Integrative analysis of histone modification landscapes of embryonic and glioblastoma stem cells

Thesis (Ph.D.)--Boston University PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.Histone modifications provide information about the transcriptional status of genes and the locations of regulatory elements. Specialized proteins catalyze the formation or removal of these modifications or bind to histone marks to translate chromatin state into regulatory effects. Recent advances in high-throughput sequencing technology have enabled the profiling of histone modifications and chromatin-associated proteins in a genome-wide, unbiased fashion, and extensive use of this technology generated global chromatin landscapes in a multitude of cell types. Here, the localization patterns of the Ezh2, Suz12 and Rnf2 Polycomb proteins were examined in mouse and human embryonic stem cells. In both cell types, Polycomb proteins bind to genes implicated in development that are repressed but amenable to activation during differentiation. I found that binding patterns differ between proteins of two Po1ycomb complexes (PRCs): while the PRC2 components Ezh2 and Suz12 localize to virtually all sites with Polycomb-related histone marks, Rnf2/PRC1 associates most strongly with developmental regulators, including many lineage-determining transcription factors (TFs). This strategy was then applied to study chromatin state in cancer stem cells (CSCs) derived from glioblastoma (GBM), the most common and aggressive form of malignant brain tumor. GBM is one of several solid tumors from which a subpopulation of cells with stem-cell characteristics and high tumorigenic potential has been isolated. These CSCs are thought to play critical roles in tumorigenicity and resistance to therapy. To identify novel regulators of GBM pathogenesis, I examined a panel of histone modification profiles in patient-derived GBM CSCs. Comparison of these profiles with those of normal neural stem cells and astrocytes revealed differentially regulated genes, miRNAs and other noncoding RNAs. In particular, developmental TFs are highly enriched among genes aberrantly activated in GBM CSCs. Together with a colleague, I showed that these TFs link intimately to Wnt signaling and correlate with clinical properties. To refine the core regulatory circuitry of malignant GBM CSCs, I further analyzed chromatin state of traditional GBM cell lines with limited tumor-initiating potential. These findings shed light on previously unappreciated regulatory hierarchies in GBM CSCs and highlight novel targets for rational therapy