Biology subjects

Fox, B.

Publications and source records attributed to Fox, B..

6 recordsLinked to original sources

bioRxiv2025

DNA extraction free whole genome sequencing of bacteriophage genomes from a single plaque

DNA sequencing is at the core of genome characterization, proteomics, and identification of novel organisms. For microorganisms such as bacteriophages, sequencing their DNA can provide key insights into their tropism, infectivity, and virulence. There remains however a critical lack of rapid sequencing techniques with the traditional process of replating and incubating individual plaques, collecting lysate, extracting DNA, preparing the DNA library, and sequencing that is labor intensive. Herein, we demonstrate the use of an adapted Nanopore Rapid PCR Barcoding protocol to sequence the bacteriophage genome directly from individual plaques. This technique provides sequencing genome assemblies with 99.88-100% (mean 99.97%) average nucleotide identity (ANI) scores when compared to the traditional methods involving phage amplification, extraction, and sequencing using Illumina. The optimization of bacteriophage identification by the technique of tagmentation directly to isolated plaques will enable rapid and cost-effective sequencing of novel phages.

microbiology↗

bioRxiv2025

Predictable modulation of a spontaneous post-translational modification in living cells

Glycation is a non-enzymatic post-translational modification associated with aging and disease. Because it occurs spontaneously, it is extremely difficult to control the extent of glycation at distinct sites within target proteins, especially in cellular systems. Here we report a chemical approach, referred to as dialAGE, that enables the site-specific control of protein glycation. This unique tool requires the introduction of just a single point mutation that modulates the glycation susceptibility of a nearby arginine. As proof-of-concept, extensive mass spectrometry analysis was performed to confirm that dialAGE can modulate site-specific glycation levels at multiple arginine residues in ubiquitin in vitro, enabling both enhanced and diminished glycation. Introduction of dialAGE point mutations and/or glycation with the biologically relevant glycating agent methylglyoxal did not affect polyubiquitin chain formation using in vitro ubiquitination assays. Furthermore, we show that dialAGE can be used to modulate ubiquitin glycation levels in living mammalian cells. We therefore anticipate that this method will be particularly useful for enabling the study of glycation as a genuine, functional, post-translational modification.

biochemistry↗

bioRxiv2023

Evolutionarily related host and microbial pathways regulate fat desaturation

Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression1-4, but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPAR in C. elegans. Untargeted metabolomics of a {beta}-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a {beta}- cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a {beta}-methyl fatty acid, bemeth#1, whose activity mimics that of microbiota-dependent becyp#1, but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated {beta}-oxidation pathway, while the endogenous bemeth#1 is metabolized via -oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPAR to regulate fat desaturation.

biochemistry↗

bioRxiv2023

Lipid nanoparticle structure and delivery route during pregnancy dictates mRNA potency, immunogenicity, and health in the mother and offspring

Treating pregnancy-related disorders is exceptionally challenging because many small molecule drugs on the market may cause maternal and fetal toxicity. This potential danger has hindered the development and clinical evaluation of new drugs for several decades. Lipid nanoparticle (LNP)-based RNA therapies with high delivery efficacy, favorable immune response, and minimal transplacental transport can quell maternal-fetal toxicity concerns and propel the development of pregnancy-safe drugs. To this extent, we report potent LNP structures that robustly deliver mRNA to maternal organs and placenta. Using structure-function analysis, we show that LNP efficacy is influenced by the polyamine headgroup, and toxicity is governed by the acrylate tail. Our lead nanoparticle shows robust protein expression via multiple clinically relevant administration routes in pregnant mice. In the placenta, it transfects trophoblasts, endothelial cells, and immune cells. Further, by varying ionizable lipid structure, we demonstrate that LNP immunogenicity affects organ expression and pup health during pregnancy. Immunogenic LNPs show lower efficacy in lymphoid organs in an IL-1{beta} dependent manner in pregnant mice. Further, pro-inflammatory immune responses provoke the infiltration of adaptive immune cells in the placenta and restrict pup growth after birth. Together, our results provide a mechanistic basis for designing safe and potent LNPs that can be administered during pregnancy.

bioengineering↗

bioRxiv2023

FcyRIIB is a novel immune checkpoint in the tumor microenvironment limiting activity of Treg-targeting antibodies

Despite pre-clinical murine data supporting T regulatory (Treg) cell depletion as a major mechanism by which anti-CTLA-4 antibodies function in vivo, the two main antibodies tested in patients (ipilimumab and tremelimumab) have failed to demonstrate similar effects. We report analogous findings in an immunocompetent murine model humanized for CTLA-4 and Fcy receptors (hCTLA-4/hFcyR mice), where both ipilimumab and tremelimumab fail to show appreciable Treg depletion. Immune profiling of the tumor microenvironment (TME) in both mice and human samples revealed upregulation of the inhibitory Fcy receptor, FcyRIIB, which limits the ability of the antibody Fc fragment of human anti-CTLA-4 antibodies to induce effective antibody dependent cellular cytotoxicty/phagocytosis (ADCC/ADCP). Blocking FcyRIIB in humanized mice rescues Treg depleting capacity and anti-tumor activity of ipilimumab. For another target, CC motif chemokine receptor 8 (CCR8), which is selectively expressed on tumor infiltrating Tregs, we show that Fc engineering to enhance binding to activating Fc receptors, while limiting binding to the inhibitory Fc receptor, leads to consistent Treg depletion and single-agent activity across multiple tumor models, including B16, MC38 and MB49. These data reveal the importance of reducing engagement to the inhibitory Fc receptor to optimize Treg depletion by TME targeting antibodies. Our results define the inhibitory FcyRIIB receptor as a novel immune checkpoint limiting antibody-mediated Treg depletion in tumors, and demonstrate Fc variant engineering as a means to overcome this limitation and augment efficacy for a repertoire of antibodies currently in use or under clinical evaluation in oncology. Highlights- Fully human anti-CTLA-4 antibodies are limited in their capacity to deplete T regulatory cells and drive durable anti-tumor immunity in humanized FcyR/hCTLA-4 mice - The inhibitory Fcy receptor, FcyRIIB, is upregulated in the tumor microenvironment in patients and in humanized FcyR/hCTLA-4 mice - Blocking FcyRIIB leads to rescue of Treg depletion in humanized murine models - Fc engineering can improve the depleting capacity and in vivo anti-tumor activity of anti-CTLA and anti-CCR8 antibodies targeting tumor infiltrating Tregs

immunology↗

bioRxiv2019

Integrative network modeling reveals mechanisms underlying T cell exhaustion

Failure to clear antigens causes CD8+ T cells to become increasingly hypo-functional, a state known as exhaustion. We combined manually extracted information from published literature with gene expression data from diverse model systems to infer a set of molecular regulatory interactions that underpin exhaustion. Topological analysis and simulation modeling of the network suggests CD8+ T cells undergo 2 major transitions in state following stimulation. The time cells spend in the earlier proliferative/pro-memory (PP) state is a fixed and inherent property of the network structure. Transition to the second state is necessary for exhaustion. Combining insights from network topology analysis and simulation modeling, we predict the extent to which each node in our network drives cells towards an exhausted state. We demonstrate the utility of our approach by experimentally testing the prediction that druginduced interference with EZH2 function increases the proportion of proliferative/pro-memory cells in the early days post-activation.

systems biology↗