Interrogating the Epigenetic Determinants of State Heterogeneity in Adult Glioblastoma
Date
2023-01-24
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Abstract
Glioblastoma is the most common malignant brain tumour in adults, and prognosis remains poor, with most patients dying in a year or two despite aggressive treatment. These tumours have high degrees of intratumoral heterogeneity, with a subpopulation of cells having stem cell properties. The drivers of this stem cell phenotype are complex, and include a large number of epigenetic and genetic factors. In this thesis, I explore glioblastoma heterogeneity in two distinct ways: I use single-cell chromatin accessibility data to explore influences of copy number alterations on the glioblastoma epigenome, and I apply functional experimental techniques and genomics to characterize macroH2A2, an epigenetic regulator in this disease. In the first part of my thesis, I develop a tool for calling copy number alterations in single-cell ATAC-seq data, called CopyscAT, and show that glioblastoma tumours have limited intratumoral genetic heterogeneity. In addition, genetic subclones share similar epigenetic profiles, but with slightly different predispositions to acquiring distinct cellular states. In the second section of the thesis, I focus on the role of macroH2A2, a histone variant involved in development and cancer. I find that expression of macroH2A2 is associated with improved prognosis in glioblastoma patients, especially in patients receiving treatment. Examining existing datasets, I find that macroH2A2 expression is enriched in neural progenitor-like cells and repressed at the leading edge of tumours, and confirm this in primary patient specimens. MacroH2A2 is associated with reduced self-renewal in vitro and in vivo and knockdown of the protein increases self-renewal markers, reduces the proportion of CD44-positive cells, and shortens mouse survival. Genome-wide, macroH2A2 knockdown results in altered accessibility, with loss of early response (FOS/AP-1) motifs, which I confirm in patient-derived single-cell ATAC-seq data. Chromatin immunoprecipitation confirms that direct effects of macroH2A2 are largely repressive in nature. Lastly, a screen of epigenetic drugs identifies a compound, MI-3, capable of increasing macroH2A2 levels, and shows that macroH2A2 repression impairs sensitivity to this compound. This work contributes novel ideas to the regulation of cell states and fates in glioblastoma.
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Keywords
epigenetics, glioblastoma, cancer, cancer biology, glioma, GBM, macroH2A
Citation
Nikolic, A. (2023). Interrogating the epigenetic determinants of state heterogeneity in adult glioblastoma (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.