Extracellular Matrix Omics

This book covers different omics aspects related to the extracellular matrix (ECM), namely specific omics resources focused on the extracellular matrix (e.g., databases, repositories and atlases), quantitative proteomics applied to specific extracellular matrices (e.g. basement membranes), biological processes such as ECM degradation (degradomics), cell-matrix interactions (adhesomes), signaling pathways, biomarker discovery and diseases, and interactomics (extracellular matrix interaction networks including not only protein-protein but also protein-glycosaminoglycan interactions). The volume also includes recent advances in glycomics and glycobioinformatics applied to proteoglycans and glycosaminoglycans, which are key biological players. The use of omics data to build dynamic models of ECM-regulated biological pathways is addressed, together with the requirement to standardize omic data, which is a prerequisite for the FAIR (Findability, Accessibility, Interoperability, and Reusability) guiding principles for scientific data management.

This book will be of great interest to a broad readership from beginners to advanced researchers, who are interested in extracellular matrix omics and will inspire future research topics.

Auteur

Sylvie Ricard-Blum is Professor of Biochemistry at the University of Lyon (France). She studies the structure, interactions and functions of the extracellular matrix (ECM) using biochemistry, biophysics, bioinformatics and systems biology. Her laboratory has developed a roadmap and tools to build and contextualize ECM interaction networks, including the database MatrixDB. She has identified several hundreds of ECM interactions, and built interaction networks of ECM proteins, bioactive ECM fragments (matricryptins), glycosaminoglycans and proteoglycans leading to the prediction of new functions for a number of them. Her current research aims at determining the role of intrinsic disorder, cross-linking, proteolysis and mutations in rewiring ECM networks in disease with a focus on matricryptins, lysyl oxidases and syndecans. She has been Secretary and President of the French Society for Matrix Biology, and serves as Associate Editor of Matrix Biology and Matrix Biology Plus, Editor of the newsletter of the International Society for Matrix Biology, and as President of the International Society for Matrix Biology (2019-2020).

Contenu

TABLE OF CONTENT

1. The extracellular matrix goes - omics: resources and tools.

2.The matrisome of model organisms: from in-silico prediction to big-data annotation

3.Detecting changes to the extracellular matrix in liver diseases

4. Characterization of Proteoglycanomes by Mass Spectrometry

5. Historical overview of integrated GAG-omics and proteomics

6.Extracellular matrix networks: from connections to functions

7. Integration of Matrisome Omics: Towards System Biology of the Tumor Matrisome

8. Proteomic and degradomic analysis of body fluids: applications, challenges and considerations

9. Regulation of Cell-Matrix Adhesion Networks: Insights from Proteomics

10. Integrative models for TGF- signaling and extracellular matrix