Significance: Epigenetic inactivation of tumor suppressor genes (TSGs) is a well-established event in cancer progression. TSG silencing is closely linked to aberrations in epigenetic mechanisms, including DNA methylation, histone modifications, and nucleosome positioning. The clinical success of DNA methylation inhibitors as a treatment for hematological malignancies has generated interest in expanding the use of these therapies. However, evidence suggests that epigenetic silencing is re-established when drug is withdrawn, often leading to disease reoccurrence and/or resistance to therapy. The broad objectives of this proposal are to determine how epigenetic alterations integrate in a gene-specific context to enforce aberrant epigenetic environments that silence or repress TSG expression.
Specific Aims and Methods:
Aim 1 is to determine the temporal sequence of molecular events associated with epigenetic resilencing. The primary goals of Aim 1 are to determine the temporospatial distribution of DNA methylation, histone modifications, and chromatin accessibility during the onset of TSG resilencing. Cultured cells will be treated with a DNA methyltransferase (DNMT) inhibitor to activate expression of epigenetically-silenced TSGs. Subsequent drug withdrawal potentiates TSG resilencing, which will be monitored in time course studies by novel epigenetic assays that we have developed. These studies will profile the appearance of epigenetic marks at four TSGs during the transition from active to repressed transcription versus two TSGs that remain active. A chief secondary objective is to develop an innovative epigenetic technology that enables investigators to assess directly if these changes map to the same or different molecules in a heterogeneous population of cells by linking chromatin immunoprecipitation and methyltransferase footprinting with bisulfite genomic sequencing.
In Aim 2, Next Gen sequencing technologies will be optimized to simultaneously query DNA methylation and chromatin accessibility at 2,000 epigenetically-regulated promoters over a time course of gene resilencing. Coupled with gene expression microarray studies, this aim tests for global patterns of gene resilencing that may point to chromosomal position, gene ontology or mechanistic regulators.
Aim 3 is to determine the extent to which epigenetic modifiers alter resilencing. The goals of this aim are to formulate working models of cause and effect in TSG silencing that will be tested by RNAi knockdown studies in pharmacologically de-repressed cells. These experiments are expected to discriminate between molecules responsible for maintenance or reprogramming of TSG silencing. Relevance: Elucidating epigenetic mechanisms that drive gene resilencing is crucial to a better understanding epigenetic dysfunction and therapy. Determining the temporal sequence of events leading to gene resilencing is expected to identify potential biomarkers of disease resistance. The mechanistic RNAi studies are expected to uncover new targets for therapeutic interventions and/or point to therapeutic strategies that will enhance the efficacy of clinically-used DNA methylation inhibitors.

Public Health Relevance

While the genetic basis of cancer is well established, epigenetic alterations have only recently been recognized as major mediators of cancer and many other diseases. Since epigenetic alterations are reversible, they represent attractive targets for disease treatment and prevention. Identifying the molecules that direct epigenetic signaling in cancer cells is crucial to understanding how to successfully prevent and treat disease.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
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Special Emphasis Panel (ZRG1-GGG-E (91))
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Okano, Paul
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University of Florida
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Stees, Jared R; Hossain, Mir A; Sunose, Tomoki et al. (2016) High Fractional Occupancy of a Tandem Maf Recognition Element and Its Role in Long-Range ?-Globin Gene Regulation. Mol Cell Biol 36:238-50
Lu, Zhengfei; Lieber, Michael R; Tsai, Albert G et al. (2015) Human lymphoid translocation fragile zones are hypomethylated and have accessible chromatin. Mol Cell Biol 35:1209-22
Pardo, Carolina E; Nabilsi, Nancy H; Darst, Russell P et al. (2015) Integrated DNA methylation and chromatin structural analysis at single-molecule resolution. Methods Mol Biol 1288:123-41
Ai, Lingbao; Kim, Wan-Ju; Alpay, Merve et al. (2014) TRIM29 suppresses TWIST1 and invasive breast cancer behavior. Cancer Res 74:4875-87
Nabilsi, Nancy H; Deleyrolle, Loic P; Darst, Russell P et al. (2014) Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma. Genome Res 24:329-39
Siebzehnrubl, Florian A; Silver, Daniel J; Tugertimur, Bugra et al. (2013) The ZEB1 pathway links glioblastoma initiation, invasion and chemoresistance. EMBO Mol Med 5:1196-212
Nabilsi, Nancy H; Ryder, Daniel J; Peraza-Penton, Ashley C et al. (2013) Local depletion of DNA methylation identifies a repressive p53 regulatory region in the NEK2 promoter. J Biol Chem 288:35940-51
Darst, Russell P; Haecker, Irina; Pardo, Carolina E et al. (2013) Epigenetic diversity of Kaposi's sarcoma-associated herpesvirus. Nucleic Acids Res 41:2993-3009
Santostefano, Katherine E; Hamazaki, Takashi; Pardo, Carolina E et al. (2012) Fibroblast growth factor receptor 2 homodimerization rapidly reduces transcription of the pluripotency gene Nanog without dissociation of activating transcription factors. J Biol Chem 287:30507-17
Darst, Russell P; Nabilsi, Nancy H; Pardo, Carolina E et al. (2012) DNA methyltransferase accessibility protocol for individual templates by deep sequencing. Methods Enzymol 513:185-204

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