Date of Award

Winter 12-15-2021

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Computational & Systems Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



The identification of recurrent genetic mutations in cancer and their functionalcharacterization has provided a strong foundation for our understanding of tumorigenesis. The more recent observation of recurrent and specific epigenetic changes also present in cancer has widened this view, now establishing cancer as a disease of both genetic and epigenetic misregulation. Enhancers, genomic regions primarily responsible for tissue-specific gene expression, have been shown to be frequent targets of both genetic and epigenetic abnormalities. The observation that DNA methylation within regulatory regions has traditionally correlated with reduced gene expression, coupled with the known role of enhancers in regulating tissuespecific gene expression, suggests that cancer cells may lose their original cellular programming while also gaining expression for genes related to foreign cell types through altered DNA methylation within enhancers. Technological advancements allowing for genome-wide methylation profiling have vastly expanded our capacity to identify DNA methylation alterations present in enhancers, previously undetected in large comparative cancer studies. In Chapter 2, we compared global methylation alterations in two distinct cancer types, endometrioid adenocarcinoma (EAC) and glioblastoma multiforme (GBM). We found that both cancer types displayed an increase in methylation over enhancers related to their cell type of origin. Recurrently hypermethylated enhancers in EAC clustered based on the presence of enriched transcription factor binding motifs. Enriched disease ontology pertaining to the majority of differentially methylated enhancer groups largely encompassed uterine-specific terms, suggesting that enhancers gaining methylation in EAC might contribute to the regulation of normal uterine function. Similarly, GBM hyperDMRs were shown to encompass a significantly greater number enhancers active in adult brain compared to those of developing brain. Further analysis of brain enhancer hyperDMRs revealed increased H3K27ac and H3K4me1 signal in adult brain compared to fetal brain, suggesting that the majority of enhancers being methylation were active in adult but not developing brain. In a second series of studies (Chapters 3 – 5), we sought to better understand the properties governing metastasis organotropism, specifically non-small cell lung cancer metastasis to brain. Reasoning that genomic, transcriptomic, and epigenomic changes might functionally contribute similar alterations, we profiled all three in a subset of 45 paired primary and metastasis samples. While few significantly mutated genes were private to metastasis, 75 genes displayed recurrent metastasis enriched variants (MEVs), largely implicated in focal adhesion and extracellular matrix receptor interactions. A similar analysis revealed increased variant allele frequencies (VAFs) in metastases over a wide range of epigenetic regulators, suggesting that epigenetic misregulation may be selected for, and possibly functionally contribute to, NSCLC metastasis to brain. Consistent with these observations, we observed widespread changes in DNA methylation as a function of disease progression, many losses of which were found within annotated brain-specific active enhancers and correlated with increased nearby gene expression. Transcriptional analyses corroborated these findings, revealing an overall increase in brain gene expression. Together these findings suggest that a potential contributor to NSCLC’s successful colonization of brain is the aberrant activation of brain transcriptional programs. To further understand how methylation changes might be contributing to metastasis, we examined DNA methylation differences across patients and found that the most recurrent and largest changes between primary and matched metastatic samples were within DNA methylation valleys (DMVs), large regions devoid of methylation in normal lung that primarily contain developmental genes. Further examination revealed that only a subset of DMVs, marked by high H3K9me3, H3K4me1, and H3K27me3 signal in normal lung, were undergoing progressive methylation gain. The known mutual exclusivity of H3K27me3 and DNA methylation within CpG islands prompted us to ask whether there was a loss of polycomb repressive complex 2 (PRC2), a multi-protein complex responsible for depositing H3K27me3, occupancy within DMVs accompanying the increased DNA methylation. The binding patterns of the PRC2 catalytic subunit, EZH2, in the non-small cell lung cancer lymph node-derived cell line, H1299, displayed a pervasive loss of EZH2 occupancy within DMVs, accompanying a large increase in DNA methylation. The mechanisms governing this epigenetic switch and its implications in metastasis are the topic of ongoing research, but may lead to the activation of encompassed developmental genes, shifting the tumor cells to a more stem-like state.


English (en)

Chair and Committee

Ting Wang

Committee Members

Barak Cohen