus on the most recent achievements in the field. In addition to highlighting the advantages of WGM sensors, we also discuss and suggest strategies to overcome their current limitations, leaving room for further development as practical tools in various applications. We aim to provide new insights and combine different knowledge and perspectives to advance the development of the next generation of WGM biosensors. With their unique advantages and compatibility with different sensing modalities, these biosensors have the potential to become major game changers for biomedical and environmental monitoring, among many other relevant target applications.
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Affiliation(s)
- Médéric Loyez
- Department of Electrical & Systems Engineering, Washington University, One Brookings Drive Green Hall 2120F, St. Louis, Missouri 63130, United States
| | - Maxwell Adolphson
- Department of Electrical & Systems Engineering, Washington University, One Brookings Drive Green Hall 2120F, St. Louis, Missouri 63130, United States
| | - Jie Liao
- Department of Electrical & Systems Engineering, Washington University, One Brookings Drive Green Hall 2120F, St. Louis, Missouri 63130, United States
| | - Lan Yang
- Department of Electrical & Systems Engineering, Washington University, One Brookings Drive Green Hall 2120F, St. Louis, Missouri 63130, United States
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9
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A Novel Blocking Enzyme-Linked Immunosorbent Assay Based on a Biotinylated Nanobody for the Rapid and Sensitive Clinical Detection of Classical Swine Fever Virus Antibodies. Microbiol Spectr 2023; 11:e0299622. [PMID: 36688674 PMCID: PMC9927282 DOI: 10.1128/spectrum.02996-22] [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] [Indexed: 01/24/2023] Open
Abstract
Monoclonal and polyclonal antibodies are mostly used for the development of traditional enzyme-linked immunosorbent assays (ELISAs), but the use of certain conventional antibodies may be limited by their low yield, the difficulty of their isolation, and their high cost. Heavy-chain antibodies derived from camelids with naturally missing light chains can overcome these deficiencies and are an excellent alternative to conventional antibodies. In this study, a nanobody (Nb)-AviTag fusion protein was constructed, and the feasibility of its use as a high-sensitivity probe in a blocking ELISA (bELISA) for classical swine fever virus (CSFV) was investigated. The CSFV E2 recombinant protein expressed by the CHO expression system exhibited good reactogenicity and immunogenicity and induced the production of high CSFV antibody levels in rabbits. Three different clones of Nbs were successfully isolated using a phage display system in alpaca, and an Nb1-AviTag fusion protein was successfully expressed using an Escherichia coli expression system. The purified Nb1-AviTag fusion protein was then biotinylated in vitro to obtain Nb1-biotin. A novel bELISA was developed for the detection of CSFV antibodies in clinical serum using Nb1-biotin as a probe. The cutoff value of bELISA was 32.18%, the sensitivity of bELISA was higher than that of the bELISA kit with IDEXX antibody, and the coincidence rate was 94.7%. A rapid, low-cost, highly sensitive and highly specific CSFV E2 antibody-based bELISA method was successfully established and can be used for the serological evaluation of CSFV E2 subunit vaccines and the ELISA-based diagnosis of CSFV infection. IMPORTANCE Currently, the epidemic situation of classical swine fever (CSF) is sporadic, and cases of atypical swine fever are on the rise in China. Therefore, it is necessary to accurately eliminate suspected cases by using highly sensitive and specific diagnostic techniques. In our study, a rapid, low-cost, highly sensitivity, highly reliable and reproducible, and highly specific classical swine fever virus (CSFV) E2 antibody-based blocking ELISA method was successfully established by using the phage display system and the Nb1-AviTag fusion expression platform. It provides a new technique for serological evaluation of CSFV vaccines and ELISA-based diagnosis of CSFV infection.
