Biology subjects

Wylie, D. C.

Publications and source records attributed to Wylie, D. C..

6 recordsLinked to original sources

bioRxiv2025

Postnatal maternal care impacts hypothalamic Esrrg gene expression, co-expression profiles, and the DNA methylome in prenatal bisphenol-exposed rats

BackgroundEnvironmental exposures co-occurring during early life have a profound influence on neurodevelopment. Our previous work in rats suggests that postnatal maternal care modulates the effects of prenatal exposure to bisphenols, an estrogenic endocrine disrupting chemical, on offspring neurodevelopment. Elevated maternal licking/grooming and prenatal bisphenol exposure have opposing effects on estrogen receptor expression in the medial preoptic area (MPOA), which could impact expression of estrogen-responsive genes. We hypothesized that maternal licking/grooming would mitigate the effects of prenatal bisphenol exposure on estrogen receptor signaling in the developing MPOA. In addition, we hypothesized that there would be interactive effects of prenatal bisphenol exposure and maternal licking/grooming on DNA methylation nearby estrogen responsive elements. ResultsOur results suggest that maternal licking/grooming normalized prenatal bisphenol-induced upregulation of estrogen-related receptor gamma (Esrrg) expression in female pups. These mitigating impacts were also evident in co-expression gene profiles that were enriched for estrogen-responsive genes. DNA methylation analyses indicated that maternal licking/grooming levels influenced the number of differentially methylated regions for prenatal bisphenol-exposed pups. These differentially methylated regions were enriched for binding sites for transcription factors that are known to interact with estrogen receptors. Finally, supplemental "licking-like" tactile stimulation normalized the DNA methylome in prenatal bisphenol-exposed female pups, with an increase and normalization of ESRRG binding to ESRRG-responsive genes. ConclusionsThese results identify a novel biological mechanism in which maternal licking/grooming can mitigate the negative neurodevelopmental impacts of prenatal bisphenol exposure and provides a proof-of-concept for postnatal tactile stimulation as a potential intervention strategy to improve neurodevelopmental outcomes.

genomics↗

bioRxiv2023

Apobec-Mediated Retroviral Hypermutation In Vivo is Dependent on Mouse Strain

Replication of the complex retrovirus mouse mammary tumor virus (MMTV) is antagonized by murine Apobec3 (mA3), a member of the Apobec family of cytidine deaminases. We have shown that MMTV-encoded Rem protein inhibits proviral mutagenesis by the Apobec enzyme, activation-induced cytidine deaminase (AID) during viral replication in BALB/c mice. To further study the role of Rem in vivo, we have infected C57BL/6 (B6) mice with a superantigen-independent lymphomagenic strain of MMTV (TBLV-WT) or a mutant strain (TBLV-SD) that is defective in Rem and its cleavage product Rem-CT. Unlike MMTV, TBLV induced T-cell tumors in {micro}MT mice, indicating that mature B cells, which express the highest AID levels, are not required for TBLV replication. Compared to BALB/c, B6 mice were more susceptible to TBLV infection and tumorigenesis. The lack of Rem expression accelerated B6 tumorigenesis at limiting doses compared to TBLV-WT in either wild-type B6 or AID-deficient mice. However, unlike proviruses from BALB/c mice, high-throughput sequencing indicated that proviral G-to-A or C-to-T changes did not significantly differ in the presence and absence of Rem expression. Ex vivo stimulation showed higher levels of mA3 relative to AID in B6 compared to BALB/c splenocytes, but effects of agonists differed in the two strains. RNA-Seq revealed increased transcripts related to growth factor and cytokine signaling in TBLV-SD-induced tumors relative to those from TBLV-WT, consistent with a third Rem function. Thus, Rem-mediated effects on tumorigenesis in B6 mice are independent of Apobec-mediated proviral hypermutation.

microbiology↗

bioRxiv2021

Massively Parallel Selection of NanoCluster Beacons

NanoCluster Beacons (NCBs) are multicolor silver nanocluster probes whose fluorescence can be activated or tuned by a proximal DNA strand called the activator. While a single-nucleotide difference in a pair of activators can lead to drastically different activation outcomes, termed the polar opposite twins (POTs), it is difficult to discover new POT-NCBs using the conventional low-throughput characterization approaches. Here we report a high-throughput selection method that takes advantage of repurposed next-generation-sequencing (NGS) chips to screen the activation fluorescence of [~]40,000 activator sequences. We find the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs and positions 4-6 and 2-4 are hotspots to generate yellow and red POTs, respectively. Based on these findings, we propose a "zipper bag model" that explains how these hotspots lead to the creation of distinct silver cluster chromophores and contribute to the difference in chromophore chemical yields. Combining high-throughput screening with machine learning algorithms, we establish a pipeline to rationally design bright and multicolor NCBs.

