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Enhanced validation of antibodies for research applications.

ABSTRACT: There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies, and capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.

SUBMITTER: Edfors F

PROVIDER: S-EPMC6175901 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Enhanced validation of antibodies for research applications.

Edfors Fredrik F Hober Andreas A Linderbäck Klas K Maddalo Gianluca G Azimi Alireza A Sivertsson Åsa Å Tegel Hanna H Hober Sophia S Szigyarto Cristina Al-Khalili CA Fagerberg Linn L von Feilitzen Kalle K Oksvold Per P Lindskog Cecilia C Forsström Björn B Uhlen Mathias M

Nature communications 20181008 1

There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strat ...[more]

PMID: 30297845

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Enhanced validation of antibodies for research applications

Project description:There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation “pillars" were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies and migration capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.

2018-08-21 | PXD010178 | Pride

Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins.

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Scaling of an antibody validation procedure enables quantification of antibody performance in major research applications.

Project description:Antibodies are critical reagents to detect and characterize proteins. It is commonly understood that many commercial antibodies do not recognize their intended targets, but information on the scope of the problem remains largely anecdotal, and as such, feasibility of the goal of at least one potent and specific antibody targeting each protein in a proteome cannot be assessed. Focusing on antibodies for human proteins, we have scaled a standardized characterization approach using parental and knockout cell lines (Laflamme et al., 2019) to assess the performance of 614 commercial antibodies for 65 neuroscience-related proteins. Side-by-side comparisons of all antibodies against each target, obtained from multiple commercial partners, demonstrates that: i) more than 50% of all antibodies failed in one or more tests, ii) yet, ~50-75% of the protein set was covered by at least one high-performing antibody, depending on application, suggesting that coverage of human proteins by commercial antibodies is significant; and iii) recombinant antibodies performed better than monoclonal or polyclonal antibodies. The hundreds of underperforming antibodies identified in this study were found to have been used in a large number of published articles, which should raise alarm. Encouragingly, more than half of the underperforming commercial antibodies were reassessed by the manufacturers, and many had alterations to their recommended usage or were removed from the market. This first such study helps demonstrate the scale of the antibody specificity problem but also suggests an efficient strategy toward achieving coverage of the human proteome; mine the existing commercial antibody repertoire, and use the data to focus new renewable antibody generation efforts.

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Generation and validation of CRISPR-engineered human natural killer cell lines for research and therapeutic applications.

Project description:Cytotoxic natural killer cells kill tumors and infected cells. We carried out CRISPR-based gene editing and transcriptional regulation in hard-to-manipulate NK-92 cells. NK-92-based therapies were found to be safe and efficacious in preclinical studies of cancers. Here, we have pioneered the generation and validation of NK-92 cells constitutively expressing Cas9 or dCas9 for knockout (CRISPRko), transcriptional activation (CRISPRa), or transcriptional repression (CRISPRi) of genes. Our CRISPR-engineered NK-92 cell platforms can be modified for research and off-the-shelf therapeutic applications.

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Theranostic applications of antibodies in oncology.

Project description:Targeted therapies, including antibodies, are becoming increasingly important in cancer therapy. Important limitations, however, are that not every patient benefits from a specific antibody therapy and that responses could be short-lived due to acquired resistance. In addition, targeted therapies are quite expensive and are not completely devoid of side-effects. This urges the need for accurate patient selection and response monitoring. An important step towards personalizing antibody treatment could be the implementation of theranostics. Antibody theranostics combine the diagnostic and therapeutic potential of an antibody, thereby selecting those patients who are most likely to benefit from antibody treatment. This review focuses on the clinical application of theranostic antibodies in oncology. It provides detailed information concerning the suitability of antibodies for theranostics, the different types of theranostic tests available and summarizes the efficacy of theranostic antibodies used in current clinical practice. Advanced theranostic applications, including radiolabeled antibodies for non-invasive functional imagining, are also addressed. Finally, we discuss the importance of theranostics in the emerging field of personalized medicine and critically evaluate recent data to determine the best way to apply antibody theranostics in the future.

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Quality Issues of Research Antibodies.

Project description:According to several recent studies, an unexpectedly high number of landmark papers seem to be not reproducible by independent laboratories. Nontherapeutic antibodies used for research, diagnostic, food analytical, environmental, and other purposes play a significant role in this matter. Although some papers have been published offering suggestions to improve the situation, they do not seem to be comprehensive enough to cover the full complexity of this issue. In addition, no obvious improvements could be noticed in the field as yet. This article tries to consolidate the remarkable variety of conclusions and suggested activities into a more coherent conception. It is concluded that funding agencies and journal publishers need to take first and immediate measures to resolve these problems and lead the way to a more sustainable way of bioanalytical research, on which all can rely with confidence.

| S-EPMC4803150 | biostudies-other

Monoclonal Antibodies against the MET/HGF Receptor and Its Ligand: Multitask Tools with Applications from Basic Research to Therapy.

Project description:Monoclonal antibodies can be seen as valuable tools for many aspects of basic as well as applied sciences. In the case of MET/HGFR, they allowed the identification of truncated isoforms of the receptor, as well as the dissection of different epitopes, establishing structure-function relationships. Antibodies directed against MET extracellular domain were found to be full or partial receptor agonists or antagonists. The agonists can mimic the effects of the different isoforms of the natural ligand, but with the advantage of being more stable than the latter. Thus, some agonist antibodies promote all the biological responses triggered by MET activation, including motility, proliferation, morphogenesis, and protection from apoptosis, while others can induce only a migratory response. On the other hand, antagonists can inhibit MET-driven biological functions either by competing with the ligand or by removing the receptor from the cell surface. Since MET/HGFR is often over-expressed and/or aberrantly activated in tumors, monoclonal antibodies can be used as probes for MET detection or as "bullets" to target MET-expressing tumor cells, thus pointing to their use in diagnosis and therapy.

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Antibody validation in estrogen receptor beta research

Project description:Three antibodies targeting estrogen receptor beta were evaluated with respect to their specificity towards the target protein, by immunoprecipitation followed by LC-Orbitrap MS.

2017-06-16 | PXD005936 | Pride

Algorithm for model validation: theory and applications.

Project description:Validation is often defined as the process of determining the degree to which a model is an accurate representation of the real world from the perspective of its intended uses. Validation is crucial as industries and governments depend increasingly on predictions by computer models to justify their decisions. We propose to formulate the validation of a given model as an iterative construction process that mimics the often implicit process occurring in the minds of scientists. We offer a formal representation of the progressive build-up of trust in the model. Thus, we replace static claims on the impossibility of validating a given model by a dynamic process of constructive approximation. This approach is better adapted to the fuzzy, coarse-grained nature of validation. Our procedure factors in the degree of redundancy versus novelty of the experiments used for validation as well as the degree to which the model predicts the observations. We illustrate the methodology first with the maturation of quantum mechanics as the arguably best established physics theory and then with several concrete examples drawn from some of our primary scientific interests: a cellular automaton model for earthquakes, a multifractal random walk model for financial time series, an anomalous diffusion model for solar radiation transport in the cloudy atmosphere, and a computational fluid dynamics code for the Richtmyer-Meshkov instability.

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