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Proteomic Assessment of the Murine Mammary Gland Extracellular Matrix

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Part of the Methods in Molecular Biology book series (MIMB,volume 2614)


The extracellular matrix (ECM) is a molecular scaffold mainly comprising fibrous proteins, glycoproteins, proteoglycans, and polysaccharides. Aside from acting as a structural support, the ECM’s composition dictates cell-matrix interactions at the biochemical and biophysical level. In the context of cancer, the ECM is a critical component of the tumor microenvironment (TME) and dysregulation of its deposition and remodelling has been shown to promote tumor onset, progression, and metastasis. Here, we describe a robust protocol for the isolation and subsequent proteomic analysis of the ECM of murine mammary glands, for downstream assays studying the role of the ECM in breast cancer. The protocol yields sufficient protein amounts to enable not only the global quantitation of protein expression but furthermore the enrichment and quantitative analysis of post-translationally modified peptides to study aberrant signalling.

Key words

  • Cancer
  • Tumor microenvironment (TME)
  • Extracellular matrix
  • Proteomics
  • Signalling

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  • DOI: 10.1007/978-1-0716-2914-7_16
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  1. Bonnans C, Chou J, Werb Z (2014) Remodelling the extracellular matrix in development and disease. Nat Rev Mol Cell Biol. 15:786–801

    CrossRef  CAS  Google Scholar 

  2. Winkler J, Abisoye-Ogunniyan A, Metcalf KJ et al (2020) Concepts of extracellular matrix remodelling in tumour progression and metastasis. Nat Commun. 11:5120

    CrossRef  CAS  Google Scholar 

  3. Naba A, Clauser KR, Hoersch S et al (2012) The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Mol Cell Proteomics 11:M111.014647

    CrossRef  Google Scholar 

  4. Naba A, Clauser KR, Ding H et al (2016) The extracellular matrix: Tools and insights for the “omics” era. Matrix Biol. 49:10–24

    CrossRef  CAS  Google Scholar 

  5. O’Brien J, Fornetti J, Schedin P (2010) Isolation of mammary-specific extracellular matrix to assess acute cell-ECM interactions in 3D culture. J Mammary Gland Biol Neoplasia 15:353–364

    CrossRef  Google Scholar 

  6. Paoletti AC, Parmely TJ, Tomomori-Sato C et al (2006) Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci 103:18928–18933

    CrossRef  CAS  Google Scholar 

  7. Tyanova S, Temu T, Sinitcyn P et al (2016) The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods 13:731–740

    CrossRef  CAS  Google Scholar 

  8. Nolte H, MacVicar TD, Tellkamp F et al (2018) Instant clue: a software suite for interactive data visualization and analysis. Sci Rep. 8:12648

    CrossRef  Google Scholar 

  9. Szklarczyk D, Franceschini A, Wyder S et al (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43:D447–D452

    CrossRef  CAS  Google Scholar 

  10. Shannon P, Markiel A, Ozier O et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498–2504

    CrossRef  CAS  Google Scholar 

  11. McIlwain S, Mathews M, Bereman MS et al (2012) Estimating relative abundances of proteins from shotgun proteomics data. BMC Bioinformatics 13:308

    CrossRef  CAS  Google Scholar 

  12. Colaert N, Vandekerckhove J, Gevaert K et al (2011) A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision. Proteomics 11:1110–1113

    CrossRef  CAS  Google Scholar 

  13. Burkhart JM, Vaudel M, Gambaryan S et al (2012) The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways. Blood 120:e73–e82

    CrossRef  CAS  Google Scholar 

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SEJP would like to acknowledge fellowships from Fonds de recherche du Québec (Santé) and the Epstein Fellowship in Women’s Health (Faculty of Medicine, McGill University). SVDR would like to thank the Canadian Institutes of Health Research (CIHR) (grants PJT-162260 and PJT-156269 to SVDR) and the Canadian Cancer Society (grant #707140 to SVDR) for financial support. CHB would like to thank Genome Canada for financial support through the Genomics Technology Platform (GTP: 264PRO), and the Segal McGill Chair in Molecular Oncology at McGill University (Montreal, Quebec, Canada). CHB would also like to thank the Warren Y. Soper Charitable Trust and the Alvin Segal Family Foundation for supporting the Jewish General Hospital (Montreal, Quebec, Canada). RPZ would like to thank the University of Manitoba and Shared Health Manitoba for financial support. The authors are also grateful for financial support from the Terry Fox Research Institute.

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Correspondence to Christoph H. Borchers or René P. Zahedi .

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Preston, S.E.J., Richard, V.R., del Rincón, S.V., Borchers, C.H., Zahedi, R.P. (2023). Proteomic Assessment of the Murine Mammary Gland Extracellular Matrix. In: Ursini-Siegel, J. (eds) The Tumor Microenvironment. Methods in Molecular Biology, vol 2614. Humana, New York, NY.

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2913-0

  • Online ISBN: 978-1-0716-2914-7

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