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Data Note

A guide to selecting high-performing antibodies for Protein-glutamine gamma-glutamyltransferase 2 (TGM2) for use in western blot, immunoprecipitation and immunofluorescence

[version 1; peer review: 2 approved with reservations]
PUBLISHED 17 May 2024
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This article is included in the YCharOS (Antibody Characterization through Open Science) gateway.

Abstract

Protein-glutamine gamma-glutamyltransferase 2 (TGM2) is a Ca2+ dependent enzyme that catalyzes transglutaminase cross-linking modifications. TGM2 is involved in various diseases, either in a protective or contributory manner, making it a crucial protein to study and determine its therapeutic potential. Identifying high-performing TGM2 antibodies would facilitate these investigations. Here we have characterized seventeen TGM2 commercial antibodies for western blot and sixteen for immunoprecipitation, and immunofluorescence. The implemented standardized experimental protocol is based on comparing read-outs in knockout cell lines against their isogenic parental controls. This study is 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 the 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.

Keywords

Uniprot ID P21980, TGM2, , TGM, Protein-glutamine gamma-glutamyltransferase 2, antibody characterization, antibody validation, western blot, immunoprecipitation, immunofluorescence

Introduction

Protein-glutamine gamma glutamyltransferase 2 (TGM2) belongs to the transglutaminase family of Ca2+ dependent enzymes, regulating various cellular processes, including cell differentiation, growth and apoptosis.13 Encoded by TGM2 gene, TGM2 protein exhibits its function through Ca2+-dependent cross-linking of substrates, thereby modulating their activity.1 TGM2’s catalytic activity is dependent on guanine nucleotides and Ca2+ binding.4 Both GTP and/or GDP act as negative regulators of TGM2, inducing a conformational change upon binding, inhibiting its cross-linking activity (closed form). Conversely, Ca2+ binding prompts a conformational change to induce TGM2 activity (open form). The proteins activity is dependent on cellular location, remaining inactive intracellularly, and becoming activated upon secretion.59

Alteration and regulation of TGM2’s activity is associated with the pathogenesis of various diseases including cancer, neurodegeneration, fibrosis, inflammatory, autoimmune disorders and liver diseases.1013 Increased TGM2 mRNA transcripts, resulting in elevated transaminase enzymatic activity, have been associated with neurodegenerative mechanism observed in Parkinson’s disease, Alzheimer’s disease and Huntington’s disease.14,15 Given that α-synuclein serves as a common substrate for TGM2, elevated activity of TGM2 results in the formation of soluble aggregates as well as insoluble inclusions; distinctive features of Parkinson’s disease pathogenesis.1518 Regulating TGM2 activity using inhibitors could positively affect the human diseases in which TGM2 is implicated.19,20 Identifying high-quality antibodies would accelerate TGM2 research and its potential as a pharmacological target.

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.2123 Here, we evaluated the performance of seventeen commercially-available antibodies for TGM2 for use in western blot, and sixteen for immunoprecipitation and immunofluorescence, enabling biochemical and cellular assessment of TGM2 properties and function. The platform for antibody characterization used to carry out this study was approved by a committee of industry, academic research. It consists of first identifying appropriate human cell lines, development/contribution of equivalent knockout cell lines and finally following antibody characterization procedures on commonly used commercial antibodies. The standardized consensus antibody characterization protocols are openly available on Protocol Exchange, DOI: 10.21203/rs.3.pex-2607/v1.24

Results and discussion

Our standard protocol involves comparing readouts from wild-type (WT) and knockout (KO) cells.25,26 The first step is to identify a cell line(s) that expresses sufficient levels of a given protein to generate a measurable signal. To this end, we examined the DepMap transcriptomics database to identify all cell lines that express the target at levels greater than 2.5 log2 (transcripts per million “TPM” + 1), which we have found to be a suitable cut-off (Cancer Dependency Map Portal, RRID:SCR_017655). Commercially available A549 cells expressed the TGM2 transcript at RNA levels above the average range of cancer cells analyzed. Parental and TGM2 KO A549 cells were obtained from Abcam (Table 1).

Table 1. Summary of the cell lines used.

