Biology subjects

Williams, D. W.

Publications and source records attributed to Williams, D. W..

14 recordsLinked to original sources

bioRxiv2026

Primary Human Macrophages Exhibit Functional CYP3A4 Activity with Marked Expression-Function Discordance and Cocaine-Induced Catalytic Activation

CYP3A4 is a phase I drug-metabolizing enzyme responsible for transformation of ~50% of clinically relevant drugs. While extensively characterized in hepatocytes, its role in immune cells remains poorly understood. Here, using primary human monocyte-derived macrophages, we identify an understudied extrahepatic site of CYP3A4-mediated drug metabolism. Macrophages from 100 independent donors expressed CYP3A4 and its transcriptional regulators, Pregnane X Receptor (PXR) and Constitutive Androstane Receptor (CAR), with substantial interindividual variability. Importantly, CYP3A4 protein expression was accompanied by measurable catalytic activity in intact macrophages, yet CYP3A4 mRNA, protein abundance, and activity lacked concordance, demonstrating that expression alone may not predict function. In vivo, CYP3A4 was expressed in rhesus macaque Kupffer cells, further supporting macrophages as a potential pharmacologic entity. We next evaluated cocaine as a potential modulator of CYP3A4, due to its role in xenobiotic clearance. Cocaine had a dichotomous effect on expression, increasing CYP3A4 in some donors while producing no change or decreases in others, a phenotype associated with PXR, CAR, and the sigma-1 cocaine receptor. Strikingly, despite these divergent expression responses, cocaine increased CYP3A4 catalytic activity in all donors, reaching or exceeding levels induced by rifampicin, a clinically relevant CYP3A4 inducer. In rhesus macaques, cocaine also decreased antiretroviral therapy tissue concentrations, coincident with increased CYP3A4 and PXR. Together, these findings establish macrophages as a functionally active extrahepatic site of CYP3A4 metabolism and reveal a critical disconnect between CYP3A4 expression and catalytic function. Moreover, our findings identify interindividual variability and expression-activity discordance as important considerations for personalized medicine and understanding clinically relevant drug-drug interactions in the context of substance use.

pharmacology and toxicology↗

bioRxiv2026

Simian Immunodeficiency Virus and Antiretroviral Therapy Impact Rhesus Macaque Brain Lipid Distribution

Human immunodeficiency virus (HIV) infection promotes considerable bioenergetic, spatially heterogenous strain to the brain that is incompletely ameliorated through viral suppression afforded by antiretroviral therapy (ART). Disrupted homeostasis of brain lipids after HIV in humans or simian immunodeficiency virus (SIV) infection in rhesus macaques occurs due to elevated energetic demands, neuroinflammation, reactive oxygen species, and barrier leakiness. Brain lipids are particularly vulnerable to HIV-associated dysregulation due to their high abundance, unique composition, and specialized functional roles. Using rhesus macaques exposed to SIV and ART (tenofovir disoproxil fumarate (TDF), emtricitabine (FTC), and dolutegravir (DTG), we investigated the spatial distribution and abundance of lipids across brain regions and metabolically relevant peripheral tissues using mass spectrometry imaging. When comparing lipid abundance, individual lipids representing a multitude of species were more varied across tissues than by treatment condition. Further, we discerned either solely SIV infection or ART outweighed one another in altering phospholipids in different tissues Presence of ART had a greater influence on phospholipid homeostasis in the temporal cortex and hippocampus than in the midbrain, possibly due to differences in penetrance and turnover of ART across brain regions. Overall, these data demonstrate ART robustly increased phospholipids across brain regions while SIV infection had a varied impact depending on the brain region. These findings inform the need to further evaluate the neurologic consequences that may result in the brain due to disrupted lipid homeostasis across ART regimens.

pharmacology and toxicology↗

bioRxiv2025

Antiviral and Anti-inflammatory Effects of Cannabidiol in HIV/SIV Infection

Persistent reservoirs and chronic immune activation are hallmarks of HIV, despite the effectiveness of antiretroviral therapy (ART) in suppressing viral replication. Here, we use rhesus macaques and primary and induced pluripotent stem cell (iPSC)-derived human immune cells to evaluate the virologic and immunologic consequences of cannabidiol (CBD) exposure during HIV/SIV infection. We show that CBD, in the absence of ART, suppresses viral replication and establishment of the viral reservoir to levels comparable with first-line therapies during acute SIV infection of rhesus macaques. This antiviral effect of CBD extended to in vitro HIV infection of human macrophages, T cells, and microglia. Immunologically, we observe CBD slowed CD4+ T cell decline and polarization, decreased CD14+CD16+ monocyte expansion, and reduced interferon-inducible cytokine release in rhesus macaques. We identify comparable effects on cytokine production with in vitro CBD treatment of human macrophages, T cells, and microglia. Importantly, we find CBD inhibits cytokines only when an immune response is elicited by HIV, suggesting it is not broadly immunosuppressive. Finally, we determine CBD regulates endocannabinoid receptors, modulators, and transporters and inhibits NF-{kappa}b and STAT1 activation when mediating its antiviral and anti-inflammatory effects. These findings show beneficial effects of CBD in laboratory models of untreated HIV, thus placebo-controlled clinical trials to evaluate the safety and effectiveness of adjunctive CBD use with ART is warranted.