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10
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Bandrowski A, Pairish M, Eckmann P, Grethe J, Martone M. The Antibody Registry: ten years of registering antibodies. Nucleic Acids Res 2023; 51:D358-D367. [PMID: 36370112 PMCID: PMC9825422 DOI: 10.1093/nar/gkac927] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/28/2022] [Accepted: 11/07/2022] [Indexed: 11/14/2022] Open
Abstract
Antibodies are ubiquitous key biological research resources yet are tricky to use as they are prone to performance issues and represent a major source of variability across studies. Understanding what antibody was used in a published study is therefore necessary to repeat and/or interpret a given study. However, antibody reagents are still frequently not cited with sufficient detail to determine which antibody was used in experiments. The Antibody Registry is a public, open database that enables citation of antibodies by providing a persistent record for any antibody-based reagent used in a publication. The registry is the authority for antibody Research Resource Identifiers, or RRIDs, which are requested or required by hundreds of journals seeking to improve the citation of these key resources. The registry is the most comprehensive listing of persistently identified antibody reagents used in the scientific literature. Data contributors span individual authors who use antibodies to antibody companies, which provide their entire catalogs including discontinued items. Unlike many commercial antibody listing sites which tend to remove reagents no longer sold, registry records persist, providing an interface between a fast-moving commercial marketplace and the static scientific literature. The Antibody Registry (RRID:SCR_006397) https://antibodyregistry.org.
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Affiliation(s)
- Anita Bandrowski
- Department of Neuroscience, UCSD, San Diego, CA 92093, USA
- SciCrunch Inc, San Diego, CA 92093, USA
| | | | - Peter Eckmann
- Department of Neuroscience, UCSD, San Diego, CA 92093, USA
- SciCrunch Inc, San Diego, CA 92093, USA
| | - Jeffrey Grethe
- Department of Neuroscience, UCSD, San Diego, CA 92093, USA
- SciCrunch Inc, San Diego, CA 92093, USA
| | - Maryann E Martone
- Department of Neuroscience, UCSD, San Diego, CA 92093, USA
- SciCrunch Inc, San Diego, CA 92093, USA
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11
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Garvin AJ, Lanz AJ, Morris JR. SUMO monoclonal antibodies vary in sensitivity, specificity, and ability to detect types of SUMO conjugate. Sci Rep 2022; 12:21343. [PMID: 36494414 PMCID: PMC9734647 DOI: 10.1038/s41598-022-25665-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
Monoclonal antibodies (MAb) to members of the Small Ubiquitin-like modifier (SUMO) family are essential tools in the study of cellular SUMOylation. However, many anti-SUMO MAbs are poorly validated, and antibody matching to detection format is without an evidence base. Here we test the specificity and sensitivity of twenty-four anti-SUMO MAbs towards monomeric and polymeric SUMO1-4 in dot-blots, immunoblots, immunofluorescence and immunoprecipitation. We find substantial variability between SUMO MAbs for different conjugation states, for detecting increased SUMOylation in response to thirteen different stress agents, and as enrichment reagents for SUMOylated RanGAP1 or KAP1. All four anti-SUMO4 monoclonal antibodies tested cross-reacted wit SUMO2/3, and several SUMO2/3 monoclonal antibodies cross-reacted with SUMO4. These data characterize the specificity of twenty-four anti-SUMO antibodies across commonly used assays, creating an enabling resource for the SUMO research community.
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Affiliation(s)
- Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Schools, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Alexander J Lanz
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Schools, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Schools, University of Birmingham, Birmingham, B15 2TT, UK.
