Nanoscale characterization of cell receptors and binding sites on cell-derived extracellular matrices

Augmenting cancer cell proteomics with cellular images - A semantic approach to understand focal adhesion

If monolayers of cancer cells are exposed to microgravity, some of the cells cease adhering to the bottom of a culture flask and join three-dimensional aggregates floating in the culture medium. Searching reasons for this change in phenotype, we performed proteome analyses and learnt that accumulation and posttranslational modification of proteins involved in cell-matrix and cell-cell adhesion are affected. To further investigate these proteins, we developed a methodology to find histological images about focal adhesion complex (FA) proteins. Selecting proteins expressed by human FTC-133 and MCF-7 cancer cells and known to be incorporated in FA, we transformed the experimental data to RDF to establish a core semantic knowledgebase. Applying iterative SPARQL queries to Linked Open Databases, we augmented these data with additional functional, transformation- and aggregation-related relationships. Using reasoning, we retrieved publications with images about the spatial arrangement of proteins incorporated in FA. Contextualizing those images enabled us to gain insights about FA of cells changing their site of growth, and to independently validate our experimental results. This new way to link experimental proteome data to biomedical knowledge from various sources via searching images may generally be applied in science when images are a tool of knowledge dissemination.

The Molecular Dance of Fibronectin: Conformational Flexibility Leads to Functional Versatility

Fibronectin, a large multimodular protein and one of the major fibrillar components of the extracellular matrix, has been the subject of study for many decades and plays critical roles in embryonic development and tissue homeostasis. Moreover, fibronectin has been implicated in the pathology of many diseases, including cancer, and abnormal depositions of fibronectin have been identified in a number of amyloid and nonamyloid lesions. The ability of fibronectin to carry all these diverse functionalities depends on interactions with a large number of molecules, including adhesive and signaling cell surface receptors, other components of the extracellular matrix, and growth factors and cytokines. The regulation and integration of such large number of interactions depends on the modular architecture of fibronectin, which allows a large number of conformations, exposing or destroying different binding sites. In this Review, we summarize the current knowledge regarding the conformational flexibility of fibronectin, with an emphasis on how it regulates the ability of fibronectin to interact with various signaling molecules and cell-surface receptors and to form supramolecular assemblies and fibrillar structures.

Effects of various extracellular matrix proteins on the growth of HL-1 cardiomyocytes

We present the physical and biochemical effects of extracellular matrixes (ECMs) on HL-1 cardiomyocytes. ECMs play major roles in cell growth, adhesion and the maintenance of native cell functions. We investigated the effects of 6 different cell culture systems: 5 different ECM-treated surfaces (fibronectin, laminin, collagen I, gelatin and a gelatin/fibronectin mixture) and 1 nontreated surface. Surface morphology was scanned and analyzed using atomic force microscopy in order to investigate the physical effects of ECMs. The attachment, growth, viability, proliferation and phenotype of the cells were analyzed using phase-contrast microscopy and immunocytochemistry to elucidate the biochemical effects of ECMs. Our study provides basic information for understanding cell-ECM interactions and should be utilized in future cardiac cell research and tissue engineering.