Novel Bifunctional Molecules Redirect Chromatin Machinery and Control Gene Expression

Chromatin regulatory pathways are commonly disrupted in many human diseases including cancer, yet much remains unknown about the mechanisms by which these pathways lead to disease pathology. To investigate and control these complex interactions in live cells, we took a fresh approach combining protein engineering with synthetic chemistry using a gene-specific manipulation strategy. We synthesized a new class of bi-functional compounds, Chemical Epigenetic Modifiers (CEM)s, with one warhead arm that engages endogenous chromatin regulators, while the other targeting arm tethers the captured epigenetic regulatory machinery to the gene of interest. Here we will present two classes of CEMs: one set that increases transcriptional activity by recruiting histone acetyltransferases and another set that decreases gene activity by recruiting histone deacetylases. To achieve gene specificity, our system uses a dCas9 (deactivated Cas9)-FKBP (FK506-binding protein) fusion protein. The FKBP portion binds the CEMs through a tight FKBP-FK506 interaction, allowing us to implement the desired enzymatic at any region of the genome to which we design a guide RNA. By refining dCas9 recruitment strategies, we have optimized our dCas9-CEMs system to activate or repress endogenous mammalian genes. We are now using our repressive CEM system to target genes driving hard-to-treat cancers, such as the androgen receptor in castration resistant prostate cancers. We hypothesize that by repressing the activity of the androgen receptor pathway at the chromatin level, the prostate cancer cells will undergo apoptosis and circumvent the drug resistance observed in the clinic. This work represents a novel mechanistic tool that is capable of modulating gene-specific expression in a reversible and dose-dependent manner and with the potential to become a new personalized therapeutic restricting broadly acting epigenetic inhibitors to relevant genetic loci.