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12
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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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13
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Russo G, Unkauf T, Meier D, Wenzel EV, Langreder N, Schneider KT, Wiesner R, Bischoff R, Stadler V, Dübel S. In vitro evolution of myc-tag antibodies: in-depth specificity and affinity analysis of Myc1-9E10 and Hyper-Myc. Biol Chem 2022; 403:479-494. [PMID: 35312243 DOI: 10.1515/hsz-2021-0405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/28/2022] [Indexed: 11/15/2022]
Abstract
One of the most widely used epitope tags is the myc-tag, recognized by the anti-c-Myc hybridoma antibody Myc1-9E10. Combining error-prone PCR, DNA shuffling and phage display, we generated an anti-c-Myc antibody variant (Hyper-Myc) with monovalent affinity improved to 18 nM and thermal stability increased by 37%. Quantification of capillary immunoblots and by flow cytometry demonstrated improved antigen detection by Hyper-Myc. Further, three different species variants of this antibody were generated to allow the use of either anti-human, anti-mouse or anti-rabbit Fc secondary antibodies for detection. We characterized the specificity of both antibodies in depth: individual amino acid exchange mapping demonstrated that the recognized epitope was not changed by the in vitro evolution process. A laser printed array of 29,127 different epitopes representing all human linear B-cell epitopes of the Immune Epitope Database allowing to chart unwanted reactivities with mimotopes showed these to be very low for both antibodies and not increased for Hyper-Myc despite its improved affinity. The very low background reactivity of Hyper-Myc was confirmed by staining of myc-tag transgenic zebrafish whole mounts. Hyper-Myc retains the very high specificity of Myc1-9E10 while allowing myc-tag detection at lower concentrations and with either anti-mouse, anti-rabbit or anti human secondary antibodies.
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Affiliation(s)
- Giulio Russo
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany.,Abcalis GmbH, Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Tobias Unkauf
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
| | - Doris Meier
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
| | - Esther Veronika Wenzel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany.,Abcalis GmbH, Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Nora Langreder
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany.,iTUBS mbH, Wilhelmsgarten 3, D-38100 Braunschweig, Germany
| | - Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
| | - Rebecca Wiesner
- Technische Universität Braunschweig, Institut für Medizinische und Pharmazeutische Chemie, Beethovenstr. 55, D-38106 Braunschweig, Germany
| | - Ralf Bischoff
- Division of Functional Genome Analysis, Research Program "Functional and Structural Genomics", German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Volker Stadler
- Pepperprint GmbH, Rischerstrasse 12, D-69123 Heidelberg, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
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14
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Katona B, Lindskog C. The Human Protein Atlas and Antibody-Based Tissue Profiling in Clinical Proteomics. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:191-206. [PMID: 34905175 DOI: 10.1007/978-1-0716-1936-0_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Immunohistochemistry (IHC) is a standard method for spatial proteomics and allows for exploration of protein expression at single-cell resolution within the intact tissue environment. Stringent procedures and proper antibody validation strategies are however needed to ensure reliability of results. Application-specific strategies have been proposed by the scientific community to ensure high quality despite variations in sample preparation between different antibody-based methods. Here, the entire workflow utilized within the Human Protein Atlas, from sample preparation to annotation of the IHC staining patterns is described in detail, with important notes on various factors that can affect the outcome of IHC. Methods include tissue microarray (TMA) production, tissue sectioning, IHC, annotation, and validation. Also, building on previously suggested validation strategies, IHC-specific orthogonal and independent validation methods are outlined.
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Affiliation(s)
- Borbala Katona
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
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15
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Pillay TS, Muyldermans S. Application of Single-Domain Antibodies ("Nanobodies") to Laboratory Diagnosis. Ann Lab Med 2021; 41:549-558. [PMID: 34108282 PMCID: PMC8203438 DOI: 10.3343/alm.2021.41.6.549] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 05/24/2021] [Indexed: 12/15/2022] Open
Abstract
Antibodies have proven to be central in the development of diagnostic methods over decades, moving from polyclonal antibodies to the milestone development of monoclonal antibodies. Although monoclonal antibodies play a valuable role in diagnosis, their production is technically demanding and can be expensive. The large size of monoclonal antibodies (150 kDa) makes their re-engineering using recombinant methods a challenge. Single-domain antibodies, such as “nanobodies,” are a relatively new class of diagnostic probes that originated serendipitously during the assay of camel serum. The immune system of the camelid family (camels, llamas, and alpacas) has evolved uniquely to produce heavy-chain antibodies that contain a single monomeric variable antibody domain in a smaller functional unit of 12–15 kDa. Interestingly, the same biological phenomenon is observed in sharks. Since a single-domain antibody molecule is smaller than a conventional mammalian antibody, recombinant engineering and protein expression in vitro using bacterial production systems are much simpler. The entire gene encoding such an antibody can be cloned and expressed in vitro. Single-domain antibodies are very stable and heat-resistant, and hence do not require cold storage, especially when incorporated into a diagnostic kit. Their simple genetic structure allows easy re-engineering of the protein to introduce new antigen-binding characteristics or attach labels. Here, we review the applications of single-domain antibodies in laboratory diagnosis and discuss the future potential in this area.
