MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities

Launay, Guillaume; Salza, Romain; Multedo, D.; Thierry‐Mieg, Nicolas; Ricard‐Blum, Sylvie

doi:10.1093/nar/gku1091

Cited by 120 publications

(76 citation statements)

References 38 publications

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“…The MatrixDB is an extracellular matrix interaction database that will continue to be useful as connections are made among ECM components. [83] In the review by Francis et.al., the Ripplinger lab discusses the interconnections among inflammation, fibrosis, and arrhythmias, highlighting the complexity of the system. [84] Understanding the interconnection between inflammation and fibrosis is an important future avenue of research.…”

Section: Future Directions and Conclusionmentioning

confidence: 99%

“…For example, fibronectin and laminin matricryptins have been studied extensively in the angiogenesis field. [83] To test for biological function, peptides 15-20 amino acids in length that are immediately upstream or downstream of the cleavage site can be commercially generated. If many cleavage sites exist, computational analysis can help to focus on the most likely candidates.…”

Section: Figurementioning

confidence: 99%

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Matrix metalloproteinases as input and output signals for post-myocardial infarction remodeling

Lindsey

Iyer

Jung

et al. 2016

Journal of Molecular and Cellular Cardiology

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Despite current optimal therapeutic regimens, approximately one in four patients diagnosed with myocardial infarction (MI) will go on to develop congestive heart failure, and heart failure has a high five-year mortality rate of 50%. Elucidating mechanisms whereby heart failure develops post-MI, therefore, is highly needed. Matrix metalloproteinases (MMPs) are key enzymes involved in post-MI remodeling of the left ventricle (LV). While MMPs process cytokine and extracellular matrix (ECM) substrates to regulate the inflammatory and fibrotic components of the wound healing response to MI, MMPs also serve as upstream signaling initiators with direct actions on cell signaling cascades. In this review, we summarize the current literature regarding MMP roles in post-MI LV remodeling. We also identify the current knowledge gaps and provide templates for experiments to fill these gaps. A more complete understanding of MMP roles, particularly with regards to upstream signaling roles, may provide new strategies to limit adverse LV remodeling.

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Section: Future Directions and Conclusionmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

Matrix metalloproteinases as input and output signals for post-myocardial infarction remodeling

Lindsey

Iyer

Jung

et al. 2016

Journal of Molecular and Cellular Cardiology

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“…Cytoscape v3.3.0 software [22] was used to build and visualize network, including additional PPI information from InnateDB [23] and MatrixDB [24] databases. This type of analysis together with our current knowledge of the existing literature allows the identification of THBS1 network-related melanoma ''hubs'', i.e.…”

Section: Interaction Network Analysismentioning

confidence: 99%

Matricellular TSP-1 as a target of interest for impeding melanoma spreading: towards a therapeutic use for TAX2 peptide

Jeanne

Boulagnon‐Rombi

Devy

et al. 2016

Clin Exp Metastasis

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Thrombospondin-1 (TSP-1) is a matricellular glycoprotein known for being highly expressed within a tumor microenvironment, where it promotes an aggressive phenotype particularly by interacting with the CD47 cell-surface receptor. While it originates from the stromal compartment in many malignancies, melanoma is an exception as invasive and metastatic melanoma cells overexpress TSP-1. We recently demonstrated that a new molecular agent that selectively prevents TSP-1 binding to CD47, called TAX2, exhibits anti-cancer properties when administered systemically by decreasing viable tumor tissue within subcutaneous B16 melanoma allografts. At the same time, emerging evidence was published suggesting a contribution of TSP-1 in melanoma metastatic dissemination and resistance to treatment. Through a comprehensive systems biology approach based on multiple genomics and proteomics databases analyses, we first identified a TSP-1-centered interaction network that is overexpressed in metastatic melanoma. Then, we investigated the effects of disrupting TSP-1:CD47 interaction in A375 human malignant melanoma xenografts. In this model, TAX2 systemic administrations induce tumor necrosis by decreasing intra-tumoral blood flow, while concomitantly making tumors less infiltrative. Besides, TAX2 treatment also drastically inhibits B16F10 murine melanoma cells metastatic dissemination and growth in a syngeneic experimental model of lung metastasis, as demonstrated by histopathological analyses as well as longitudinal and quantitative µCT follow-up of metastatic progression. Altogether, the results obtained by combining bioinformatics and preclinical studies strongly suggest that targeting TSP-1/CD47 axis may represent a valuable therapeutic alternative for hampering melanoma spreading.

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“…Hussenet, Orend and collaborators used such an approach to identify a matrisome signature enriched in the transcriptome of angiogenic vs non-angiogenic oncogenic pancreatic islets, which they termed the “angiomatrix” signature [34]. Once identified, ECM signatures (of a given tissue or disease state) can be further analyzed with pathway or interaction analysis tools such as MatrixDB [35, 36]. …”

Section: Introductionmentioning

confidence: 99%

The extracellular matrix: Tools and insights for the “omics” era

et al. 2016

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The extracellular matrix (ECM) is a fundamental component of multicellular organisms that provides mechanical and chemical cues that orchestrate cellular and tissue organization and functions. Degradation, hyperproduction or alteration of the composition of the ECM cause or accompany numerous pathologies. Thus, a better characterization of ECM composition, metabolism, and biology can lead to the identification of novel prognostic and diagnostic markers and therapeutic opportunities. The development over the last few years of high-throughput (“omics”) approaches has considerably accelerated the pace of discovery in life sciences. In this review, we describe new bioinformatic tools and experimental strategies for ECM research, and illustrate how these tools and approaches can be exploited to provide novel insights in our understanding of ECM biology. We also introduce a web platform “the matrisome project” and the database MatrisomeDB that compiles in silico and in vivo data on the matrisome, defined as the ensemble of genes encoding ECM and ECM-associated proteins. Finally, we present a first draft of an ECM atlas built by compiling proteomics data on the ECM composition of 14 different tissues and tumor types.

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MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities

Cited by 120 publications

References 38 publications

Matrix metalloproteinases as input and output signals for post-myocardial infarction remodeling

Matrix metalloproteinases as input and output signals for post-myocardial infarction remodeling

Matricellular TSP-1 as a target of interest for impeding melanoma spreading: towards a therapeutic use for TAX2 peptide

The extracellular matrix: Tools and insights for the “omics” era

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