Site-specific epigenetic activation of TP53 to improve cancer therapy

ABSTRACTThe disruption of epigenetic pathways are key driving mechanisms that contribute to myriad human diseases. Recent advances in chromatin biology and high-throughput genetic sequencing have discovered that such disruptions underlie a substantial number of cancers. While the affected epigenetic pathways that contribute to cancer pathophysiology are quite diverse, a common theme among them is that aberrant regulation of epigenetic enzymes can lead to dysregulated expression of key disease driver genes. For example, aberrant DNA methylation, histone H3 methylation and/or histone H3 deacetylation can repress genes, and lead to a more deleterious disease phenotype. Indeed, broad-acting pan-epigenetic inhibitors have shown initial promise clinically by grossly disrupting disease signaling pathways by altering the expression profile of key genes. However, a fundamental issue related to the mechanism of these traditional epigenetic inhibitors centers on their potential to affect thousands of genes simultaneously (both on- and off-target). Thus, while treatment with histone deacetylase (HDAC) inhibitors causes the desired effect of activation of specific target genes, this activation also comes with off-target activation of potentially hundreds to thousands of additional genes. Recently, technological advancements on the CRISPR/Cas9 system have been developed to allow for induction of site-specific chromatin modifications that can modulate gene expression. Our technological advancements build on these approaches and allow for the possibility of developing targeted, epigenetically based gene therapeutics with real potential for clinical translation.Here, we outline an approach that leverages a site-specific dCas9-FKBP fusion protein, coupled with a synthetic bifunctional chemical epigenetic modifier (CEM). The CEM consists of three modular components: (1) FK506 (which binds FKBP); (2) a short inert chemical polyethylene glycol (PEG) linker; and (3) a chemical entity that interacts with host epigenetic machinery. Ultimately, the dCas9-FKBP CEM has the ability to target any locus in the genome, and “activate” epigenetic activity to modulate gene expression. We propose to implement this strategy to a clinically relevant target: TP53. Our proposed technology seeks to target endogenous histone acetylation enzymes to the TP53 locus to reverse its epigenetic repression, and thus increase the sensitivity of tumor cells to chemotherapeutic agents. As a first step, we propose to evaluate our technology in preclinical models of colorectal cancer. Colorectal cancer is the third most commonly diagnosed cancer and third cancer most common cause of cancer-related death among both men and women. Additionally, colorectal cancer is known to be driven by both mutated and epigenetically silenced TP53, and there are available preclinical model systems that recapitulate was is observed clinically. Long-term our novel platform could represent an innovative and curative treatment for many epigenetically driven human cancers.NARRATIVE While the pathways underlying cancer is quite diverse, a common theme among them is the inappropriate repression of tumor suppressor genes or activation of oncogenes (i.e., abnormal epigenetic regulation). Technologies that can specifically restore the normal state of these otherwise normal genes would provide a new way to treat cancer. Our proposed technology will make a novel contribution to cancer research by offering a new personalized epigenome-based approach therapeutic that treats cancer through a novel mechanism at the root of the gene mis-regulation.