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Affiliation(s)
- Tahir S Pillay
- Department of Chemical Pathology and NHLS- Tshwane Academic Division, University of Pretoria, Pretoria, South Africa.,Division of Chemical Pathology, University of Cape Town, Cape Town, South Africa.,Department of Chemical Pathology, University of Pretoria, Prinshof Campus, Pretoria, South Africa
| | - Serge Muyldermans
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium.,Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, China
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16
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Lengfeld J, Zhang H, Stoesz S, Murali R, Pass F, Greene MI, Goel PN, Grover P. Challenges in Detection of Serum Oncoprotein: Relevance to Breast Cancer Diagnostics. BREAST CANCER-TARGETS AND THERAPY 2021; 13:575-593. [PMID: 34703307 PMCID: PMC8524259 DOI: 10.2147/bctt.s331844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/02/2021] [Indexed: 11/23/2022]
Abstract
Breast cancer is a highly prevalent malignancy that shows improved outcomes with earlier diagnosis. Current screening and monitoring methods have improved survival rates, but the limitations of these approaches have led to the investigation of biomarker evaluation to improve early diagnosis and treatment monitoring. The enzyme-linked immunosorbent assay (ELISA) is a specific and robust technique ideally suited for the quantification of protein biomarkers from blood or its constituents. The continued clinical relevancy of this assay format will require overcoming specific technical challenges, including the ultra-sensitive detection of trace biomarkers and the circumventing of potential assay interference due to the expanding use of monoclonal antibody (mAb) therapeutics. Approaches to increasing the sensitivity of ELISA have been numerous and include employing more sensitive substrates, combining ELISA with the polymerase chain reaction (PCR), and incorporating nanoparticles as shuttles for detection antibodies and enzymes. These modifications have resulted in substantial boosts in the ability to detect extremely low levels of protein biomarkers, with some systems reliably detecting antigen at sub-femtomolar concentrations. Extensive utilization of mAb therapies in oncology has presented an additional contemporary challenge for ELISA, particularly when both therapeutic and assay antibodies target the same protein antigen. Resolution of issues such as epitope overlap and steric hindrance requires a rational approach to the design of diagnostic antibodies that takes advantage of modern antibody generation pipelines, epitope binning techniques and computational methods to strategically target biomarker epitopes. This review discusses technical strategies in ELISA implemented to date and their feasibility to address current constraints on sensitivity and problems with interference in the clinical setting. The impact of these recent advancements will depend upon their transformation from research laboratory protocols into facile, reliable detection systems that can ideally be replicated in point-of-care devices to maximize utilization and transform both the diagnostic and therapeutic monitoring landscape.
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Affiliation(s)
- Justin Lengfeld
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Hongtao Zhang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven Stoesz
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology; Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Franklin Pass
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Mark I Greene
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peeyush N Goel
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Payal Grover
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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17
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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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18
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Saavedra JM. Angiotensin Receptor Blockers Are Not Just for Hypertension Anymore. Physiology (Bethesda) 2021; 36:160-173. [PMID: 33904788 DOI: 10.1152/physiol.00036.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Beyond blood pressure control, angiotensin receptor blockers reduce common injury mechanisms, decreasing excessive inflammation and protecting endothelial and mitochondrial function, insulin sensitivity, the coagulation cascade, immune responses, cerebrovascular flow, and cognition, properties useful to treat inflammatory, age-related, neurodegenerative, and metabolic disorders of many organs including brain and lung.
