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A guide to selecting high-performing antibodies for PKN2 (UniProt ID: Q16513) for use in western blot and flow cytometry [version 1; peer review: awaiting peer review]
Дата публикации: 06-08-2026 10:41:20
Idiopathic pulmonary fibrosis is a chronic, progressive interstitial lung disease characterised by fibrotic remodelling of the distal alveolar interstitium and irreversible loss of lung function. Rapid decline in forced vital capacity has been significantly associated with rs115982800, a single nucleotide polymorphism in PKN2. Identifying high-quality research antibodies is therefore essential to enable robust investigation of PKN2 biology and its translational potential. Here, we systematically evaluated eleven commercial antibodies for western blot and flow cytometry using a standardised knockout-validation approach in human HCT 116 cells, comparing readouts in PKN2 knockout lines with isogenic parental controls. These experiments are part of a broader collaborative initiative addressing antibody reproducibility by characterising commercial antibodies for human proteins and making the results openly available. While antibody performance and protocol conditions may vary between laboratories, this study provides a resource to guide selection of the most suitable reagents for investigations of PKN2 in health and disease.
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Biddle M, Cooper J, Jones C et al. A guide to selecting high-performing antibodies for PKN2 (UniProt ID: Q16513) for use in western blot and flow cytometry [version 1; peer review: awaiting peer review]. F1000Research 2026, 15:1311 (https://doi.org/10.12688/f1000research.185471.1)
Data Note
[version 1; peer review: awaiting peer review]
https://orcid.org/0000-0002-9853-8815
1, Jemma Cooperhttps://orcid.org/0009-0007-8915-379X
1, Carolyn Jones1, Katie Dixonhttps://orcid.org/0009-0007-1014-0866
1, Harvinder Virkhttps://orcid.org/0000-0002-9739-9593
1https://orcid.org/0000-0002-9853-8815
1, Jemma Cooperhttps://orcid.org/0009-0007-8915-379X
1, [...] Carolyn Jones1, Katie Dixonhttps://orcid.org/0009-0007-1014-0866
1, Harvinder Virkhttps://orcid.org/0000-0002-9739-9593
11 University of Leicester College of Life Sciences, Leicester, England, UK
Michael Biddle
Roles: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Project Administration, Resources, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing
Jemma Cooper
Roles: Data Curation, Formal Analysis, Investigation, Methodology, Validation, Writing – Review & Editing
Carolyn Jones
Roles: Investigation, Methodology, Project Administration, Writing – Review & Editing
Katie Dixon
Roles: Data Curation, Writing – Original Draft Preparation, Writing – Review & Editing
Harvinder Virk
Roles: Conceptualization, Funding Acquisition, Project Administration, Resources, Supervision
OPEN PEER REVIEW
REVIEWER STATUS AWAITING PEER REVIEW
Abstract
Idiopathic pulmonary fibrosis is a chronic, progressive interstitial lung disease characterised by fibrotic remodelling of the distal alveolar interstitium and irreversible loss of lung function. Rapid decline in forced vital capacity has been significantly associated with rs115982800, a single nucleotide polymorphism in PKN2. Identifying high-quality research antibodies is therefore essential to enable robust investigation of PKN2 biology and its translational potential. Here, we systematically evaluated eleven commercial antibodies for western blot and flow cytometry using a standardised knockout-validation approach in human HCT 116 cells, comparing readouts in PKN2 knockout lines with isogenic parental controls. These experiments are part of a broader collaborative initiative addressing antibody reproducibility by characterising commercial antibodies for human proteins and making the results openly available. While antibody performance and protocol conditions may vary between laboratories, this study provides a resource to guide selection of the most suitable reagents for investigations of PKN2 in health and disease.
Keywords
Q16513, idiopathic pulmonary fibrosis, IPF, PKN2, Serine/threonine-protein kinase N2, antibody validation, western blot, flow cytometry.
Corresponding authors: Michael Biddle, Harvinder Virk Competing interests: HV and MB have received funding for a research studentship from Abcam Ltd, and contributions in kind for manufacturers that contribute to the YCharOS Inc. consortium. The remaining authors declare no competing interests. These relationships did not influence the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Grant information: This work was supported by a grant from the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs) and MRC (NC3Rs Ref: NC/NAM0019/1, MRC UKRI076) alongside support from the Institute for Precision Health, University of Leicester.
