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Improved sensitivity in cell surface protein detection by combining chemical labeling with mechanical lysis in a colorectal cancer cell model

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Abstract

Objective

To develop a new technique for improved cell surface protein detection and analysis by combining chemical labeling with mild cell lysis using model HCT 116 colorectal cancer cells.

Results

We found that Dounce homogenization by hand, rather than the typical sonication or syringe lysis method, recovered surface/membrane proteins more consistently and effectively. This was indicated by marker membrane proteins such as claudin-4 and EGFR (epidermal growth factor receptor) that span the typical 20–200 kD range. As monitored by Western blotting (WB), the Dounce lysis method combined with cell surface biotinylation showed consistent recovery of the marker proteins claudin-4 and EGFR. This lysis method was combined with a cell surface biotinylation strategy to enrich cell surface/membrane proteins using affinity bead-based purification with four-fold less cells compared to prior work. Subsequent LC/MS/MS analysis identified 49 additional surface/membrane proteins for the first time from HCT 116 cells.

Conclusion

This combination of methodologies may fit into an advanced workflow for identifying new and elusive cell surface proteins. It can increase the protein coverage for biomarker discovery for colorectal cancer or other cancers. This new detection/analysis approach may also promote new applications in surface display systems as well as cell screening, selection, and binding processes.

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References

  • Baker MS et al (2017) Accelerating the search for the missing proteins in the human proteome. Nat Commun 8:14271

    Article  CAS  Google Scholar 

  • Cordwell SJ, Thingholm TE (2010) Technologies for plasma membrane proteomics. Proteomics 10:611–627

    Article  CAS  Google Scholar 

  • Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26:1367–1372

    Article  CAS  Google Scholar 

  • Dolai S, Xu Q, Liu F, Molloy MP (2011) Quantitative chemical proteomics in small-scale culture of phorbol ester stimulated basal breast. Cancer Cells Proteomics 11:2683–2692. https://doi.org/10.1002/pmic.201000801

    Article  CAS  PubMed  Google Scholar 

  • Dounce AL, Witter RF, Monty KJ, Pate S, Cottone MA (1955) A method for isolating intact mitochondria and nuclei from the same homogenate, and the influence of mitochondrial destruction on the properties of cell nuclei. J Cell Biol 1:139–153

    Article  CAS  Google Scholar 

  • Elia G (2008) Biotinylation reagents for the study of cell. Surf Proteins Proteomics 8:4012–4024

    CAS  Google Scholar 

  • Elschenbroich S, Kim Y, Medin JA, Kislinger T (2010) Isolation of cell surface proteins for mass spectrometry-based proteomics. Expert Rev Proteomics 7:141–154

    Article  CAS  Google Scholar 

  • Grabski AC (2009) Advances in preparation of biological extracts for protein purification. Methods in enzymology 463 Elsevier, Amsterdam, pp 285–303

    Google Scholar 

  • Hahn-Strömberg V, Askari S, Ahmad A, Befekadu R, Nilsson TK (2017) Expression of claudin 1, claudin 4, and claudin 7 in colorectal cancer and its relation with CLDN DNA methylation patterns. Tumour Biol. https://doi.org/10.1177/1010428317697569

    Article  PubMed  Google Scholar 

  • Han C-L, Chien C-W, Chen W-C, Chen Y-R, Wu C-P, Li H, Chen Y-J (2008) A multiplexed quantitative strategy for membrane proteomics opportunities for mining therapeutic targets for autosomal dominant polycystic kidney disease. Mol Cell Proteomics 7:1983–1997

    Article  CAS  Google Scholar 

  • Hörmann K, Stukalov A, Müller AC, Heinz LX, Superti-Furga G, Colinge J, Bennett KL (2016) A surface biotinylation strategy for reproducible plasma membrane protein purification and tracking of genetic and drug-induced alterations. J Proteome Res 15:647–658

    Article  Google Scholar 

  • Kamath KS et al (2016) Pseudomonas aeruginosa cell membrane protein expression from phenotypically diverse cystic fibrosis isolates demonstrates host-specific adaptations. J Proteome Res 15:2152–2163. https://doi.org/10.1021/acs.jproteome.6b00058

    Article  CAS  PubMed  Google Scholar 

  • Kavousipour S, Khademi F, Zamani M, Vakili B, Mokarram P (2017) Novel biotechnology approaches in colorectal cancer diagnosis and therapy. Biotechnol Lett 39:785–803. https://doi.org/10.1007/s10529-017-2303-8

    Article  CAS  PubMed  Google Scholar 

  • Kischel P et al (2008) Cell membrane proteomic analysis identifies proteins differentially expressed in osteotropic human breast. Cancer Cells Neoplasia 10:1014-N1011

    Article  CAS  Google Scholar 

  • Leth-Larsen R, Lund RR, Ditzel HJ (2010) Plasma membrane proteomics and its application in clinical cancer biomarker discovery . Mol Cell Proteomics 9:1369–1382