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Affiliation(s)
- Juan M Saavedra
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, District of Columbia
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19
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Tabatabaee MS, Kerkovius J, Menard F. Design of an Imaging Probe to Monitor Real-Time Redistribution of L-type Voltage-Gated Calcium Channels in Astrocytic Glutamate Signaling. Mol Imaging Biol 2021; 23:407-416. [PMID: 33432518 DOI: 10.1007/s11307-020-01573-x] [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] [Received: 09/07/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 11/29/2022]
Abstract
PURPOSE In the brain, astrocytes are non-excitable cells that undergo rapid morphological changes when stimulated by the excitatory neurotransmitter glutamate. We developed a chemical probe to monitor how glutamate affects the density and distribution of astrocytic L-type voltage-gated calcium channels (LTCC). PROCEDURES The imaging probe FluoBar1 was created from a barbiturate ligand modified with a fluorescent coumarin moiety. The probe selectivity was examined with colocalization analyses of confocal fluorescence imaging in U118-MG and transfected COS-7 cells. Living cells treated with 50 nM FluoBar1 were imaged in real time to reveal changes in density and distribution of astrocytic LTCCs upon exposure to glutamate. RESULTS FluoBar1 was synthesized in ten steps. The selectivity of the probe was demonstrated with immunoblotting and confocal imaging of immunostained cells expressing the CaV1.2 isoform of LTCCs proteins. Applying FluoBar1 to astrocyte model cells U118-MG allowed us to measure a fivefold increase in fluorescence density of LTCCs upon glutamate exposure. CONCLUSIONS Imaging probe FluoBar1 allows the real-time monitoring of LTCCs in living cells, revealing for first time that glutamate causes a rapid increase of LTCC membranar density in astrocyte model cells. FluoBar1 may help tackle previously intractable questions about LTCC dynamics in cellular events.
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Affiliation(s)
- Mitra Sadat Tabatabaee
- Department of Biochemistry & Molecular Biology, I.K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Jeff Kerkovius
- Department of Chemistry, I.K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Frederic Menard
- Department of Biochemistry & Molecular Biology, I.K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada. .,Department of Chemistry, I.K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada.
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20
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Sivertsson Å, Lindström E, Oksvold P, Katona B, Hikmet F, Vuu J, Gustavsson J, Sjöstedt E, von Feilitzen K, Kampf C, Schwenk JM, Uhlén M, Lindskog C. Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins. J Proteome Res 2020; 19:4766-4781. [PMID: 33170010 PMCID: PMC7723238 DOI: 10.1021/acs.jproteome.0c00486] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The localization of proteins at a
tissue- or cell-type-specific
level is tightly linked to the protein function. To better understand
each
protein’s role in cellular systems, spatial information constitutes
an important complement to quantitative data. The standard methods
for determining the spatial distribution of proteins in single cells
of complex tissue samples make use of antibodies. For a stringent
analysis of the human proteome, we used orthogonal methods and independent
antibodies to validate 5981 antibodies that show the expression of
3775 human proteins across all major human tissues. This enhanced
validation uncovered 56 proteins corresponding to the group of “missing
proteins” and 171 proteins of unknown function. The presented
strategy will facilitate further discussions around criteria for evidence
of protein existence based on immunohistochemistry and serves as a
useful guide to identify candidate proteins for integrative studies
with quantitative proteomics methods.