The funders have no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Copyright: © 2026 Biddle M et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite: Biddle M, Cooper J, Jones C et al. A guide to selecting high-performing antibodies for PKN2 (UniProt ID: Q16513) for use in western blot and flow cytometry [version 1; peer review: awaiting peer review]. F1000Research 2026, 15:1311 (https://doi.org/10.12688/f1000research.185471.1) First published: 06 Aug 2026, 15:1311 (https://doi.org/10.12688/f1000research.185471.1) Latest published: 06 Aug 2026, 15:1311 (https://doi.org/10.12688/f1000research.185471.1)
Introduction
Idiopathic pulmonary fibrosis is a chronic and progressive interstitial lung disease characterised by fibrosis of the distal alveolar interstitium, leading to progressive decline in lung function. Approved therapeutics such as pirfenidone and nintedanib reduce the rate of lung function decline; however, they do not halt or reverse established fibrosis.1 As such, tailored therapies targeting disease pathogenesis and progression through precision medicine approaches may improve treatment outcomes and support the identification of patients with increased disease susceptibility. One approach to identify candidate therapeutic targets is the investigation of disease-associated single nucleotide polymorphisms (SNPs), such as variants in PKN2 (rs115982800), which have been associated with rapid decline in forced vital capacity.2 The encoded protein, Serine/threonine-protein kinase N2 (PKN2), is a downstream effector of Rho GTPases, mediating actin cytoskeletal organisation.3 However, detailed investigation of PKN2 biology and its potential role in disease requires well-validated research tools, including reliable antibodies for protein detection and characterisation.
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 characterising commercial antibodies for human proteins using standardised protocols4 and openly sharing the data.5 Here we evaluated the performance of eleven commercial antibodies for PKN2 for use in western blot and flow cytometry, enabling biochemical and cellular assessment of PKN2 properties and function. The platform for antibody characterisation used to carry out this study was endorsed by a committee of industry and academic representatives. 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 characterisation procedures using most commercially available renewable antibodies against the corresponding protein. The standardised consensus antibody characterisation protocols are openly available on Protocols.io (DOI: dx.doi.org/10.21203/rs.3.pex-2607/v1).
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 characterisation data independently, enabling them to make informed choices regarding the most suitable antibodies for their specific experimental needs. Guidelines on how to interpret the antibody characterisation data found in this study are featured on the YCharOS gateway.6
Results and discussion
Our standard protocol involves comparing readouts from WT (wild type) and KO cells.7–9 The first step is 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 transcriptomics database to identify all cell lines that express the target at levels greater than 2.5 log2 (transcript per million “TPM” + 1), which we have found to be a suitable cut-off (Cancer Dependency Map Portal, RRID:SCR_017655). The HCT 116 cell line expresses the PKN2 transcript at 5.1 log2 TPM + 1, and a PKN2 KO HCT 116 cell line was obtained from Abcam ( Table 1).
Table 1. Summary of the cell lines used.InstitutionCatalogue numberRRID (Cellosaurus)Cell line GenotypeAbcamab255451CVCL_0291HCT 116WTAbcamab266894CVCL_B1DYHCT 116PKN2 KO
To screen all eleven PKN2 antibodies by western blot, protein lysates from both HCT 116 WT and PKN2 KO cell lines were run on SDS-PAGE, transferred onto nitrocellulose membranes and probed in parallel with eleven PKN2 antibodies ( Figure 1).
Figure 1. PKN2 antibody screening by western blot using protein lysates.
Protein lysates from HCT 116 WT and PKN2 KO cells were collected, and 30 μg of protein was used for western blot with the indicated PKN2 antibodies. The Ponceau stained transfers of each blot are presented to show equal loading of WT and KO samples. Antibody dilutions were chosen according to the recommendations of the antibody supplier. Antibody dilutions used: ab138514** at 1/1000, ab314021** at 1/1000, A19746** at 1/1000, ARP61894_P050 at 1/500, 8697** at 1/1000, 14608–1-AP at 1/1000, MAB5686* at 1/500, MA5–15887* at 1/1000, MA5–37978** at 1/1000, MA5–44818** at 1/1000, and MA5–49998** at 1/1000. Predicted band size: 112.0 kDa. ** = recombinant antibody, * = monoclonal antibody.
