ARID1A is a member of the ARID family of DNA-binding proteins. ¹ As a subunit of the SWI/SNF complex, ² ARID1A is essential for remodelling chromatin, thereby controlling its accessibility to RNA polymerase II and transcriptional regulators. ³ This protein contains two functional domains: the ARID domain for DNA binding and the BAF250_C domain for interactions with other proteins including subunits of the chromatin remodeling complexes. ⁴ ARID1A functions at DNA damage sites by controlling the cellular response. ⁵ It also helps repress cell cycle-specific genes, leading to cell cycle arrest in differentiating cells and during DNA damage repair. ^{4, 6} ARID1A acts as a tumor suppressor, and its downregulation or mutation is associated with poor prognosis in many types of cancer. ⁷

This research is part of a broader collaborative initiative in which academics, funders and commercial antibody manufacturers are working together to address antibody reproducibility issues by characterizing commercial antibodies for human proteins using standardized protocols, and openly sharing the data. ⁸ It consists of identifying human cell lines with adequate target protein expression and the development/contribution of equivalent knockout (KO) cell lines, followed by antibody characterization procedures using most commercially available renewable antibodies against the corresponding protein. ⁸ Here we characterized fourteen commercial ARID1A antibodies, selected and donated by participant antibody manufacturers, for use in western blot, immunoprecipitation, and immunofluorescence (also referred to as immunocytochemistry), enabling biochemical and cellular assessment of ARID1A properties and function.

The authors do not engage in result analysis or offer explicit antibody recommendations. Our primary aim is to deliver top-tier data to the scientific community, grounded in Open Science principles. This empowers experts to interpret the characterization data independently, enabling them to make informed choices regarding the most suitable antibodies for their specific experimental needs. Guidelines on how to interpret antibody characterization data found in this study are featured on the YCharOS gateway ⁹ and in Table 4 of this data note. ⁸

Our standard protocol involves comparing readouts from wild type (WT) and KO cells. ^{10, 11} The first step was to identify a cell line(s) that expresses sufficient levels of a given protein to generate a measurable signal using antibodies. To this end, we examined the DepMap (Cancer Dependency Map Portal, RRID: SCR_017655) transcriptomics database to identify all cell lines that express the target at levels greater than 2.5 log ₂ (transcripts per million “TPM” + 1), which we have found to be a suitable cut-off. ¹² The HAP1 expresses the ARID1A transcript at 4.7 log ₂ TPM + 1, and an ARID1A KO HAP1 cell line was obtained from Horizon Discovery ( Table 1). Moreover, as seen on DepMap, the HAP1 does not carry mutations in the ARID1A that could affect antibody–epitope binding.

To screen all fourteen antibodies by western blot, WT and ARID1A KO protein lysates were ran on SDS-PAGE, transferred onto nitrocellulose membranes, and then probed with the fourteen ARID1A antibodies in parallel ( Figure 1).

We then assessed the capability of all fourteen antibodies to capture ARID1A from HAP1 protein extracts using immunoprecipitation techniques, followed by western blot analysis. For the immunoblot step, a specific ARID1A antibody identified previously (refer to Figure 1) was selected. Equal amounts of the starting material (SM) and the unbound fractions (UB), as well as the whole immunoprecipitate (IP) eluates were separated by SDS-PAGE ( Figure 2).

For immunofluorescence, fourteen antibodies were screened using a mosaic strategy. First, HAP1 WT and ARID1A KO cells were labelled with different fluorescent dyes in order to distinguish the two cell lines, and the ARID1A antibodies were evaluated. Both WT and KO lines imaged in the same field of view to reduce staining, imaging and image analysis bias ( Figure 3). Quantification of immunofluorescence intensity in hundreds of WT and KO cells was performed for each antibody tested, and the images presented in Figure 3 are representative of this analysis. ⁸

In conclusion, we have screened fourteen ARID1A commercial antibodies by western blot, immunoprecipitation, and immunofluorescence by comparing the signal produced by the antibodies in human HAP1 WT and ARID1A KO cells. To assist users in interpreting antibody performanyce, Table 4 outlines various scenarios in which antibodies may perform in all three applications. ¹² High-quality and renewable antibodies that successfully detect ARID1A were identified in all applications. Researchers who wish to study ARID1A in a different species are encouraged to select high-quality antibodies, based on the results of this study, and investigate the predicted species reactivity of the manufacturer before extending their research.

Inherent limitations are associated with the antibody characterization platform used in this study. Firstly, the YCharOS project focuses on renewable (recombinant and monoclonal) antibodies and does not test all commercially available ARID1A antibodies. YCharOS partners provide approximately 80% of all renewable antibodies, but some top-cited polyclonal antibodies may not be available through these partners. We encourage readers to consult vendor documentation to identify the specific antigen each antibody is raised against, where such information is available.

Secondly, the YCharOS effort employs a non-biased approach that is agnostic to the protein for which antibodies have been characterized. The aim is to provide objective data on antibody performance without preconceived notions about how antibodies should perform or the molecular weight that should be observed in western blot. As the authors are not experts in ARID1A, only a brief overview of the protein’s function and its relevance in disease is provided. ARID1A experts are invited to analyze and interpret observed banding patterns in western blots and subcellular localization in immunofluorescence.

Thirdly, YCharOS experiments are not performed in replicates primarily due to the use of multiple antibodies targeting various epitopes. Once a specific antibody is identified, it validates the protein expression of the intended target in the selected cell line, confirms the lack of protein expression in the KO cell line and supports conclusions regarding the specificity of the other antibodies. All experiments are performed using master mixes, and meticulous attention is paid to sample preparation and experimental execution. In IF, the use of two different concentrations serves to evaluate antibody specificity and can aid in assessing assay reliability. In instances where antibodies yield no signal, a repeat experiment is conducted following titration. Additionally, our independent data is performed subsequently to the antibody manufacturers internal validation process, therefore making our characterization process a repeat.

Lastly, as comprehensive and standardized procedures are respected, any conclusions remain confined to the experimental conditions and cell line used for this study. The use of a single cell type for evaluating antibody performance poses as a limitation, as factors such as target protein abundance significantly impact results. Additionally, the use of cancer cell lines containing gene mutations poses a potential challenge, as these mutations may be within the epitope coding sequence or other regions of the gene responsible for the intended target. Such alterations can impact the binding affinity of antibodies. This represents an inherent limitation of any approach that employs cancer cell lines.

The standardized protocols used to carry out this KO cell line-based antibody characterization platform was established and approved by a collaborative group of academics, industry researchers and antibody manufacturers. The detailed materials and step-by-step protocols used to characterize antibodies in western blot, immunoprecipitation and immunofluorescence are openly available on Protocols.io ( protocols.io/view/a-consensus-platform-for-antibody-characterization ). ⁸ Brief descriptions of the experimental setup used to carry out this study can be found below.