InstitutionCatalog numberRRID (Cellosaurus)Cell lineSpecies of originGenotype
Abcamab275463CVCL_0023A549Homo sapiens (Human)WT
Abcamab261876CVCL_B1I0A549Homo sapiens (Human)TGM2 KO

For western blot experiments, we resolved proteins from WT and TGM2 KO cell extracts and probed them side-by-side with all antibodies in parallel on lysate and culture medium (Figures 1 and 2).

e371354b-73e7-4a5a-a902-38d595ac4bd2_figure1.gif

Figure 1. TGM2 antibody screening by western blot on lysate.

Lysates of A549 (WT and TGM2 KO) were prepared and 40 μg of protein were processed for western blot with the indicated TGM2 antibodies. The Ponceau stained transfers of each blot are presented to show equal loading of WT and KO lysates and protein transfer efficiency from the acrylamide gels to the nitrocellulose membrane. Antibody dilutions were chosen according to the recommendations of the antibody supplier. Antibody dilution used: ab109121** at 1/1000, ab109200** at 1/10000, ab2386* at 1/500, ab310333** at 1/1000, ab421 at 1/500, ABCD_AI748** at 1/10, A21184** at 1/10000, ARP47471 at 1/500, ARP47472 at 1/500, AF4376 at 1/400, MAB4376* at 1/200, 3557** at 1/500, GTX111702 at 1/500, 15100-1-AP at 1/6000, 68006-1-Ig* at 1/10000, MA5-32819** at 1/500, MA5-12739* at 1/200. Predicted band size: 77 kDa. *Monoclonal antibody, **Recombinant antibody.

e371354b-73e7-4a5a-a902-38d595ac4bd2_figure2.gif

Figure 2. TGM2 antibody screening by western blot on culture medium.

A549 WT and TGM2 KO were cultured in serum free media, and 40 μg of protein from concentrated culture media were processed for western blot with the indicated TGM2 antibodies. The Ponceau stained transfers of each blot are shown. Antibody dilution used: ab109121** at 1/1000, ab109200** at 1/10000, ab2386* at 1/500, ab310333** at 1/1000, ab421 at 1/500, ABCD_AI748** at 1/10, A21184** at 1/10000, ARP47471 at 1/500, ARP47472 at 1/500, AF4376 at 1/400, MAB4376* at 1/200, 3557** at 1/500, GTX111702 at 1/500, 15100-1-AP at 1/6000, 68006-1-Ig* at 1/10000, MA5-32819** at 1/500, MA5-12739* at 1/200. Predicted band size: 77 kDa. *Monoclonal antibody, **Recombinant antibody.

As per our standard procedure, we next used the antibodies to immunoprecipitate TGM2 from A549 cell extracts. To evaluate the performance of each antibody, the TGM2 protein was detected in extracts, in each extract unbound to the antibody and corresponding immunoprecipitate (Figure 3). To detect TGM2, a western blot was performed with an antibody successful under the conditions tested in Figure 1.

e371354b-73e7-4a5a-a902-38d595ac4bd2_figure3.gif

Figure 3. TGM2 antibody screening by immunoprecipitation on lysate.

A549 lysates were prepared, and immunoprecipitation was performed using 2.0 μg of the indicated TGM2 antibodies pre-coupled to Dynabeads protein A or protein. Samples were washed and processed for western blot with the indicated TGM2 antibody. For western blot, A21184** was used at 1/10000. The Ponceau stained transfers of each blot are shown. SM=4% starting material; UB=4% unbound fraction; IP=immunoprecipitate; n/s=non-specific signal. *Monoclonal antibody, **Recombinant antibody.

For immunofluorescence, antibodies were screened using a mosaic strategy, as per our standard procedure. First, A549 WT and TGM2 KO were labelled with different fluorescent dyes in order to distinguish the two cell lines, and TGM2 antibodies were evaluated. Cells were imaged in the same field of view to reduce staining, imaging and image analysis bias (Figure 4). Quantification of immunofluorescence intensity in hundreds of WT and KO cells was performed for each antibody tested. The images presented in Figure 4 are representative of the results of this analysis.

e371354b-73e7-4a5a-a902-38d595ac4bd2_figure4.gif

Figure 4. TGM2 antibody screening by immunofluorescence.