For flow cytometry, HCT 116 WT and PKN2 KO cells were labelled with distinct fluorescent dyes and combined at a 1:1 ratio. Both cell lines were fixed, permeabilised and blocked in the same tube prior to antibody staining to reduce bias. Eleven PKN2 antibodies were then evaluated, with fluorescence intensity assessed using the Attune NxT flow cytometer. Antibody staining in both WT and KO lines was then quantified using FlowJo software, with representative histograms presented in Figure 2.
Figure 2. PKN2 antibody screening by flow cytometry.
HCT 116 WT and PKN2 KO cells were labelled with a green or violet fluorescent dye, respectively. WT and KO cells were mixed in a 1:1 ratio, fixed in 4% PFA and permeabilised in 0.1% saponin. 400,000 cells were stained with the indicated PKN2 antibodies and corresponding Multi-rAb CoraLite Plus 647 secondary antibodies. Antibody staining was quantified using the Attune NxT Flow Cytometer with representative images showing the staining intensity in the KO population (pink histogram, dashed line) compared to the WT cells (green histogram, solid line). Histograms with dotted lines represent secondary antibody-only controls in both WT and KO cells. Antibody dilutions used: ab138514** at 1/1000, ab314021** at 1/4000, A19746** at 1/4000, ARP61894_P050 at 1/500, 8697** at 1/1000, 14608–1-AP at 1/4500, MAB5686* at 1/500, MA5–15887* at 1/1000, MA5–37978** at 1/4000, MA5–44818** at 1/10000, and MA5–49998** at 1/4000. ** = recombinant antibody, * = monoclonal antibody.
In conclusion, we screened eleven PKN2 commercial antibodies by western blot and flow cytometry by comparing the signal produced using human HCT 116 WT and PKN2 KO cells. High-quality and renewable antibodies capable of successfully detecting PKN2 were identified.
Limitations
Inherent limitations are associated with the antibody characterisation platform used in this study. Firstly, the YCharOS project focuses on renewable (recombinant and monoclonal) antibodies and does not test all commercially available PKN2 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 an unbiased approach that is agnostic to the protein for which antibodies have been characterised. 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 PKN2, only a brief overview of the protein’s function and its relevance in disease is provided. PKN2 experts are invited to analyse and interpret observed banding patterns in western blots. Thirdly, YCharOS experiments are not performed in replicate 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 instances where antibodies yield no signal, a repeat experiment is conducted following titration. Additionally, our independent characterisation is performed subsequent to the antibody manufacturer’s internal validation process, therefore making our characterisation process a repeat.
Lastly, as comprehensive and standardised 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 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.
Methods
The standardised protocols used to carry out this KO cell line-based antibody characterisation platform were established and approved by a collaborative group of academics, industry researchers and antibody manufacturers. The detailed materials and step-by-step protocols used to characterise antibodies in western blot, immunoprecipitation and immunofluorescence are openly available on Protocols.io (DOI: dx.doi.org/10.21203/rs.3.pex-2607/v1).
Antibodies
All PKN2 antibodies are listed in Table 2, together with their corresponding Research Resource Identifiers (RRID), to ensure antibodies are cited properly.10 Secondary antibodies used in this study are provided in Table 3. To ensure consistency with manufacturer recommendations and account for proprietary formulations (where antibody concentrations are not disclosed), antibody usage is reported as dilution ratios rather than absolute concentrations.
