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Revised

A guide to selecting high-performing antibodies for human Midkine for use in Western blot and immunoprecipitation

[version 4; peer review: 2 approved]
Previously titled: The identification of high-performing antibodies for Midkine for use in Western blot and immunoprecipitation
PUBLISHED 01 Aug 2024
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This article is included in the Cell & Molecular Biology gateway.

This article is included in the YCharOS (Antibody Characterization through Open Science) gateway.

Abstract

Midkine is a secreted protein that acts as a growth factor or cytokine involved in cell survival and inflammatory processes. It accumulates in amyloid plaques, which are hallmarks of Alzheimer’s Disease (AD). The reproducibility of Midkine research would be enhanced if the community had access to well-characterized anti-Midkine antibodies. In this study, we characterized 8 commercial Midkine antibodies for Western blot and immunoprecipitation, using a standardized experimental protocol based on comparing read-outs in a knockout cell line and isogenic parental control. These studies are part of a larger, collaborative initiative seeking to address the antibody reproducibility issue 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.

Keywords

Uniprot #P21741, MDK, Midkine, antibody validation, antibody characterization, Western blot, immunoprecipitation

Revised Amendments from Version 3

In our efforts to ensure reproducibility, version 4 includes amendments to the Methods and Figure 1 legend to provide detailed information on how the HAP1 WT and MDK KO cells were prepared prior to Western blot evaluation.

See the authors' detailed response to the review by Jean-Pierre Bellier
See the authors' detailed response to the review by Jens-Ulrich Rahfeld

Introduction

The neurotrophic and developmental factor Midkine is a secreted heparin-binding cytokine.1 It mediates its diverse physiological functions by binding to cell-surface proteoglycan receptors via their chondroitin sulfate groups, thereby regulating cell proliferation, migration and differentiation.24

Midkine is involved in numerous processes that promote cell growth, and may contribute to the pathogenesis of inflammatory diseases.1,4 Proteomic analyses have found that Midkine is highly enriched in amyloid-beta plaques, indicating its potential as a biomarker and/or therapeutic target for Alzheimer’s Disease (AD).57 Mechanistic studies would be greatly facilitated by the availability of high-quality antibodies for Midkine.

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.810 Here, we compared the performance of a range of commercially available antibodies for Midkine use in Western Blot and immunoprecipitation. This article serves as a valuable guide to help researchers select high-quality antibodies for their specific needs, facilitating the biochemical and cellular assessment of Midkine properties and function.

Results and discussion

Our standard protocol involves comparing readouts from wild-type and knockout cells.1113 The first step is to identify a human 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 human HAP1 cells expressed the Midkine transcript at RNA levels above the average range of cancer cells analyzed.14 Parental and MDK knockout human HAP1 cells were obtained from Horizon Discovery (Table 1).

Table 1. Summary of the cell lines used.

InstitutionCatalog numberRRID (Cellosaurus)Cell lineGenotype
Horizon DiscoveryC631CVCL_Y019HAP1WT
Horizon DiscoveryHZGHC007906c008CVCL_C6Y2HAP1MDK KO

Midkine is predicted to be a secreted protein. Accordingly, we collected concentrated culture media from both wild-type and MDK KO cells and used the conditioned media to probe the performance of the antibodies (Table 2) side-by-side by Western blot and immunoprecipitation. The profiles of the tested antibodies are shown in Figures 1 and 2.

Table 2. Summary of the Midkine antibodies tested.

CompanyCatalog numberLot numberRRID (Antibody Registry)ClonalityClone IDHostConcentration (μg/μl)Initial vendors recommended applications
GeneTexGTX10843939855AB_1950903polyclonal-rabbit0.33Wb
GeneTexGTX116089a40597AB_11165850polyclonal-rabbit1.00Wb
Bio-TechneAF-258-PBWE0519091AB_2143400polyclonal-goat0.20Wb
Bio-TechneMAB2582**CMHR0219071AB_2893288recombinant-mono1011522mouse0.50IF
Bio-TechneMAB2583*CMLT0120031AB_2893289monoclonal1011622mouse0.50-
Bio-TechneNBP2-66948**aHN0907AB_2893290recombinant-monoJF096-5rabbit1.00Wb, IP
ThermoMA5-32538**WD3265256AB_2809815recombinant-monoJF096-5rabbit1.00Wb
Abcamab52637**GR3315059-2AB_880698recombinant-monoEP1143Yrabbit0.10Wb, IP, IF

* Monoclonal antibody.

