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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, have demonstrated that: (i) more than 50% of all antibodies failed in one or more applications, (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 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.

Letter to the Editor

Matrix metallopeptidase 7 (MMP7, also known as matrilysin) is a secreted zinc-dependent endopeptidase implicated in extracellular matrix remodelling and fibrotic processes. Elevated MMP7 expression is a hallmark of idiopathic pulmonary fibrosis and other interstitial lung diseases, where it has emerged as a candidate biomarker for disease progression. Identifying high-quality research antibodies is therefore essential to enable robust investigation of MMP7 biology and its translational potential. In this study, we systematically evaluated ten commercial antibodies for western blot and immunoprecipitation using a standardized knockout validation approach in human A549 cells, comparing readouts in MMP7 knockout lines with isogenic parental controls. These experiments form part of a larger collaborative initiative to address antibody reproducibility by characterizing commercial antibodies for human proteins and making the results openly available to the community. While antibody use and protocol conditions will vary between laboratories, this report provides a resource to guide selection of the most suitable reagents for studies of MMP7 in health and disease.

A single event can completely change the direction of a career in science; four researchers share their stories.A single event can completely change the direction of a career in science; four researchers share their stories.

Antibodies are used in many areas of biomedical and clinical research, but many of these antibodies have not been adequately characterized, which casts doubt on the results reported in many scientific papers. This problem is compounded by a lack of suitable control experiments in many studies. In this article we review the history of the 'antibody characterization crisis', and we document efforts and initiatives to address the problem, notably for antibodies that target human proteins. We also present recommendations for a range of stakeholders - researchers, universities, journals, antibody vendors and repositories, scientific societies and funders - to increase the reproducibility of studies that rely on antibodies.

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.

Synaptotagmin-1 is a synaptic vesicle transmembrane protein that senses calcium influx via its tandem C2-domains, triggering synchronous neurotransmitter release. Disruption to SYT1 is associated with neurodevelopmental disorders, highlighting the importance of identifying high-quality research reagents to enhance understanding of Synaptotagmin-1 in health and disease. Here we have characterized thirteen Synaptotagmin-1 commercial antibodies for western blot, immunoprecipitation, immunofluorescence and flow cytometry using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a larger, collaborative initiative seeking to address antibody reproducibility issues by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While use of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs.

Alpha-1-antitrypsin (A1AT), encoded by the SERPINA1 gene, is a circulating serine protease inhibitor that protects the lung from neutrophil elastase–mediated tissue damage. Mutations in SERPINA1 cause alpha-1-antitrypsin deficiency, one of the most common hereditary causes of respiratory disease, leading to early-onset emphysema and chronic obstructive pulmonary disease, as well as hepatic complications. Given the clinical significance of A1AT and its widespread use as a biomarker, there is a critical need for high-quality antibodies to ensure reliable detection and mechanistic insights. Here we systematically characterised eighteen commercial antibodies for western blot, immunoprecipitation, and flow cytometry using a standardized knockout validation approach in human Hep G2 cells, comparing readouts in a SERPINA1 knockout line with its isogenic parental control. This work is part of a broader collaborative initiative aimed at addressing antibody reproducibility by characterising commercial antibodies for human proteins and openly sharing the results with the community. While antibody use and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific experimental needs.

RNA-binding protein Fused-in Sarcoma (FUS) plays an essential role in various cellular processes. Mutations in the C-terminal domain region, where the nuclear localization signal (NLS) is located, causes the redistribution of FUS from the nucleus to the cytoplasm. In neurons, neurotoxic aggregates are formed as a result, contributing to neurogenerative diseases. Well-characterized anti-FUS antibodies would enable the reproducibility of FUS research, thereby benefiting the scientific community. In this study, we characterized ten FUS commercial antibodies for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. We identified many high-performing antibodies and encourage readers to use this report as a guide to select the most appropriate antibody for their specific needs.

Titanium and its alloys are used to make different blood-contacting medical devices such as stents, artificial heart valves, and catheters for cardiovascular diseases due to their superior biocompatibility. Thrombus formation begins on the surface of these devices as soon as they encounter blood. This leads to the formation of blood clots, which obstructs the flow of blood that leads to severe complications. Recent advancements in nanoscale fabrication and superhydrophobic surface modification techniques have demonstrated that these surfaces have antiadhesive properties and the ability to reduce thrombosis. In this study, the interaction of erythrocytes and whole blood clotting kinetics on superhydrophobic titanium nanostructured surfaces was investigated. These surfaces were characterized for their wettability (contact angle), surface morphology and topography (scanning electron microscopy (SEM)), and crystallinity (glancing angled X-Ray diffraction (GAXRD)). Erythrocyte morphology on different surfaces was characterized using SEM and overall cell viability was demonstrated through fluorescence microscopy. The hemocompatibility of these surfaces was characterized using commercially available assays: thrombin generation assay → thrombin generation, hemolytic assay → hemolysis, and complement convertase assay → complement activity. The results indicate that superhydrophobic titanium nanostructured surfaces had lower erythrocyte adhesion, less morphological changes in adhered cells, lower thrombin generation, lower complement activation, and were less cytotoxic compared to control surfaces. Thus, superhydrophobic titanium nanostructured surfaces may be a promising approach to prevent thrombosis for several blood-contacting medical devices.