Table 2. Summary of the PKN2 antibodies tested.CompanyCatalogue numberLot numberRRID (Antibody Registry)ClonalityClone IDHostStock concentration (μg/mL)Vendor recommended applicationsAbcamab138514**1037490–5AB_3668835 Monoclonal RecombinantEPR5490Rabbit-ICC/IF, WBAbcamab314021**1075349–3AB_3668836 Monoclonal Recombinant20A8Rabbit400Intra-FC, ICC/IF, IHC, WBABclonalA19746**4000002274AB_3668860 Monoclonal RecombinantARC2274Rabbit400ELIAS, WBAviva Systems BiologyARP61894_P050QC32618–40750AB_3741052 Polyclonal-Rabbit500WBCell Signaling Technology8697**1AB_2797651 Monoclonal RecombinantD10A10Rabbit100IP, WBProteintech14608–1-AP00011209AB_10638487 Polyclonal-Rabbit450ELISA, FC, ICC/IF, IHC, IP, WBR & D SystemsMAB5686*CBZH0124031AB_2163979 Monoclonal509105Mouse500WBThermo Fisher ScientificMA5–15887*ZJ4521294AB_11155620 Monoclonal1D1Mouse-ELISA, FC, ICC/IF, IHC, WBThermo Fisher ScientificMA5–37978**ZJ4521739AB_2897896 Monoclonal RecombinantARC2274Rabbit400ELISA, ICC/IF, WBThermo Fisher ScientificMA5–44818**ZJ4520956CAB_2931275 Monoclonal RecombinantJE62–44Rabbit1000ICC/IF, IHC, WBThermo Fisher ScientificMA5–49998**ZJ4520724AAB_3092493 Monoclonal Recombinant20A8Rabbit400ELISA, FC, ICC/IF, IHC, WB
Table 3. Summary of the secondary antibodies used.CompanySecondary antibodyCatalogue numberRRID (Antibody Registry)ClonalityApplicationStock concentration (μg/mL)Working concentration (μg/mL)ProteintechHRP-Goat Anti-Rabbit (H + L)RGAR001AB_3073505 Recombinant PolyclonalWestern blot10000.1ProteintechHRP-Goat Anti-Mouse (H + L)RGAM001AB_3068333 Recombinant PolyclonalWestern blot10000.1ProteintechCoraLite Plus 647- Goat Anti-Rabbit (H + L)RGAR005AB_3073509 Recombinant PolyclonalFlow cytometry5000.625ProteintechCoraLite Plus 647- Goat Anti-Mouse (H + L)RGAM005AB_3073503 Recombinant PolyclonalFlow cytometry5000.625
Cell culture
All cell lines used in this study are listed in Table 1, alongside their corresponding RRIDs, to ensure proper citation.11 Cells were cultured in DMEM (Capricorn Scientific #DMEM-HPSTA) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific #A5256801) and 1% antibiotic/antimycotic solution (Capricorn Scientific #AAS-B). All cell lines used in this study were routinely tested for mycoplasma contamination and were confirmed to be mycoplasma-free.
Antibody screening by western blot
For lysate preparation, HCT 116 WT and PKN2 KO cells were washed three times in phosphate buffered saline (PBS) (Thermo Fisher Scientific #70011044) and lysed in RIPA buffer containing 1 × of protease inhibitor cocktail, sodium orthovanadate and phenylmethylsulfonyl fluoride (Santa Cruz Biotechnology #sc-24948). Lysates were sonicated (40% amplitude for 5 seconds) three times and incubated for 30 minutes on ice prior to centrifugation at 20,000 × g for 1 hour at 4 °C.
Protein concentration was confirmed using the Pierce BCA protein assay (Thermo Fisher Scientific #23225) and 30 μg of protein was used. Samples were combined with Laemmli sample buffer (Bio-Rad #1610747) containing 2-mercaptoethanol (final concentration 355 mM) (Sigma Aldrich #M7522) before being heated at 65 °C for 10 minutes. Samples were then loaded in precast 4–20% WedgeWell Tris-Glycine Plus midi gels (Thermo Fisher Scientific #WTG42020BOX) alongside Prime-Step prestained broad range protein ladder (BioLegend #773302). SDS-PAGE was then performed in SureLock Tandem Midi Gel tanks (Thermo Fisher Scientific #STM1001) and run at 200 V for 1 hour with Tris/Glycine/SDS buffer (Bio-Rad #1610772). Proteins were then transferred to 0.2 μm supported nitrocellulose membranes (Cytiva #10600015) using a Criterion blotter with plate electrodes (Bio-Rad #17004070) run at 85 V for 45 minutes. Proteins on the blot were then visualised with Ponceau S stain (Thermo Fisher Scientific #161470250) which was scanned to show alongside individual western blots. Blots were blocked with 5% milk for 1 hour except for antibody 8697 which was blocked in 5% BSA in Tris-buffered saline containing 0.1% Tween 20 (TBST) (Thermo Fisher Scientific #J77500.K2). Primary antibodies ( Table 2) were then incubated overnight at 4 °C in 5% milk TBST with gentle shaking. Following three ten-minute washes with TBST, horseradish peroxidase (HRP) conjugated secondary antibodies ( Table 3) were incubated at a dilution of 1/10000 (0.1 μg/mL) in TBST with 5% milk for 1 hour at room temperature followed by three ten-minute washes with TBST. Membranes were then incubated with either Pierce ECL (Thermo Fisher Scientific #32106) or Clarity Western ECL substrate (Bio-Rad #1705061) prior to detection with the ImageQuant LAS 4000.
