An integrative analysis of gene regulation in mesenchymal differentiation and soft-tissue sarcomas

Aberrant gene regulatory networks drive the progression and metastasis of many cancers. In soft-tissue sarcomas, rare cancers that resemble connective tissues, the aetiology and pathogenesis are poorly understood. Increasing evidence suggests dedifferentiation is analogous to disease progression as a result of aberrant gene regulatory networks within mesenchymal progenitor cells. Characterising gene regulatory mechanisms that control the process of mesenchymal stem cell (MSC) differentiation may reveal functional roles in tumours that are related to disease progression and patient outcomes. This thesis explores the relationship between MSC differentiation and oncogenesis in sarcoma. Firstly, I investigated networks of small non-coding RNAs, microRNAs (miRNAs), that regulate the expression of genes involved in critical cellular processes such as differentiation, proliferation, and apoptosis. I employed an integrative bioinformatics approach to interrogate dysregulated microRNA signatures of mesenchymal differentiation and downstream regulatory networks associated with patient prognosis. From this, I applied gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to identify miRNA mediators for the enriched pathways and progenitor cell phenotypes that may play a role in disease progression. Secondly, since gene regulation is cell-specific, I continued to investigate phenotypic and genotypic changes in MSCs isolated from tumour and patient-matched normal tissue. Under MSC-specific culture conditions, I found that tumour-derived stem cell populations were phenotypically similar to normal tissue-derived MSCs. At the molecular level, using wholeexome sequencing and RNA-sequencing, it was found that gene expression and regulation of MSCs derived from liposarcomas were distinctly different from that derived from adjacent normal tissue. The cultured cells lacked characteristic mutations of soft-tissue sarcomas, suggesting that they are not tumourigenic themselves, but rather, differences were related to the unique microenvironment and may play an indirect role in promoting the tumourigenic potential of sarcoma cells. These findings deepen the existing knowledge of miRNA-mediated gene regulation in sarcoma and enrich the understanding of concomitant stem cell populations within human primary liposarcomas