** Recombinant antibody.

a Antibodies that have been discontinued subsequent to the release of this study.

c477576a-b14c-4aba-8bc1-073353e8047f_figure1.gif

Figure 1. Midkine antibody screening by Western blot on culture media.

A) Schematic of the protocol used to concentrate the culture media. B) Concentrated media of HAP1 (WT and MDK KO) were prepared, and ~30 μg of protein was processed for Western blot with the indicated Midkine 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. An exceptions was given to antibody GTX116089, which was titrated to 1/1000, as the signal was too weak when following the supplier’s recommendations. When suppliers did not recommend dilutions, we tested the antibodies at 1/200. Antibody dilution used: GTX108439 at 1/1000; GTX116089 at 1/100; AF-258-PB at 1/100; MAB2582** at 1/200; MAB2583* at 1/200; NBP2-66948** at 1/500; MA5-32538** at 1/500; ab52637** at 1/500. Predicted band size: 15 kDa. *Monoclonal antibody, **Recombinant antibody.

c477576a-b14c-4aba-8bc1-073353e8047f_figure2.gif

Figure 2. Midkine antibody screening by immunoprecipitation on culture media.

Concentrated culture media were prepared as in 1A). Immunoprecipitation was performed using 1.0 μg of the indicated Midkine antibodies pre-coupled to either protein A or protein G magnetic beads. Samples were washed and processed for Western blot with the indicated Midkine antibody. For Western blot, AF-258-PB was used at 1/500, NBP2-66948** at 1/500, MA5-32538** at 1/200 and ab52637** at 1/200. The Ponceau stained transfers of each blot are shown. SM = 10% starting material; UB = 10% unbound fraction; IP = immunoprecipitate; HC = antibody heavy chain. *Monoclonal antibody, **Recombinant antibody.

In conclusion, we screened eight Midkine commercial antibodies by Western blot and immunoprecipitation. Several high-quality antibodies that successfully detect Midkine under our standardized experimental conditions can be identified. 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. However, 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.

Antibodies GTX 116089 and NBP2-66948 were removed from the commercial antibody market and are no longer available. Antibody MA5-32538 has the same clone ID as NBP2-66948, and is still available on the market as an alternative.

Methods

Antibodies

All Midkine antibodies are listed in Table 2. Peroxidase-conjugated goat anti-rabbit, anti-mouse and donkey anti-goat antibodies are from Thermo Fisher Scientific (cat. number 65-6120, 62-6520 and A15999, respectively).

Cell culture

Cells were cultured in DMEM high-glucose (GE Healthcare cat. number SH30081.01) containing 10% fetal bovine serum (Wisent, cat. number 080450), 2 mM L-glutamate (Wisent cat. number 609065, 100 IU penicillin and 100 μg/ml streptomycin (Wisent cat. number 450201). Cells were starved in DMEM high glucose containing L-glutamate and penicillin/streptomycin.

Antibody screening by Western blot on culture medium

HAP1 cells (WT and MDK KO) were grown in 20 ml complete medium to 80% confluence in 150 mm dishes. At 80% confluency, HAP1 cells were at a density of ~1.0 × 106/ml (~20.0 × 106/20 ml). To prepare for protein extraction, cells were washed 3× with PBS and starved for ~18 hrs. Culture media were collected and centrifuged for 10 min at 500 × g to eliminate cells and larger contaminants, then for 10 min at 4500 × g to eliminate smaller contaminants.