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Affiliation(s)
- Åsa Sivertsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Emil Lindström
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Per Oksvold
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Borbala Katona
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Feria Hikmet
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Jimmy Vuu
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Jonas Gustavsson
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden.,Atlas Antibodies AB, 16869 Bromma, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
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21
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Increased Cytoplasmic CD138 Expression Is Associated with Aggressive Characteristics in Prostate Cancer and Is an Independent Predictor for Biochemical Recurrence. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5845374. [PMID: 33195694 PMCID: PMC7641694 DOI: 10.1155/2020/5845374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/27/2020] [Accepted: 09/30/2020] [Indexed: 01/11/2023]
Abstract
Syndecan-1 (CD138) is a transmembrane proteoglycan expressed in various normal and malignant tissues. It is of interest due to a possible prognostic effect in tumors and its role as a target for the antibody-drug conjugate indatuximab ravtansine. Here, we analyzed 17,747 prostate cancers by immunohistochemistry. Membranous and cytoplasmic CD138 staining was separately recorded. In normal prostate glands, CD138 staining was limited to basal cells. In cancers, membranous CD138 positivity was seen in 19.6% and cytoplasmic CD138 staining in 11.2% of 12,851 interpretable cases. A comparison with clinico-pathological features showed that cytoplasmic CD138 staining was more linked to unfavorable tumor features than membranous staining. Cytoplasmic CD138 immunostaining was associated with high tumor stage (p < 0.0001), high Gleason grade (p < 0.0001), nodal metastases (p < 0.0001), positive surgical margin (p < 0.0001), and biochemical recurrence (p < 0.0001). This also holds true for both V-ets avian erythroblastosis virus E26 oncogene homolog (ERG) fusion positive and ERG fusion negative tumors although the cytoplasmic CD138 expression was markedly more frequent in ERG positive than in ERG negative tumors (p < 0.0001). Comparison with 11 previously analyzed chromosomal deletions identified a conspicuous association between cytoplasmic CD138 expression and 8p deletions (p < 0.0001) suggesting a possible functional interaction of CD138 with one or several 8p genes. Multivariate analysis revealed the cytoplasmic CD138 expression as an independent prognostic parameter in all cancers and in the ERG positive subgroup. In summary, our study indicates the cytoplasmic CD138 expression as a strong and independent predictor of poor prognosis in prostate cancer. Immunohistochemical measurement of CD138 protein may thus—perhaps in combination with other parameters—become clinically useful in the future.
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22
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Gray A, Bradbury ARM, Knappik A, Plückthun A, Borrebaeck CAK, Dübel S. Animal-free alternatives and the antibody iceberg. Nat Biotechnol 2020; 38:1234-1239. [DOI: 10.1038/s41587-020-0687-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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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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24
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Animal-derived-antibody generation faces strict reform in accordance with European Union policy on animal use. Nat Methods 2020; 17:755-756. [DOI: 10.1038/s41592-020-0906-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Kim YS, Lim J, Sung J, Cheong Y, Lee EY, Kim J, Oh H, Kim YS, Cho NH, Choi S, Kang SM, Nam JH, Chae W, Seong BL. Built-in RNA-mediated chaperone (chaperna) for antigen folding tailored to immunized hosts. Biotechnol Bioeng 2020; 117:1990-2007. [PMID: 32297972 PMCID: PMC7262357 DOI: 10.1002/bit.27355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 01/25/2023]
Abstract
High‐quality antibody (Ab) production depends on the availability of immunologically relevant antigens. We present a potentially universal platform for generating soluble antigens from bacterial hosts, tailored to immunized animals for Ab production. A novel RNA‐dependent chaperone, in which the target antigen is genetically fused with an RNA‐interacting domain (RID) docking tag derived from the immunized host, promotes the solubility and robust folding of the target antigen. We selected the N‐terminal tRNA‐binding domain of lysyl‐tRNA synthetase (LysRS) as the RID for fusion with viral proteins and demonstrated the expression of the RID fusion proteins in their soluble and native conformations; immunization predominantly elicited Ab responses to the target antigen, whereas the “self” RID tag remained nonimmunogenic. Differential immunogenicity of the fusion proteins greatly enriched and simplified the screening of hybridoma clones of monoclonal antibodies (mAbs), enabling specific and sensitive serodiagnosis of MERS‐CoV infection. Moreover, mAbs against the consensus influenza hemagglutinin stalk domain enabled a novel assay for trivalent seasonal influenza vaccines. The Fc‐mediated effector function was demonstrated, which could be harnessed for the design of next‐generation “universal” influenza vaccines. The nonimmunogenic built‐in antigen folding module tailored to a repertoire of immunized animal hosts will drive immunochemical diagnostics, therapeutics, and designer vaccines.