    Article  CAS  Google Scholar 

  • Liu F et al (2016) Systems proteomics view of the endogenous human claudin protein family. J Proteome Res 15:339–359

    Article  CAS  Google Scholar 

  • Lu X, Zhu H (2005) Tube-gel digestion a novel proteomic approach for high throughput analysis of membrane proteins . Mol Cell Proteomics 4:1948–1958

    Article  CAS  Google Scholar 

  • Nagano K, Shinkawa T, Kato K, Inomata N, Yabuki N, Haramura M (2011) Distinct cell surface proteome profiling by biotin labeling and glycoprotein capturing. J Proteomics 74:1985–1993

    Article  CAS  Google Scholar 

  • Pollock SB et al (2018) Highly multiplexed and quantitative cell-surface protein profiling using genetically barcoded antibodies. Proc Natl Acad Sci 115:2836–2841. https://doi.org/10.1073/pnas.1721899115

    Article  CAS  PubMed  Google Scholar 

  • Rouet R, Jackson KJL, Langley DB, Christ D (2018) Next-generation sequencing of antibody display repertoires. Front Immunol.https://doi.org/10.3389/fimmu.2018.00118

    Article  PubMed  PubMed Central  Google Scholar 

  • Rybak JN, Scheurer SB, Neri D, Elia G (2004) Purification of biotinylated proteins on streptavidin resin: a protocol for quantitative elution . Proteomics 4:2296–2299

    Article  CAS  Google Scholar 

  • Sasaki T, Hiroki K, Yamashita Y (2013) The role of epidermal growth factor receptor in cancer metastasis and microenvironment biomed. Res Int 2013:546318. https://doi.org/10.1155/2013/546318

    Article  CAS  Google Scholar 

  • Shin BK et al (2003) Global profiling of the cell surface proteome of cancer cells uncovers an abundance of proteins with chaperone function. J Biol Chem 278:7607–7616

    Article  CAS  Google Scholar 

  • Shukla HD, Vaitiekunas P, Cotter RJ (2012) Advances in membrane proteomics and cancer biomarker discovery: current status and future perspective. Proteomics 12:3085–3104

    Article  CAS  Google Scholar 

  • Smolders K, Lombaert N, Valkenborg D, Baggerman G, Arckens L (2015) An effective plasma membrane proteomics approach for small tissue samples. Sci Rep. https://doi.org/10.1038/srep10917

    Article  PubMed  PubMed Central  Google Scholar 

  • Tan S, Tan HT, Chung M (2008) Membrane proteins and membrane proteomics. Proteomics 8:3924–3932

    Article  CAS  Google Scholar 

  • Weekes MP, Antrobus R, Lill JR, Duncan LM, Hör S, Lehner PJ (2010) Comparative analysis of techniques to purify plasma membrane proteins. J Biomol Tech JBT 21:108

    PubMed  Google Scholar 

  • Winter D, Steen H (2011) Optimization of cell lysis and protein digestion protocols for the analysis of HeLa S3 cells by LC-MS/MS. Proteomics 11:4726–4730

    Article  CAS  Google Scholar 

  • Wu C, Xu Q, Liu F, Nevalainen KM (2007) Activity-based identification of secreted serine proteases of the filamentous fungus. Ophiostoma Biotechnol Lett 29:937–943. https://doi.org/10.1007/s10529-007-9333-6

    Article  CAS  PubMed  Google Scholar 

  • Zhao M, Wei W, Cheng L, Zhang Y, Wu F, He F, Xu P (2016) Searching missing proteins based on the optimization of membrane protein enrichment and digestion process. J Proteome Res 15:4020–4029

    Article  CAS  Google Scholar 

  • Zhao Q et al (2017) In-depth proteome coverage by improving efficiency for membrane p[roteome analysis. Anal Chem 89:5179–5185. https://doi.org/10.1021/acs.analchem.6b04232

    Article  CAS  PubMed  Google Scholar 

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Funding

We thank Macquarie University (MQRDG-9201601650) and international Macquarie University research excellence scholarship (iMQRES) for supporting this project. We also thank the Australian proteome analysis facility (APAF) for technical support and Md Kawsar Khan for supporting with data visualizations.

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Authors and Affiliations

  1. Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia

    Payal Barua, Abidali Mohamedali & Fei Liu

  2. Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia

    Seong Beom Ahn

Authors
  1. Payal Barua
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  2. Seong Beom Ahn
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  3. Abidali Mohamedali
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  4. Fei Liu
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Correspondence to Fei Liu.

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The author declares that they have no conflicts of interest.

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This work has been approved by Institutional Biosafety Committee (IBC) on behalf of Macaquarie University under the project ID 0340–520180340968.

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Barua, P., Ahn, S.B., Mohamedali, A. et al. Improved sensitivity in cell surface protein detection by combining chemical labeling with mechanical lysis in a colorectal cancer cell model. Biotechnol Lett 42, 683–695 (2020). https://doi.org/10.1007/s10529-020-02824-1

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  • DOI: https://doi.org/10.1007/s10529-020-02824-1

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