Culture media were initially concentrated using Amicon Ultra-15 Centrifugal Filter Units (MilliporeSigma cat. number UFC9010) by centrifuging at 4000 × g for 15 min. The resulting 500 μl of concentrated media from each filter unit were centrifuged again at 4000 × g for 15 min using Amicon Ultra- 0.5 Centrifugal Filter Units (MilliporeSigma cat. number UFC5010) to 200 μl. The final protein concentration was 0.3 mg/ml and 100 μl (30 μg) of media were used for each blot.

Western blots were performed as described in our standard operating procedure.13,15 A Bradford reagent assay was performed to determine the protein concentration of the culture medium. The concentration was then adjusted to ensure equal amounts of protein were loaded in each gel. Western blots were performed with large 10-20% gradient polyacrylamide gels, loaded with 30 μg of protein in each lane and then transferred on nitrocellulose membranes. Proteins on the blots were visualized with Ponceau staining which is scanned to show together with individual Western blot. Blots were blocked with 5% milk for 1 hr, and antibodies were incubated overnight at 4°C with 5% bovine serum albumin in TBS with 0.1% Tween 20 (TBST). Following three washes with TBST, the peroxidase conjugated secondary antibody was incubated at a dilution of ~0.2 μg/ml in TBST with 5% milk for 1 hr at room temperature followed by three more washes with TBST. Membranes were incubated with ECL from Pierce (cat. number 32106) prior to detection with HyBlot CL autoradiography films from Denville (cat. number 1159T41).

Antibody screening by immunoprecipitation on culture medium

Immunoprecipitation was performed as described in our standard operating procedure.13,16 Antibody-bead conjugates were prepared by adding 1.0 μg of antibody to 500 μl of Pierce IP Lysis from Thermo Fisher Scientific (cat. number 87788) in a microcentrifuge tube, together with 30 μl of Dynabeads protein A - (for rabbit antibodies) or protein G - (for mouse and goat antibodies) from Thermo Fisher Scientific (cat. number 10002D and 10004D, respectively). Tubes were rocked overnight at 4°C followed by two washes with the Pierce IP Buffer to remove unbound antibodies. Pierce IP Lysis Buffer (25 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% NP-40 and 5% glycerol) was supplemented with 1× Halt Protease and Phosphatase Inhibitor Cocktail from Thermo Fisher Scientific (cat. number 78446).

Starved HAP1 WT culture media were concentrated as described above. The concentrated culture media were diluted in Pierce IP Lysis Buffer, and 1ml aliquots at 0.3 mg/ml of lysate were incubated with an antibody-bead conjugate for ~2 hrs at 4°C. The unbound fractions were collected, and beads were subsequently washed three times with 1.0 ml of IP Buffer and processed for SDS-PAGE and immunoblot on 10-20% polyacrylamide gels. Prot-A: HRP was used as a secondary detection system (MilliporeSigma, cat. number P8651) at a dilution of 0.4 μg/ml for an experiment where a rabbit antibody was used for both immunoprecipitation and its corresponding Western Blot.

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Ayoubi R, Southern K, Laflamme C and NeuroSGC/YCharOS Collaborative Group. A guide to selecting high-performing antibodies for human Midkine for use in Western blot and immunoprecipitation [version 4; peer review: 2 approved]. F1000Research 2024, 12:148 (https://doi.org/10.12688/f1000research.130587.4)
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 3
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PUBLISHED 23 Jul 2024
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Reviewer Report 31 Jul 2024
Jens-Ulrich Rahfeld, Fraunhofer Institute for Cell Therapy and Immunology, Department Molecular Drug Biochemistry and Therapy, Weinbergweg 22, 06120, Halle, Germany 
Approved
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Okay, no further comments! 
... Continue reading
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Rahfeld JU. Reviewer Report For: A guide to selecting high-performing antibodies for human Midkine for use in Western blot and immunoprecipitation [version 4; peer review: 2 approved]. F1000Research 2024, 12:148 (https://doi.org/10.5256/f1000research.169429.r306188)
NOTE: 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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Reviewer Report 13 May 2024
Jens-Ulrich Rahfeld, Fraunhofer Institute for Cell Therapy and Immunology, Department Molecular Drug Biochemistry and Therapy, Weinbergweg 22, 06120, Halle, Germany 
Approved with Reservations
VIEWS 20
The results of the publication are very helpful for the selection of suitable Midkine antibodies. 