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Affiliation(s)
- Young-Seok Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jongkwan Lim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jemin Sung
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yucheol Cheong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Eun-Young Lee
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Jihoon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Hana Oh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yeon-Sook Kim
- Division of Infectious Diseases, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seongil Choi
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sang-Moo Kang
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia
| | - Jae-Hwan Nam
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Wonil Chae
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Baik L Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
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26
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Budhathoki-Uprety J, Shah J, Korsen JA, Wayne AE, Galassi TV, Cohen JR, Harvey JD, Jena PV, Ramanathan LV, Jaimes EA, Heller DA. Synthetic molecular recognition nanosensor paint for microalbuminuria. Nat Commun 2019; 10:3605. [PMID: 31399600 PMCID: PMC6689023 DOI: 10.1038/s41467-019-11583-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/19/2019] [Indexed: 01/16/2023] Open
Abstract
Microalbuminuria is an important clinical marker of several cardiovascular, metabolic, and other diseases such as diabetes, hypertension, atherosclerosis, and cancer. The accurate detection of microalbuminuria relies on albumin quantification in the urine, usually via an immunoturbidity assay; however, like many antibody-based assessments, this method may not be robust enough to function in global health applications, point-of-care assays, or wearable devices. Here, we develop an antibody-free approach using synthetic molecular recognition by constructing a polymer to mimic fatty acid binding to the albumin, informed by the albumin crystal structure. A single-walled carbon nanotube, encapsulated by the polymer, as the transduction element produces a hypsochromic (blue) shift in photoluminescence upon the binding of albumin in clinical urine samples. This complex, incorporated into an acrylic material, results in a nanosensor paint that enables the detection of microalbuminuria in patient samples and comprises a rapid point-of-care sensor robust enough to be deployed in resource-limited settings.
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Affiliation(s)
- Januka Budhathoki-Uprety
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Department of Textile Engineering, Chemistry, and Science, North Carolina State University, Raleigh, NC, 27695, United States
| | - Janki Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
| | - Joshua A Korsen
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Weill Cornell Medical College, New York, NY, 10065, United States
| | - Alysandria E Wayne
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Washington University in St. Louis, St. Louis, MO, 63130, United States
| | - Thomas V Galassi
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Weill Cornell Medical College, New York, NY, 10065, United States
| | - Joseph R Cohen
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
| | - Jackson D Harvey
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Weill Cornell Medical College, New York, NY, 10065, United States
| | - Prakrit V Jena
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
| | | | - Edgar A Jaimes
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Weill Cornell Medical College, New York, NY, 10065, United States
| | - Daniel A Heller
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States.
- Weill Cornell Medical College, New York, NY, 10065, United States.
