The Matrisome: In Silico Definition and In Vivo Characterization by Proteomics of Normal and Tumor Extracellular Matrices
Open accessAbstract
The extracellular matrix (ECM) is a complex meshwork of cross-linked proteins providing both biophysical and biochemical cues that are important regulators of cell proliferation, survival, differentiation, and migration. We present here a proteomic strategy developed to characterize the in vivo ECM composition of normal tissues and tumors using enrichment of protein extracts for ECM components and subsequent analysis by mass spectrometry. In parallel, we have developed a bioinformatic approach to predict the in silico "matrisome" defined as the ensemble of ECM proteins and associated factors. We report the characterization of the extracellular matrices of murine lung and colon, each comprising more than 100 ECM proteins and each presenting a characteristic signature. Moreover, using human tumor xenografts in mice, we show that both tumor cells and stromal cells contribute to the production of the tumor matrix and that tumors of differing metastatic potential differ in both the tumor- and the stroma-derived ECM components. The strategy we describe and illustrate here can be broadly applied and, to facilitate application of these methods by others, we provide resources including laboratory protocols, inventories of ECM domains and proteins, and instructions for bioinformatically deriving the human and mouse matrisome.
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Hynes and Naba first presented the matrisomics concept in 2012, establishing a matrisome database that classifies ECM into core matrisome proteins (collagens, proteoglycans, and glycoproteins) and matrisome-associated proteins (secreted factors, regulators, and ECM-affiliated proteins), providing a reliable reference for comprehensive dECM analysis.
“Hynes and Naba first presented the matrisomics concept in 2012, establishing a matrisome database (http://matrisomeproject.mit.edu/) which classifies ECM into core matrisome proteins, including collagens, proteoglycans, and glycoproteins, and matrisome‐associated proteins, encompassing secreted factors, regulators, and ECM‐affiliated proteins, thus providing a reliable reference for comprehensive”
From Bioactive scaffolds for tissue engineering: A review of decellularized extracellular matrix applications and innovations (2025) · cites this paper as [117]
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Experimental — accuracy not yet measuredTSC2−/− astrocytes show high expression of extracellular matrix synthesis and remodelling genes including COL3A1, MMP14, DCN, CD44 and TIMP2.
“In addition, we observed high expression of several genes associated with extracellular matrix synthesis and remodelling, including COL3A1, MMP14, DCN, CD44 and TIMP237 (Fig. 2m, Extended Data Fig. 2b,d and Supplementary Table 8).”
From mTORC1 drives cell-autonomous astrocyte reactivity in tuberous sclerosis (2026) · cites this paper as [37]
The Results (page unavailable) classify collagens and proteoglycans as core extracellular-matrix components and matrix metalloproteinases and their regulators as ECM regulators. This supports the cited paper’s role in identifying ECM-related gene categories, but our copy does not explicitly classify all five named genes. The high expression in TSC2−/− astrocytes is presented as the citing authors’ own observation, not a finding attributed to this source. (LLM, conf=0.83)
Experimental — accuracy not yet measuredPreceding and accompanying invasion, cancer-associated fibroblasts (CAFs) may deposit fibronectin, collagen type I or type IV, or proteoglycans, resulting in stiffened, ECM-rich fibrous connective tissue.
“Preceding and accompanying invasion, cancer-associated fibroblasts (CAFs) may deposit fibronectin, collagen type I or type IV, or proteoglycans, resulting in stiffened, ECM-rich fibrous connective tissue [17,18].”
From Cancer-on-chip models for metastasis: importance of the tumor microenvironment (2024) · cites this paper as [18]
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- Authors
- Naba, A., Clauser, K. R., Hoersch, S., Liu, H., Carr, S. A., & Hynes, R. O.
- Affiliations
- Howard Hughes Medical Institute (US)
- Broad Institute (US)
- Max Delbrück Center (DE)
- Corresponding author
- Carr, Steven A.
- Hynes, Richard O.
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2012-04
- Volume
- 11
- Issue
- 4
- Pages
- M111.014647
- ISSN
- 1535-9476 (ISSN-L)
- PMC
- PMC3322572
- OpenAlex
- W2131495509
- Cited by
- 1,354
- References
- 58
- Citations by year
- 2026: 125 · 2025: 124 · 2024: 141 · 2023: 153 · 2022: 146 · 2021: 151 · 2020: 136 · 2019: 87 · 2018: 77 · 2017: 61 · 2016: 43 · 2015: 40 · 2014: 31 · 2013: 21 · 2012: 14
- FWCI
- 9.85
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular & Cellular Proteomics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- Howard Hughes Medical Institute
- Broad Institute
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
- National Cancer Institute (U54CA163109, U54CA126515, P30CA014051)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Health Sciences › Medicine › Rheumatology › Bone and Dental Protein Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Protease and Inhibitor Mechanisms
- Keywords
- matrisome, extracellular matrix, ECM proteomics, tumor stroma, tumor xenografts, lung cancer, colon cancer, metastasis
- MeSH terms
- Proteoglycan Link Protein, Animals, Colon, Extracellular Matrix, Humans, Lung, Male, Mice, Mutant Strains, Neoplasm Proteins, Neoplasm Transplantation, Neoplasms, Proteoglycans, Extracellular Matrix Proteins, Stromal Cells, Proteomics, Cell Line, Tumor, Mice, Tandem Mass Spectrometry
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