Epigenetic modifications play a key role in tumor origin and progression. Oncogenic transcription factors (TFs) are frequently over-expressed in breast cancers, while being silenced in normal epithelial cells. TFs can switch entire transcriptional gene cascades, resulting in tumor initiation and progression. Since most TFs do not have intrinsic enzymatic activities and they lack small-molecule-binding pockets, these targets have been refractory to drug design. The oncogenic TFs Sox2 is over-expressed in breast cancers of advanced stage, while the gene is silenced and hyper-methylated in normal epithelial cells. As a stable repressive mark, DNAme catalyzed by DNA-methyltransferases, is regarded as a key player in epigenetic silencing. DNAme orchestrate other epigenetic modifications, shaping the architecture of the promoter and driving chromatin condensation and gene silencing. A hallmark of DNAme is that it is hereditary and thereby transmitted over cell generations. In many developmentally regulated TFs, such as Sox2, DNAme constitute an epigenetic switch, which changes cells from an active mitogenic state towards a G0/G1 arrest and differentiation. In this application, our objective is to target DNAme into the promoter of Sox2, which is highly expressed in breast cancer cell lines, with levels comparable or superior to embryonic stem cells. To direct specific DNAme, we will fuse engineered DNA-binding proteins made of sequence-specific Zinc Finger (ZF) domains with a catalytically active DNA-methyltransferase domain (Dnmt3a). Our objective is to restore the hereditable epigenetic silencing in the Sox2 promoter of the tumor cell in a pattern that is similar to breast epithelial cells. We hypothesize that ZFs-Dnmt3a fusions are able to target DNAme marks into the Sox2 oncogenic promoter, resulting in transmission of these marks over cell generations. This epigenetic memory will be accompanied by the maintenance of the transcriptional silencing and tumor cell growth inhibition.
In Aim1 we propose the construction of 6ZF proteins linked to the Dnmt3a and inactive mutants, to assess whether these engineered proteins deposit specific silencing marks into the Sox2 promoter, resulting in oncogenic silencing.
In Aim2 we monitor the longevity of the silencing implemented by the 6ZF- silencers. We will express the 6ZF constructs using inducible vectors to "pulse" and "chase" DNAme in cell culture and breast tumor models. Next, to move the technology towards a pre-clinical phase, we will deliver ATF mRNAs using nanoparticles that will be injected in mouse models of breast cancer (Aim 3). While RNAi technology can be used to knock-down oncogenes, its therapeutic effect is transient because of the short-lived time of the small RNA. The significance of this application is the potential of the ZF agent to induce an endogenous epigenetic reprogramming of the target TF, which is expected to maintain the longevity of the therapeutic effect. Thus, this work will be of vital importance to develop stable, inherited, oncogenic silencing methods, to suppress oncogenic expression in tumor cells.

Public Health Relevance

Oncogenic Transcription Factors (TFs) play a critical role in the initiation and progression of human tumors. These genes are often epigenetically dysregulated, being aberrantly hypomethylated and over-expressed in cancer cells, relative to normal tissues. Due to their lack of small-molecule binding pockets, TFs are very refractory to small molecule-based approaches. Our work provides a new strategy to suppress the expression of these classically undruggable targets. We propose the design of zinc finger proteins linked to catalytically active DNA-methyltransferase domain to restore the epigenetic silencing these genes. By reprogramming the epigenetic silencing of tumor cells we hope to promote inherited changes in the epigenome of cancer cells and ultimately induce a more stable anti-tumor and therapeutic effect, helping minimize tumor relapse even if the ZF agent is discontinued. This work will provide sequence-specific molecular devices to stably restore the epigenetic silencing of oncogenic TFs. Our work will lead to the development of novel therapeutic agents for the treatment of aggressive breast and ovarian cancers, for which no cure is available.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA170370-03
Application #
8817228
Study Section
Special Emphasis Panel (ZCA1-SRLB-9 (M1))
Program Officer
Okano, Paul
Project Start
2012-08-01
Project End
2016-05-31
Budget Start
2014-06-01
Budget End
2015-05-31
Support Year
3
Fiscal Year
2014
Total Cost
$134,377
Indirect Cost
$16,102
Name
University of Western Australia
Department
Type
DUNS #
889328519
City
Crawley
State
Country
Australia
Zip Code
6009
Grimmer, Matthew R; Stolzenburg, Sabine; Ford, Ethan et al. (2014) Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. Nucleic Acids Res 42:10856-68