Antibody screening by flow cytometry
HCT 116 WT and PKN2 KO cells were detached, and five million cells were labelled with CellTracker green or violet fluorescent dyes, respectively (Thermo Fisher Scientific, #C7025 and #C10094). WT and KO cells were centrifuged at 300 × g for 10 minutes and resuspended in PBS containing 1% bovine serum albumin (BSA) (Sigma-Aldrich, A9647). The two populations were combined at a 1:1 ratio, centrifuged and fixed on ice for 20 minutes using 800 μL of 4% PFA in PBS (Thermo Fisher Scientific #J19943.K2). Following fixation, 1.2 mL of 1% BSA in PBS was added to the tube, vortexed and centrifuged at 600 × g for 15 minutes at 4 °C. Cells were then permeabilised in 400 μL PBS with 0.1% saponin (Sigma-Aldrich #558255) for 10 minutes at room temperature, centrifuged at 600 × g for 15 minutes at 4 °C and then blocked with 5% goat serum (Sigma-Aldrich #G6767), 1% BSA, 0.1% saponin in PBS for 30 minutes on ice. After the blocking step, 400,000 cells were aliquoted into individually labelled tubes, centrifuged at 600 × g for 15 minutes at 4 °C and incubated in 150 μL of 1% BSA, 0.1% saponin PBS with primary PKN2 antibodies ( Table 2) for 30 minutes on ice. 500 μL of 1% BSA, 0.1% saponin PBS was then added to each tube, vortexed and centrifuged at 600 × g for 15 minutes at 4 °C. Cells were then incubated with their corresponding Multi-rAb CoraLite Plus 647 secondary antibodies ( Table 3) in 150 μL of 1% BSA, 0.1% saponin PBS for 30 minutes on ice. 500 μL of 1% BSA, 0.1% saponin PBS was then added to each tube, vortexed and centrifuged at 600 × g for 15 minutes at 4 °C.
Tubes were then resuspended in 1 mL of 1% BSA in PBS and data was acquired using the Attune NxT flow cytometer. Data was analysed using FlowJo with the following gates. The cell population was first gated on FSC-A vs SSC-A, within that gate single cells were selected by FSC-A vs FSC-H and then KO and WT cells were isolated by BL1-A vs VL1-A using a quadrant gate. Quantification of antibody staining was then observed in the RL1-A channel and histograms merged to demonstrate the staining intensity between the two populations compared to the two secondary only controls. The figure was then assembled using Adobe Illustrator 2024.
Data availability
Acknowledgments
This is a summary of independent research funded by both the NC3Rs and MRC and carried out at the National Institute for Health and Care Research (NIHR) Leicester Biomedical Research Centre (BRC). The views expressed are those of the author(s) and not necessarily those of the NC3Rs, the MRC, the NIHR or the Department of Health and Social Care.
We gratefully acknowledge the support of Dr. Carl Laflamme and Dr. Riham Ayoubi, whose technical expertise was invaluable to this work.
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HV and MB have received funding for a research studentship from Abcam Ltd, and contributions in kind for manufacturers that contribute to the YCharOS Inc. consortium. The remaining authors declare no competing interests. These relationships did not influence the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
This work was supported by a grant from the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs) and MRC (NC3Rs Ref: NC/NAM0019/1, MRC UKRI076) alongside support from the Institute for Precision Health, University of Leicester.
The funders have no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
© 2026 Biddle M et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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