Biology subjects

Fox, S. D.

Publications and source records attributed to Fox, S. D..

3 recordsLinked to original sources

bioRxiv2024

5hmC enhances PARP trapping and restores PARP inhibitor sensitivity in chemoresistant BRCA1/2-deficient cells

Mutations in BRCA1 and BRCA2 genes are the leading cause of hereditary breast and ovarian cancer. BRCA1/2-mutant cells are defective in repairing damaged DNA by homologous recombination and are characterized by hypersensitivity to PARP inhibitors. PARP inhibitors can trap PARP proteins on the chromatin, a mechanism that can contribute to the death of BRCA1/2-deficient cells. The FDA has approved multiple PARP inhibitors for the treatment of metastatic breast and ovarian cancers, but despite the success of PARP inhibitors in treating BRCA1/2-mutant cancers, drug resistance is a major challenge. Here, we report that 5hmC enhances PARP1 trapping on the chromatin in olaparib-treated cells. Elevated PARP trapping generates replication gaps, leading to the restoration of PARP inhibitor sensitivity in chemoresistant BRCA1/2-deficient cells. Our findings suggest that combining 5hmC with olaparib can restore the sensitivity of chemoresistant BRCA1/2-deficient cells.

cancer biology↗

bioRxiv2021

Protonation-Dependent Sequencing of 5-Formylcytidine in RNA

Chemical modification of cytidine in non-coding RNAs plays a key role in regulating translation and disease. However, the distribution and dynamics of many of these modifications remains unknown due to a lack of sensitive site-specific sequencing technologies. Here we report a protonation-dependent sequencing reaction for detection of 5-formylcytidine (5fC) and 5-carboxycytidine (5caC) in RNA. First, we evaluate how protonation combined with electron-withdrawing substituents alters the molecular orbital energies and reduction of modified cytidine nucleosides, highlighting 5fC and 5caC as reactive species. Next, we apply this reaction to detect these modifications in synthetic oligonucleotides as well as endogenous human tRNA. Finally, we demonstrate the utility of our method to characterize a patient-derived model of 5fC-deficiency, where it enables facile monitoring of both pathogenic loss and exogenous rescue of NSUN3-dependent 5fC within the wobble base of human mitochondrial tRNAMet. These studies showcase the ability of protonation to enhance the reactivity and sensitive detection of 5fC in RNA, and provide a molecular foundation for applying optimized sequencing reactions to better understand the role of oxidized RNA cytidine nucleobases in disease.

biochemistry↗

bioRxiv2019

A systems chemoproteomic analysis of acyl-CoA signaling networks

Acyl-CoA/protein interactions are required for many functions essential to life including membrane synthesis, oxidative metabolism, and macromolecular acetylation. However, despite their importance, the global scope and selectivity of these protein-metabolite interactions remains undefined. Here we describe the development of CATNIP (CoA/AcetylTraNsferase Interaction Profiling), a chemoproteomic platform for the high-throughput analysis of acyl-CoA/protein interactions in endogenous proteomes. First, we apply CATNIP to identify acetyl-CoA-binding proteins through unbiased clustering of competitive dose-response data. Next, we use this method to profile diverse protein-CoA metabolite interactions, identifying biological processes susceptible to altered acetyl-CoA levels. Finally, we apply systems-level analyses to assess the features of novel protein networks that may interact with acyl-CoAs, and demonstrate a strategy for high-confidence proteomic annotation of acetyl-CoA binding proteins. Overall our studies illustrate the power of integrating chemoproteomics and systems biology, and provide a resource for understanding the roles of acyl-CoA metabolites in biology and disease.

biochemistry↗