DNA methylation is a vital epigenetic process that acts as a major control mechanism for gene expression. In addition to its essential role in many normal cellular processes, it is also implicated in a wide variety of disease states and processes including cancer. Along with genetic mutations, aberrant DNA methylation patterns, specifically the inappropriate DNA methylation or demethylation of CpG residues, may activate oncogenes or suppress tumor suppressor genes, respectively. These changes can generate or facilitate the progression of tumorigenesis and tend to accumulate throughout the development of cancer. Although they play such a major role in cancer and in other diseases, it remains unclear what causes these epigenetic revisions to occur. This dissertation will focus on uncovering mechanisms that are sources of epigenetic revision, specifically as they relate to cancer. Due to rapid cell division and increased DNA damage, cells are increasingly dependent on DNA repair as they continue on a path of tumorigenic progression. We hypothesize that DNA repair, specifically the repair of DNA double strand breaks (DSB) by Non-Homologous End Joining (NHEJ) may play a role in inappropriate epigenetic revision. Using a GFP reporter system inserted into the genome of HeLa cells, we are able to induce targeted DNA damage that enables the cells, after successfully undergoing NHEJ repair, to express WT GFP. These GFP+ cells were segregated into two expression classes, one with robust expression (Bright) and the other with reduced expression (Dim). Using a DNA hypomethylating drug (AzadC) we were able to demonstrate that the different GFP expression levels was due to differential methylation statuses of CpGs in regions on either side of the break site. Deep sequencing analysis of this area in sorted Bright and Dim populations revealed a collection of different epi-alleles that display patterns of DNA methylation following repair by NHEJ. These patterns differ between Bright and Dim cells which are hypo- and hypermethylated, respectively, and between the post-repair populations and the original, uncut cells. These data suggest that NHEJ repair facilitates a rewrite of the methylation landscape in repaired genes, elucidating one potential source for the altered methylation patterns seen in cancer cells. The Dim cells generated during this study are known to have a hypermethylated GFP gene that is correlated with reduced expression, allowing it to be used as a screening tool for hypomethylating agents. We used this tool to screen the blood serum of patients with head and neck squamous cell carcinoma (HNSCC). We found that the serum from HNSCC patients, but not from healthy individuals, contains some factor that causes hypomethylation in exposed cells. Further, we were able to identify this factor as a protein capable of effecting changes in DNA methylation, gene expression, and miRNA levels in the treated Dim cells. The novel concept presented in this study has immense implications on the study of cancer progression as it evidences circulating proteins, presumably released by cancer cells, which are able to effect gene expression in cells that are distal to the location of the cancer. Further, the fact that these proteins are in circulation makes them a potential target for use in diagnostics. Changes in DNA methylation play a major role in the development of cancer and understanding the mechanisms by which this occurs could provide new therapeutic targets for preventing this process from contributing to tumorigenesis. This dissertation presents potential sources of epigenetic revision in cancer and thus provides answers to a major question that has yet to be answered in the area of cancer research.


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Graduation Date





Masternak, Michal


Doctor of Philosophy (Ph.D.)


College of Medicine


Burnett School of Biomedical Sciences

Degree Program

Biomedical Sciences









Release Date

May 2022

Length of Campus-only Access

5 years

Access Status

Doctoral Dissertation (Open Access)

Included in

Biology Commons