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27
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Kiskova T, Mytsko Y, Schepelmann M, Helmer H, Fuchs R, Miedl H, Wadsack C, Ellinger I. Expression of the neonatal Fc-receptor in placental-fetal endothelium and in cells of the placental immune system. Placenta 2019; 78:36-43. [PMID: 30955709 DOI: 10.1016/j.placenta.2019.02.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/21/2019] [Accepted: 02/22/2019] [Indexed: 02/04/2023]
Abstract
INTRODUCTION Starting from the second trimester of pregnancy, passive immunity is provided to the human fetus by transplacental transfer of maternal IgG. IgG transfer depends on the neonatal Fc receptor, FcRn. While FcRn localization in the placental syncytiotrophoblast (STB) has been demonstrated unequivocally, FcRn expression in placental-fetal endothelial cells (pFECs), which are part of the materno-fetal barrier, is still unclear. Therefore, this study aimed to elucidate the spatio-specific expression pattern of FcRn in placental tissue. METHODS FcRn expression was investigated by western blotting in term placentas and in isolated human placental arterial and venous endothelial cells (HPAEC, HPVEC) using a validated affinity-purified polyclonal anti-peptide antibody against the cytoplasmic tail of FcRn α-chain. In situ localization of FcRn and IgG was studied by immunofluorescence microscopy on tissue sections of healthy term placentas. RESULTS FcRn expression was demonstrated in placental vasculature particularly, in HPAEC, and HPVEC. FcRn was localized in cytokeratin 7+ STB and in CD31+ pFECs in terminal as well as stem villi in situ. Additionally, CD68+ placental macrophages exhibited FcRn expression in situ. Endogenous IgG partially co-localized with FcRn in STB, pFECs, and in placental macrophages. DISCUSSION Placental FcRn expression in endothelial cells and macrophages is analogous to the expression pattern in other organs. FcRn expression in pFECs suggests an involvement of FcRn in IgG transcytosis and/or participation in recycling/salvaging of maternal IgG present in the fetal circulation. FcRn expression in placental macrophages may account for recycling of monomeric IgG and/or processing and presentation of immune complexes.
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Affiliation(s)
- Terezia Kiskova
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Yuliya Mytsko
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Martin Schepelmann
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Hanns Helmer
- Division of Obstetrics and Feto-Maternal Medicine, University Department of Obstetrics and Gynaecology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Renate Fuchs
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Heidi Miedl
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Christian Wadsack
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Isabella Ellinger
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
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Sfanos KS, Yegnasubramanian S, Nelson WG, Lotan TL, Kulac I, Hicks JL, Zheng Q, Bieberich CJ, Haffner MC, De Marzo AM. If this is true, what does it imply? How end-user antibody validation facilitates insights into biology and disease. Asian J Urol 2019; 6:10-25. [PMID: 30775245 PMCID: PMC6363603 DOI: 10.1016/j.ajur.2018.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 12/30/2022] Open
Abstract
Antibodies are employed ubiquitously in biomedical sciences, including for diagnostics and therapeutics. One of the most important uses is for immunohistochemical (IHC) staining, a process that has been improving and evolving over decades. IHC is useful when properly employed, yet misuse of the method is widespread and contributes to the "reproducibility crisis" in science. We report some of the common problems encountered with IHC assays, and direct readers to a wealth of literature documenting and providing some solutions to this problem. We also describe a series of vignettes that include our approach to analytical validation of antibodies and IHC assays that have facilitated a number of biological insights into prostate cancer and the refutation of a controversial association of a viral etiology in gliomas. We postulate that a great deal of the problem with lack of accuracy in IHC assays stems from the lack of awareness by researchers for the critical necessity for end-users to validate IHC antibodies and assays in their laboratories, regardless of manufacturer claims or past publications. We suggest that one reason for the pervasive lack of end-user validation for research antibodies is that researchers fail to realize that there are two general classes of antibodies employed in IHC. First, there are antibodies that are "clinical grade" reagents used by pathologists to help render diagnoses that influence patient treatment. Such diagnostic antibodies, which tend to be highly validated prior to clinical implementation, are in the vast minority (e.g. < 500). The other main class of antibodies are "research grade" antibodies (now numbering >3 800 000), which are often not extensively validated prior to commercialization. Given increased awareness of the problem, both the United States, National Institutes of Health and some journals are requiring investigators to provide evidence of specificity of their antibody-based assays.
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Affiliation(s)
- Karen S. Sfanos
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - William G. Nelson
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tamara L. Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ibrahim Kulac
- Department of Pathology, Koc Universitesi Tip Fakultesi, Istanbul, Turkey
| | - Jessica L. Hicks
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Qizhi Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles J. Bieberich
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Michael C. Haffner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Angelo M. De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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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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30
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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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31
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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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