The Matrisome: In Silico Definition and In Vivo Characterization by Proteomics of Normal and Tumor Extracellular Matrices

Abstract

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.

Quantitative proteomics identify Tenascin-C as a promoter of lung cancer progression and contributor to a signature prognostic of patient survival

“…1A). To systematically characterize the matrisome of normal lung, fibrotic lung, primary lung adenocarcinoma, and associated lymph node metastases, we used a recently developed proteomics-based approach (9,13). The four sample types-normal lungs, fibrotic lungs, primary tumors, and metastatic tumors-were first subjected to a decellularization procedure to remove the soluble intracellular proteins and to enrich for ECM proteins (Fig.…”

“…In the present study, we implemented a label-based, quantitative mass spectrometry (MS) approach to elucidate the compositional changes in the ECM accompanying lung cancer progression by profiling the matrisome of normal lung, primary lung tumors, and lung tumor metastases to the lymph nodes. The matrisome is defined as the ensemble of core ECM proteins (e.g., collagens, proteoglycans) and ECM-associated proteins, which include ECM-affiliated proteins (e.g., annexins, lectins), ECM regulators (proteases, their inhibitors, and cross-linking enzymes) and secreted factors (e.g., chemokines, growth factors, S100 proteins) (9).…”

Complementary, Semiautomated Methods for Creating Multidimensional PEG-Based Biomaterials

“…We quantified cell area ( Figure 2e) and LAP is an efficient photoinitiator to synthesize 2D PEG-PC hydrogels in a 96-well plate format. In addition to protein composition, [30][31] every tissue has a specific stiffness range [32][33] that can be mimicked using hydrogels. We had developed a 2D PEG-PC hydrogel that is polymerized with Irgacure 2959 (Irgacure), 34 a commonly used photoinitiator in hydrogel synthesis.…”

When is a thrombogenic matrix not thrombogenic?

“…8 In a mouse model of breast cancer, primary tumor growth and metastasis of isografted breast cancer cells was inhibited in EphA4-knockout mice vs control wild-type littermates. 9 In chronic lymphocytic leukemia, evidence has been presented that EphA4, including soluble EphA4, may contribute to nodal dissemination. 10 As increasing attention focuses on the role of the tumor microenvironment in pathogenesis, it seems likely that important insights will be gained by study of the modulation of Eph/ephrin signaling by viral infection.…”

“…Proteomic approaches have recently been developed to characterize the composition of the ECM, or matrisome. 9 This type of nonbiased approach would determine whether the absence of TSP2 results in few or many changes to the ECM. Whereas several recent studies have highlighted the importance of thrombospondins in the structure of the ECM, the study by Kristofik et al underscores their importance in the function of the ECM.…”