bioengineering↗

bioRxiv2019

Identification of peptide coatings that enhance diffusive transport of nanoparticles through the tumor microenvironment

In solid tumors, increasing drug penetration promotes their regression and improves the therapeutic index of compounds. However, the heterogeneous extracellular matrix (ECM) acts a steric and interaction barrier that hinders effective transport of therapeutics, including nanomedicines. Specifically, the interactions between the ECM and surface physicochemical properties of nanomedicines (e.g. charge, hydrophobicity) impedes their diffusion and penetration. To address the challenges using existing surface chemistries, we used peptide-presenting phage libraries as a high-throughput approach to screen and identify peptides as coatings with desired physicochemical properties that improve diffusive transport through the tumor microenvironment. Through iterative screening against the ECM and identification by next-generation DNA sequencing and analysis, we selected individual clones and measured their transport by diffusion assays. Here, we identified a net-neutral charge, hydrophilic peptide P4 that facilitates significantly higher diffusive transport of phage than negative control through in vitro tumor ECM. Through alanine mutagenesis, we confirmed that the hydrophilicity, charge, and their spatial ordering impact diffusive transport. P4 phage clone exhibited almost 200-fold improved uptake in ex vivo pancreatic tumor xenografts compared to the negative control. Nanoparticles coated with P4 exhibited [~]40-fold improvement in diffusivity in pancreatic tumor tissues, and P4-coated particles demonstrated less hindered diffusivity through the ECM compared to particles functionalized with gold standard poly(ethylene) glycol or iRGD peptide ligand. By leveraging the power of molecular diversity using phage display, we can greatly expand the chemical space of surface chemistries that can improve the transport of nanomedicines through the complex tumor microenvironment to ultimately improve their efficacy.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC=\"FIGDIR/small/659524v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (23K):\norg.highwire.dtl.DTLVardef@18bc04forg.highwire.dtl.DTLVardef@1feb597org.highwire.dtl.DTLVardef@14403e5org.highwire.dtl.DTLVardef@5bbf6c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2019

A combinatorial biomolecular strategy to identify peptides for improved transport across the sputum of cystic fibrosis patients and the underlying epithelia

Drugs and drug delivery systems have to traverse multiple biological barriers to achieve therapeutic efficacy. In diseases of mucosal-associated tissues such as cystic fibrosis (CF), successful delivery of gene and drug therapies remains a significant challenge due to an abnormally concentrated viscoelastic mucus, which prevents ~99% of all drugs and particles from penetrating the mucus barrier and the underlying epithelia for effective therapy, resulting in decreased survival. We used combinatorial peptide-presenting phage libraries and next-generation sequencing to identify hydrophilic, close to net-neutral charged peptides that penetrate the mucus barrier ex vivo in sputum from CF patients with ~600-fold better penetration than a positively charged control. After mucus penetration, nanoparticles conjugated with our selected peptides successfully translocated into lung epithelial cells derived from CF patients and demonstrated up to three-fold improved cell uptake compared to non-modified carboxylated- and gold standard PEGylated-nanoparticles. The selected peptides act as surface chemistries with synergistic functions to significantly improve the ability of drug delivery systems to overcome the human mucosal barriers and provide efficient cellular internalization. Our screening strategy provides a biologically-based discovery assay that directly addresses transport through mucus and cell barriers and has the potential to advance drug and gene delivery to multiple mucosal barriers.

bioengineering↗

bioRxiv2017

SArKS: Discovering Gene Expression Regulatory Motifs And Domains By Suffix Array Kernel Smoothing

MotivationWe set out to develop an algorithm that can mine differential gene expression data to identify candidate cell type-specific DNA regulatory sequences. Differential expression is usually quantified as a continuous score--fold-change, test-statistic, p-value--comparing biological classes. Unlike existing approaches, our de novo strategy, termed SArKS, applies nonparametric kernel smoothing to uncover promoter motifs that correlate with elevated differential expression scores. SArKS detects motifs by smoothing sequence scores over sequence similarity. A second round of smoothing over spatial proximity reveals multi-motif domains (MMDs). Discovered motifs can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.\n\nResultsWe applied SArKS to published gene expression data representing distinct neocortical neuron classes in M. musculus and interneuron developmental states in H. sapiens. When benchmarked against several existing algorithms for correlative motif discovery using a cross-validation procedure, SArKS identified larger motif sets that formed the basis for regression models with higher correlative power.\n\nAvailabilityhttps://github.com/denniscwylie/sarks.\n\nContactdenniswylie@austin.utexas.edu.\n\nSupplementary informationappended to document.

bioinformatics↗