Chemical Biology Platforms to Define the Metabolism-Epigenetics Interface

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

The goal of this project is to characterize and control novel modification-based regulatory mechanisms that drive altered gene activity in cancer. The majority of our initial efforts in this area have focused on the study of protein and nucleic acid acetylation. Using a suite of novel chemical biology platforms that allow us to study cellular acetylation mechanisms, we have discovered new enzymatic and non-enzymatic acetylation mechanisms that are highly elevated in cancer. In addition, we have made substantial progress characterizing the activity, druggability, and metabolic regulation of these mechanisms. These advances are grouped according to three specific aims. 1. Discovery and characterization of novel acetyltransferase enzymes. Chemoproteomic profiling studies in our lab led to the discovery that a relatively uncharacterized acetyltransferase, NAT10, is highly upregulated in a variety of cancer cell lines, and also sensitive to the metabolic state of the cell. Subsequent work has revealed the primary function of NAT10 is the catalysis of RNA cytidine acetylation, which evidence suggests extends to diverse elements of the transcriptome including ribosomal RNA and transfer RNA. Over the past year we have applied multiscale chemical approaches developed in our lab (Bartee et al. JACS 2022, Link et al. Biochemistry 2022) to biologically, biophysically, and biochemically characterize cytidine acetyltransferase activity across the tree of life. This is being used to gain novel insights into the mechanisms by which RNA acetylation is installed (Bortolin-Cavaille et al., Nucleic Acids Research 2021, Gamage et al. NAR 2022) as well as its role in cancer development and progression. We are also using knowledge developed in these studies to understand how base modifications influence RNA-protein interactions in synthetic mRNA therapeutic such as the COVID-19 vaccines, a topic of substantial public interest (Nance et al., ACS Central Science 2021, Nance et al. Cell Chemical Biology 2022). 2. Characterization of acetyltransferase inhibitors. Targeting the cellular acetylation machinery is an emerging paradigm in oncology. However, relatively few small molecule inhibitors of acetyltransferases are known. To address this unmet need, our group has developed biochemical, chemoproteomic, and cell-based assays that can be used to unambiguously interrogate the activity of small molecule acetyltransferase inhibitors. These methods enabled the first evidence for cellular occupancy and on-target activity of a small molecule lysine acetyltransferase inhibitor as well as N-terminal acetyltransferase inhibitors. Currently we are applying these approaches in collaboration with industry to define the selectivity of novel classes of acetyltransferase inhibitors (Kung et al. ACS Med Chem Lett, 2020; Jing et al. ACS Chem Biol 2021, Lieberman et al. biorxiv 2022, Crawford et al. biorxiv 2023) and aid the pre-clinical and clinical development of these compounds for cancer treatment. Finally, we continue to apply our methods to characterize the pan-assay interference features of reported acetyltransferase inhibitors (Dahlin et al. Nat Comm 2023). These studies critical are crucial to aiding the interpretation of the activity of these molecules in cellular assays and providing impetus for the discovery of drug-like acetyltransferase inhibitors. 3. Metabolic regulation of epigenetics. Emerging evidence indicates that metabolism itself may function as a modification-based regulatory or "epigenetic" mechanism, through the ability of metabolites to modulate the activity of enzymes involved in epigenetic and epitranscriptomic regulation of gene expression, as well as directly react with amino acid residues leading to the deposition of non-enzymatic protein posttranslational modifications. Our previous work has focused on the development of technologies for studying the metabolic regulation of acetylation. Over the past two years, we have extended these methods to study the mechanism of action of oncometabolites, a class of cancer metabolites that can directly trigger tumorigenic signaling. Using the oncometabolite fumarate which accumulates in the hereditary cancer syndrome predisposition HLRCC as an initial model, we have shown that chemoproteomic methods can be used to identify hotspots of oncometabolite reactivity and target them via a principle we have cubbed 'covalent collateral lethality' (Perez et al., ACS Chem Biol, 2022). In our current and future work we are extending these approaches to pathway discovery in biological systems driven by non-covalent oncometabolite-protein interactions, including cancer and inborn errors of metabolism (Head et al., J. Inherit. Metab. Dis. 2023).