Biology subjects

Nguyen, P. A.

Publications and source records attributed to Nguyen, P. A..

4 recordsLinked to original sources

bioRxiv2025

Discovery and characterization of FX-909, a covalent inverse agonist of PPARG rationally designed to impose a powerful repressive bias in PPARG for the treatment of PPARG/RXRA-activated muscle-invasive urothelial cancers

We report our mechanistic investigation into the conformationally-driven activation bias of PPARG in muscle-invasive urothelial cancer (MIUC) and our efforts to pharmacologically reverse this activation bias through covalent PPARG inverse agonism. We utilized studies into tumor-associated mutations in both PPARG and RXRA, as well as a combination of structure-based drug design merged with insights from biochemical mechanistic studies to discover FX-909, a first-in-class clinical PPARG inverse agonist that robustly enforces a conformationally repressive state of PPARG, even in highly activated contexts such as RXRA S427F mutation and PPARG amplification. FX-909 is a potent, highly selective, and powerful suppressor of PPARG transcriptional activity through enhancement of PPARG nuclear corepressor binding (NCOR) affinity. Treatment with FX-909 resulted in selective growth inhibition in PPARG-activated MIUC cell lines. Further, FX-909 achieved durable regressions in xenograft models of MIUC through inverse agonism of PPARG. FX-909 is the first chemical tool available to the community that is capable of recapitulating PPARG genetic knockout in vivo and is currently in clinical development for the treatment of intractable MIUC.

cancer biology↗

bioRxiv2020

Comprehensive synthetic genetic array analysis of alleles that interact with mutation of the Saccharomyces cerevisiae RecQ helicases Hrq1 and Sgs1

Most eukaryotic genomes encode multiple RecQ family helicases, including five such enzymes in humans. For many years, the yeast Saccharomyces cerevisiae was considered unusual in that it only contained a single RecQ helicase, named Sgs1. However, it has recently been discovered that a second RecQ helicase, called Hrq1, resides in yeast. Both Hrq1 and Sgs1 are involved in genome integrity, functioning in processes such as DNA inter-strand crosslink repair, double-strand break repair, and telomere maintenance. However, it is unknown if these enzymes interact at a genetic, physical, or functional level as demonstrated for their human homologs. Thus, we performed synthetic genetic array (SGA) analyses of hrq1{Delta} and sgs1{Delta} mutants. As inactive alleles of helicases can demonstrate dominant phenotypes, we also performed SGA analyses on the hrq1-K318A and sgs1-K706A ATPase/helicase-null mutants, as well as all combinations of deletion and inactive double mutants. We crossed these eight query strains (hrq1{Delta}, sgs1{Delta}, hrq1-K318A, sgs1-K706A, hrq1{Delta} sgs1{Delta}, hrq1{Delta} sgs1-K706A, hrq1-K318A sgs1{Delta}, and hrq1-K318A sgsl-K706A) to the S. cerevisiae single gene deletion and temperature-sensitive allele collections to generate double and triple mutants and scored them for synthetic positive and negative genetic effects based on colony growth. These screens identified hundreds of synthetic interactions, supporting the known roles of Hrq1 and Sgs1 in DNA repair, as well as suggesting novel connections to rRNA processing, mitochondrial DNA maintenance, transcription, and lagging strand synthesis during DNA replication.

genetics↗

bioRxiv2020

The genetic and physical interactomes of the Saccharomyces cerevisiae Hrq1 helicase

The human genome encodes five RecQ helicases (RECQL1, BLM, WRN, RECQL4, and RECQL5) that participate in various processes underpinning genomic stability. Of these enzymes, the disease-associated RECQL4 is comparatively understudied due to a variety of technical challenges. However, Saccharomyces cerevisiae encodes a functional homolog of RECQL4 called Hrq1, which is more amenable to experimentation and has recently been shown to be involved in DNA inter-strand crosslink (ICL) repair and telomere maintenance. To expand our understanding of Hrq1 and the RecQ4 subfamily of helicases in general, we took a multi-omics approach to define the Hrq1 interactome in yeast. Using synthetic genetic array analysis, we found that mutations of genes involved in processes such as DNA repair, chromosome segregation, and transcription synthetically interact with deletion of HRQ1 and the catalytically inactive hrq1-K318A allele. Pull-down of tagged Hrq1 and mass spectrometry identification of interacting partners similarly underscored links to these processes and others. Focusing on transcription, we found that hrq1 mutant cells are sensitive to caffeine and that mutation of HRQ1 alters the expression levels of hundreds of genes. In the case of hrq1-K318A, several of the most highly upregulated genes encode proteins of unknown function whose expression levels are also increased by DNA ICL damage. Together, our results suggest a heretofore unrecognized role for Hrq1 in transcription, as well as novel members of the Hrq1 ICL repair pathway. These data expand our understanding of RecQ4 subfamily helicase biology and help to explain why mutations in human RECQL4 cause diseases of genomic instability.

genetics↗

bioRxiv2018

Phenotypes associated with genes encoding drug targets are predictive of clinical trial side effects

Biomedical scientists face major challenges in developing novel drugs for unmet medical needs. Only a small fraction of early drug programs progress to the market, due to safety and efficacy failures, despite extensive efforts to predict drug and target safety as early as possible using a variety of assays in vitro and in preclinical species. In principle, characterizing the effect of natural variation in the genes encoding drug targets should present a powerful alternate approach to predict not only whether a protein will be an effective drug target, but also whether a protein will be an inherently safe drug target, while avoiding the challenges of translating biology from experiments in non-human species. We have embarked on a retrospective analysis, demonstrating for the first time a statistical link between the organ systems involved in genetic syndromes of drug target genes and the organ systems in which side effects are observed clinically. Across 1,819 drugs and 21 organ system phenotype categories analyzed, drug side effects are more likely to occur in organ systems where there is genetic evidence of a link between the drug target and a phenotype involving that organ system, compared to when there is no such genetic evidence (30.0% vs 19.2%; OR = 1.80). Conversely, we find that having genetic evidence of a Mendelian syndrome involving a drug target in which a certain organ system is unaffected decreases the likelihood that side effects will manifest in that organ system, relative to having no informative syndrome (18.5% vs 20.2%; OR = 0.89). We find a relationship between genetics and side effects even when controlling for known confounders such as drug delivery route and indication. We highlight examples where genetics of drug targets could have anticipated side effects observed during clinical trials. This result suggests that human genetic data should be routinely used to predict potential safety issues associated with novel drug targets. This may lead to selection of better targets, appropriate monitoring of putative side effects early in development, reduction of the use of preclinical animal experiments, and ultimately increased success of molecules. Furthermore, deeply phenotyping human knockouts will be critically important to understand the full spectrum of effects that a new drug may elicit.

genetics↗