Transcriptome profiling to unravel bio-instructive materials

Spinal fusions and the repair of large bone defects resulting from trauma, tumors, infections or abnormal skeletal development are frequent surgeries in the clinic. These bone defects do not heal spontaneously and require grafts to bridge the defect, provide support to the surrounding tissue, and regenerate the missing bone. Although autografts are still perceived as the gold-standard for bone grafting, a wide array of alternatives available on the market has expanded, and research in search for improved alternatives has intensified in the last decade. In spite of the advances within this field of biomaterials for bone regeneration applications, the limitations in terms of material properties have not been solved and their mechanisms of action have yet to be elucidated. In this thesis I present a genomics approach to biomaterial research to help further advances within this field. The context and description of alternative bone graft substitutes are briefly summarized in chapter 1. Chapter 2 is a review dedicated to introduce materiomics as the holistic approach in materials research that considers a material as a complex system from which all the properties contribute to the overall (biological) capacity. Developments in the field of biomaterials are often hampered by the lack of adequate in vitro models due to an incomplete understanding of in vivo mechanisms following biomaterial-cell and -tissue interactions. Therefore, in chapter 3, we defined a suitable cell type to study biomaterials in vitro by comparing and studying the transcriptional profiles of five different cell lines exposed to three well characterized biomaterials. Osteosarcoma-derived MG-63 cells were selected based on their ability to reflect the in vivo bone forming capacity of these three biomaterials in their transcriptome. This cell line was then employed throughout this thesis to study biomaterials with the aim of elucidating the instructive effect of biomaterials and biomaterial surfaces. To do so, we employed genomics tools and considered that the genome-wide transcriptional profiles illustrate the cellular state in response to the presented materials. As such, in chapter 4, we compared the cellular responses to various diverse, but commonly studied and clinically employed materials for bone regeneration applications in relation to material properties. Specific signalling pathways such as TGF-β and Focal Adhesion Kinase correlated to the bone forming capacity of biomaterials and are therefore hypothesized to play a role in material-induced bone regeneration in vivo. This specific correlation was further elucidated in chapter 5, in which we studied a selected subset of genes in relation to this bone-inducing property. The results not only confirm the complexity of biomaterials and their properties, but also point towards a role of the extracellular matrix composition for successful bone formation. Lastly, we compared in chapter 6 the transcriptional responses with morphological characteristics of cells when exposed to four materials with distinct surface roughness to explore the potential of high content morphological imaging as a tool to study, compare and screen biomaterials in a non-invasive manner. Chapter 7 includes final remarks discussing the envisioned approaches for successful developments in the field of biomaterials for (bone) tissue regeneration, to which the work presented in this thesis contributes.