Bioinformatics approaches to studying mesenchymal stem cell behaviour on artificial extracellular matrices

Gurden, Ross Brian (2017) Bioinformatics approaches to studying mesenchymal stem cell behaviour on artificial extracellular matrices. PhD thesis, University of Glasgow.

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Abstract

Stem cells have potential use in tissue engineering and regenerative medicine, and as they underlie the development and maintenance of tissues throughout life, how they function is also of interest. The extracellular matrix presents a variety of physical and chemical signals to stem cells to regulate their behaviour in vivo. Recapitulation of these signals in vitro could enable the control of explanted stem cells to facilitate their study. Biomaterials that display extracellular-matrix inspired cues are one way to do this. By combining surface chemistry and fibronectin, an extracellular matrix protein with cell binding and growth factor binding domains, the conformation of fibronectin was controlled to create artificial extracellular matrices. Adsorbed on a film of poly(ethyl acrylate), fibronectin adopted a network-like conformation which ostensibly increased the exposure of its functional domains, whereas on poly(methyl acrylate) it had an unconnected organisation with more concealed domains. The growth factors bone morphogenetic protein 2 and vascular endothelial growth factor, known to bind to fibronectin, were adsorbed to the network conformation. Prior studies have reported that these artificial extracellular matrices differentially affected cell behaviour. In this work, the growth and differentiation of human bone marrow stromal cell surface marker-1 positive mesenchymal stem cells was characterised on these substrates. It was shown that all combinations of fibronectin conformation and growth factors supported cell adhesion and growth. A high-content image processing and analysis pipeline was developed to take advantage of automated fluorescence microscopy to show that cytoskeletal, nuclei, and differentiation-associated protein features distinguished cells cultured on the artificial extracellular matrices. Those on the isolated conformation and the network conformation with vascular endothelial growth factor were particularly distinct. Further, metabolomics revealed several metabolic pathways that differed in activity between the fibronectin conformations. To analyse the metabolomics data a Quick Results web application was built, which extended the existing Polyomics integrated Metabolomics Pipeline. The application improves the visualisation and interpretation of untargeted liquid chromatography—mass spectrometry metabolomics data. This work gives insights into how these artificial extracellular matrices can control stem cell behaviour, and developed and demonstrated several tools to improve the understanding of these biomaterials and the use of metabolomics data.

Item Type: Thesis (PhD)
Qualification Level: Doctoral
Keywords: Stem cells, metabolomics, biomaterials, bioinformatics.
Subjects: Q Science > QH Natural history
Colleges/Schools: College of Medical Veterinary and Life Sciences > Institute of Molecular Cell and Systems Biology
Funder's Name: Biotechnology and Biological Sciences Research Council (BBSRC)
Supervisor's Name: Dalby, Prof. Matthew and Salmeron-Sanchez, Prof. Manuel and Daly, Dr. Ronan and Burgess, Dr. Karl
Date of Award: 2017
Depositing User: Mr Ross B Gurden
Unique ID: glathesis:2017-9039
Copyright: Copyright of this thesis is held by the author.
Date Deposited: 09 May 2018 12:13
Last Modified: 15 Jun 2018 13:06
URI: http://theses.gla.ac.uk/id/eprint/9039

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