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DNA methylation dynamics underlying therapy resistance in cancer

Boek - Dissertatie

Plentiful DNA methylation changes have been associated with the cellular response to anti-cancer therapeutic pressure. However, it has not systematically been assessed how these changes arise, whether and how they causally contribute to therapeutic resistance and what their impact in the clinic is. In this study, we therefore investigate if and how DNA methylation patterns can underlie the cellular expression and phenotype changes that allow cellular populations to survive therapeutic pressures that are otherwise lethal. The mechanisms we examine appear to span several cancer and drug types, and may therefore be commonly applicable and of broad clinical interest. In particular, we first search for the origins of intratumoural heterogeneity as well as its biological consequences and clinical impact using publicly available data from over 7000 cancer patients. Cellular heterogeneity and plasticity allow the acquisition of resistance to therapy by augmenting the number of available cancer cell phenotypes hence increasing the chance that some cells may survive the selective pressures associated with therapeutic pressure. Since there is no consensus to date, we start by establishing and characterizing metrics suitable for the assessment of cancer-cell intrinsic intratumoural heterogeneity. We show that DNA methylome disarray is increased at active and regulatory genomic regions and that it associates with tumour progression and poor overall survival. Further, we provide evidence that it is likely the aberrant expression of epigenetic modifier enzymes - among which the Ten-Eleven-Translocation (TET) enzymes and the DNA methyltransferases (DNMT) - that underlie DNA methylation dysregulation. Lastly, we find several relevant biological processes to be affected by enhanced DNA methylome heterogeneity, among which the Epithelial-to-Mesenchymal Transition (EMT), a highly plastic cellular process during which cancer cells dedifferentiate and acquire stem cell-like properties such as pluripotency, hence severely increasing cellular heterogeneity. In a second part of this study, we assess the role of DNA methylation during EMT, which recurrently has been shown to underlie therapeutic resistance in cancer. We use cell lines (n=10) from diverse tissues of origin that acquired resistance to various targeted and chemotherapy-based treatments through EMT and explore whether and how DNA methylation changes could causally underlie the EMT phenotype. We show that common DNA methylation dynamics, potentially mediated by the demethylating TET enzymes, drive a reversible EMT-mediated phenotype of therapy resistance to a wide array of therapeutic agents. We show that the loss of EMT expression and/or DNA methylation profiles results in the loss of resistance to therapy. Additionally, we clinically validate that DNA methylation changes drive EMT-mediated resistance to sorafenib in patients with advanced hepatocellular cancer (HCC). We develop a capture-based protocol to interrogate DNA methylation in low amounts of circulating tumour DNA (ctDNA) in HCC patients treated with sorafenib. By monitoring methylation changes in EMT genes in serially-sampled ctDNA, we are able to predict tumour response and acquired resistance to sorafenib. Together, our in silico, in vitro and patient data demonstrate the importance of DNA methylation in driving tumour heterogeneity and plasticity, tumour progression and the acquisition of resistance through EMT.
Jaar van publicatie:2020
Toegankelijkheid:Closed