A549 WT and TGM2 KO cells were labelled with a green or a deep-red fluorescent dye, respectively. WT and KO cells were mixed and plated to a 1:1 ratio in a 96-well plate with optically clear flat-bottom. Cells were stained with the indicated TGM2 antibodies and with the corresponding Alexa-fluor 555 coupled secondary antibody including DAPI. Acquisition of the blue (nucleus-DAPI), green (identification of WT cells), red (antibody staining) and deep-red (identification of KO cells) channels was performed. Representative images of the merged blue and red (grayscale) channels are shown. WT and KO cells are outlined with green and magenta dashed line, respectively. When the concentration was not indicated by the supplier, which was the case for all antibodies tested, except ab310333**, ABCD_AI748 and A21184**, we tested antibodies at using the dilutions listed below. At these concentrations, the signal from each antibody was in the range of detection of the microscope used. Antibody dilution used: ab109121** at 1/1000, ab109200** at 1/300, ab2386* at 1/1000, ab310333** at 1/500, ab421 at 1/1000, ABCD_AI748** at 1/1000, A21184** at 1/1000, ARP47471 at 1/500, ARP47472 at 1/250, AF4376 at 1/100, MAB4376* at 1/100, 3557** at 1/500, GTX111702 at 1/1000, 15100-1-AP at 1/300, 68006-1-Ig* at 1/500, MA5-32819** at 1/1000. Bars = 10 μm. *Monoclonal antibody, **Recombinant antibody.

In conclusion, we have screened seventeen TGM2 commercial antibodies by western blot, and sixteen by immunoprecipitation, and immunofluorescence, comparing the signal produced by the antibodies in human A549 WT and TGM2 KO cells. Several high-quality antibodies that successfully detect TGM2 under our standardized experimental protocol can be identified. Researchers who wish to study TGM2 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.

In our effort to address the antibody reliability and reproducibility challenges in scientific research, the authors recommend the antibodies that demonstrated to be underperforming under our standard procedure be removed from the commercial antibody market. Following the release of the antibody characterization, ab421 was removed from the manufacturer’s antibody catalog.

The authors do not engage in result analysis or offer explicit antibody recommendations. A limitation of this study is the use of universal protocols - any conclusions remain relevant within the confines of the experimental setup and cell line used in this study. 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.27

The underlying data for this study can be found on Zenodo, an open-access repository for which YCharOS has its own collection of antibody characterization reports.28,29

Methods

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 Protocol Exchange, a repository dedicated to openly sharing scientific research protocols, DOI: 10.21203/rs.3.pex-2607/v1.24

Antibodies and cell line used

Cell lines used and primary antibodies tested in this study are listed in Table 1 and 2, respectively. To ensure that the cell lines and antibodies are cited properly and can be easily identified, we have included their corresponding Research Resource Identifiers, or RRID.30,31

Table 2. Summary of the TGM2 antibodies tested.

CompanyCatalog numberLot numberRRID (Antibody Registry)ClonalityClone IDHostConcentration (μg/μL)Vendors recommended applications
Abcamab109121**1058833-3AB_10861115Recombinant-monoEPR2956rabbit2.79Wb
Abcamab109200**1044092-1AB_10860177Recombinant-monoEP2957rabbit0.30Wb
Abcamab2386*1051063-6AB_2287299MonoclonalCUB 7402mousen/aWb, IF
Abcamab310333**1056093-5AB_3076417Recombinant-monoEPR28142-86rabbit0.50Wb, IF
Abcamab4211034725-7AB_304372Polyclonal-rabbitn/aWb, IF
ABCDABCD_AI748**10/27/2023AB_3076341Recombinant-mono679-14-E06rabbit0.12Others
AbclonalA21184**3522042510AB_3083448Recombinant-monoARC52843rabbit1.30Wb, IF
Aviva Systems BiologyARP47471QC18320-43546AB_1107120Polyclonal-rabbit0.50Wb
Aviva Systems BiologyARP47472QC16720AB_1088480Polyclonal-rabbit0.50Wb
R&D Systems (a Bio-Techne brand)AF4376CFGU0119031AB_10890213Polyclonal-sheep0.20Wb
R&D Systems (a Bio-Techne brand)MAB4376*CFNO0119031AB_10971763Monoclonal716620mouse0.20Wb
Cell Signaling Technology3557**3AB_2202883Recombinant-monoD11A6rabbit0.02Wb
GeneTexGTX11170244524AB_1952227Polyclonal-rabbit1.05Wb, IF
Proteintech15100-1-AP00081307AB_2202885Polyclonal-rabbit0.60Wb, IP, IF
Proteintech68006-1-Ig*10023724AB_2918753Monoclonal2D4C11mouse1.00Wb, IF
Thermo Fisher ScientificMA5-32819**YJ4089240AB_2810095Recombinant-monoJU30-02rabbit1.00Wb
Thermo Fisher ScientificMA5-12739*ZA4176225AB_10985077MonoclonalCUB 7402mouse0.20Wb, IP, IF