However, there are ambiguities in the experimental and methodological part: 
The protocol mentions that the cell culture supernatants were obtained from ... Continue reading
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HOW TO CITE THIS REPORT
Rahfeld JU. Reviewer Report For: A guide to selecting high-performing antibodies for human Midkine for use in Western blot and immunoprecipitation [version 4; peer review: 2 approved]. F1000Research 2024, 12:148 (https://doi.org/10.5256/f1000research.160165.r269176)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Author Response 23 Jul 2024
    Kathleen Southern, Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Canada
    23 Jul 2024
    Author Response
    Thank you to Dr. Jens-Ulrich Rahfeld for your comprehensive review of this article which presents as a guide to selecting high-performing antibodies for Midkine to progress research of this target ... Continue reading
  • Author Response 01 Aug 2024
    Kathleen Southern, Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Canada
    01 Aug 2024
    Author Response
    The authors would like to clarify our response to Jens-Ulrich Rahfeld in regards to  cell density and amount of protein used. 

    HAP1 cells (WT and MDK KO) were grown in ... Continue reading
COMMENTS ON THIS REPORT
  • Author Response 23 Jul 2024
    Kathleen Southern, Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Canada
    23 Jul 2024
    Author Response
    Thank you to Dr. Jens-Ulrich Rahfeld for your comprehensive review of this article which presents as a guide to selecting high-performing antibodies for Midkine to progress research of this target ... Continue reading
  • Author Response 01 Aug 2024
    Kathleen Southern, Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Canada
    01 Aug 2024
    Author Response
    The authors would like to clarify our response to Jens-Ulrich Rahfeld in regards to  cell density and amount of protein used. 

    HAP1 cells (WT and MDK KO) were grown in ... Continue reading
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Reviewer Report 18 Jan 2024
Jean-Pierre Bellier, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA 
Approved
VIEWS 8
I have ... Continue reading
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CITE
HOW TO CITE THIS REPORT
Bellier JP. Reviewer Report For: A guide to selecting high-performing antibodies for human Midkine for use in Western blot and immunoprecipitation [version 4; peer review: 2 approved]. F1000Research 2024, 12:148 (https://doi.org/10.5256/f1000research.160165.r231070)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
Version 1
VERSION 1
PUBLISHED 09 Feb 2023
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Reviewer Report 29 Nov 2023
Jean-Pierre Bellier, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA 
Approved with Reservations
VIEWS 21
In this manuscript, Ayoubi et al. investigated the specificity of eight commercially available antibodies directed against the human Midkine protein. Midkine is a secreted pleiotropic protein involved in cell proliferation, survival, and the regulation of inflammation. It is often associated ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Bellier JP. Reviewer Report For: A guide to selecting high-performing antibodies for human Midkine for use in Western blot and immunoprecipitation [version 4; peer review: 2 approved]. F1000Research 2024, 12:148 (https://doi.org/10.5256/f1000research.143357.r208220)
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 Jan 2024
    Kathleen Southern, Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Canada
    18 Jan 2024
    Author Response
    Dear Jean-Pierre Bellier,

    Thank you for your feedback. We have submitted a modified version of this manuscript, with your requested modifications included. We trust that the refinements made meet ... Continue reading
COMMENTS ON THIS REPORT
  • Author Response 18 Jan 2024
    Kathleen Southern, Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Canada
    18 Jan 2024
    Author Response
    Dear Jean-Pierre Bellier,

    Thank you for your feedback. We have submitted a modified version of this manuscript, with your requested modifications included. We trust that the refinements made meet ... Continue reading

Comments on this article Comments (0)

Version 4
VERSION 4 PUBLISHED 09 Feb 2023
Comment
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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