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Ayoubi R, Fotouhi M, Alende C et al. A guide to selecting high-performing antibodies for Protein-glutamine gamma-glutamyltransferase 2 (TGM2) for use in western blot, immunoprecipitation and immunofluorescence [version 1; peer review: 2 approved with reservations]. F1000Research 2024, 13:481 (https://doi.org/10.12688/f1000research.150684.1)
NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article.
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ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions
Version 1
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PUBLISHED 17 May 2024
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Reviewer Report 15 Jul 2024
Nicoletta Bianchi, University of Ferrara, Ferrara, Italy 
Approved with Reservations
VIEWS 7
Dear Editorial Team,
I find this work extremely interesting. The authors tested the efficacy and specificity of commercial antibodies that can be used to study TGM2.
Unfortunately, only one cell line and its KO were used, this is ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Bianchi N. Reviewer Report For: A guide to selecting high-performing antibodies for Protein-glutamine gamma-glutamyltransferase 2 (TGM2) for use in western blot, immunoprecipitation and immunofluorescence [version 1; peer review: 2 approved with reservations]. F1000Research 2024, 13:481 (https://doi.org/10.5256/f1000research.165276.r293962)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Author Response 30 Jul 2024
    Kathleen Southern, Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, H3A 2B4, Canada
    30 Jul 2024
    Author Response
    Dear Nicoletta Bianchi,

    Thank you for reviewing the article “A guide to selecting high-performing antibodies for Protein-glutamine gamma-glutamyltransferase 2 (TGM2) for use in western blot, immunoprecipitation and immunofluorescence” recently ... Continue reading
COMMENTS ON THIS REPORT
  • Author Response 30 Jul 2024
    Kathleen Southern, Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, H3A 2B4, Canada
    30 Jul 2024
    Author Response
    Dear Nicoletta Bianchi,

    Thank you for reviewing the article “A guide to selecting high-performing antibodies for Protein-glutamine gamma-glutamyltransferase 2 (TGM2) for use in western blot, immunoprecipitation and immunofluorescence” recently ... Continue reading
Views
11
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Reviewer Report 03 Jul 2024
Michael A Rieger, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Goethe University, Cardio-Pulmonary-Institute, Frankfurt Cancer Institute, Frankfurt am Main, Germany;  Hospital of the Goethe University Frankfurt Department of Medicine II Hematology Oncology Rheumatology Infectious Diseases HIV Therapy, Frankfurt, Hesse, Germany 
Approved with Reservations
VIEWS 11
The authors of this study have tested 17 different commercially available antibodies against human Transglutaminase 2 (TGM2) on their specificity and feasibility for different biochemical and cell biological applications. They rigorously tested the antibodies for their suitability in Western blotting, ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Rieger MA. Reviewer Report For: A guide to selecting high-performing antibodies for Protein-glutamine gamma-glutamyltransferase 2 (TGM2) for use in western blot, immunoprecipitation and immunofluorescence [version 1; peer review: 2 approved with reservations]. F1000Research 2024, 13:481 (https://doi.org/10.5256/f1000research.165276.r289998)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Author Response 18 Jul 2024
    Kathleen Southern, Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, H3A 2B4, Canada
    18 Jul 2024
    Author Response
    Dear Michael A. Rieger,
    The authors would like extend our gratitude for having taken the time to review this article and provide concrete feedback. Please see our response to your ... Continue reading
COMMENTS ON THIS REPORT
  • Author Response 18 Jul 2024
    Kathleen Southern, Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, H3A 2B4, Canada
    18 Jul 2024
    Author Response
    Dear Michael A. Rieger,
    The authors would like extend our gratitude for having taken the time to review this article and provide concrete feedback. Please see our response to your ... Continue reading

Comments on this article Comments (0)

Version 2
VERSION 2 PUBLISHED 17 May 2024
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Alongside their report, reviewers assign a status to the article:
Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
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