microbiology↗

bioRxiv2024

Octopamine signals coordinate the spatial pattern of presynaptic machineries in the Drosophila mushroom bodies

Neurons need to adjust synaptic output according to the targets. However, the target-specific synaptic structures within individual neurons in the central nervous system remains unresolved. Applying the CRISPR/Cas9-mediated split-GFP tagging, we visualized the endogenous active zone scaffold protein, Bruchpilot (Brp), in specific cells. This technology enabled the spatial characterization of presynaptic machineries only within the Kenyon cells (KCs) of the Drosophila mushroom bodies. We found the patterned accumulation of Brp among the compartments of axon terminals, where a KC synapses onto different postsynaptic neurons. Mechanistically, the localized octopaminergic modulation along {gamma} KC terminals regulate this compartmental Brp heterogeneity via Oct{beta}2R and cAMP signaling. We further found that acute food deprivation reorganizes this spatial pattern in an octopamine-dependent manner. Such coordinated regulation of local synaptic machineries thus explains how the mushroom bodies integrate changing physiological states. This subcellular information processing represents an elegant solution to expand computational capacity of the circuit.

neuroscience↗

bioRxiv2024

Rapid and cost-effective production of high-quality insect genome sequences

Insects are the most diverse group of animals on earth, with nearly 1 million species described to date, yet this variation is not reflected within the ranks of genomes currently available. In the current age of genetics, the generation of high-quality reference genomes is invaluable, often necessary and expensive. We prove that insect genomes do not need to come at a large cost. We demonstrate a cost-efficient method for producing high-quality insect genomes, with comparisons to current reference assemblies.

genomics↗

bioRxiv2024

Drug Metabolism and Transport Capacity of Endothelial Cells, Pericytes, and Astrocytes: Implications for CNS Drug Disposition

Therapeutically targeting the brain requires interactions with endothelial cells, pericytes, and astrocytes at the blood brain barrier (BBB). We evaluated regional and cell-type specific drug metabolism and transport mechanisms using rhesus macaques and in vitro treatment of primary human cells. Here, we report heterogenous distribution of representative drugs, tenofovir (TFV), emtricitabine (FTC), and their active metabolites, which cerebrospinal fluid measures could not reflect. We found that all BBB cell types possessed functional drug metabolizing enzymes and transporters that promoted TFV and FTC uptake and pharmacologic activation. Pericytes and astrocytes emerged as pharmacologically dynamic cells that rivaled hepatocytes and were uniquely susceptible to modulation by disease and treatment. Together, our findings demonstrate the importance of considering the BBB as a unique pharmacologic entity, rather than viewing it as an extension of the liver, as each cell type possesses distinct drug metabolism and transport capacities that contribute to differential brain drug disposition.

pharmacology and toxicology↗

bioRxiv2024

Hemilineage-specific expression of the RHG genes Grim and Reaper sculpt neural network composition during Drosophila neurogenesis

During development, nervous systems generate an incredible diversity of different cell types. One mechanism that appears critical for controlling whether a specific subtype is present or absent, and ensuring that neuronal numbers are appropriate for specific regions, is programmed cell death. Here we show that the precisely patterned hemilineage-based cell death found in the ventral nerve cord of Drosophila melanogaster is controlled by the transcription of the pro-apoptotic RHG genes reaper and grim. Using smFISH we show that reaper and grim, but not hid, are expressed in postembryonic lineages during neurogenesis. By generating novel T2A-GAL4 knock-in tools we have been able to map reaper and grim expression on a lineage-by-lineage basis and show diverse expression patterns within different hemilineage populations. Analysis of null mutants for both genes reveal a division of labour with distinct combinations being important in sculpting the nervous system. Investigation of a specific sexually dimorphic lineage reveals temporal patterning of hemilineage-specific programmed cell death through Grim and Reaper function underpins the development of sex-specific circuitry in the VNC. Our findings suggest that the precisely patterned expression of these pro-apoptotic genes is a critical fate determinant that generates segmental-specific circuity and instructs the appropriate assembly of sexually dimorphic neural circuits in the VNC.

developmental biology↗

bioRxiv2023

Roadmap for Canonical and Extended Endocannabinoid System Receptors in Peripheral Organs of Preclinical Animal Models

The endocannabinoid system is widely expressed throughout the body and is comprised of receptors, ligands, and enzymes that maintain metabolic, immune, and reproductive homeostasis. Increasing interest in the endocannabinoid system has arisen due to these physiologic roles, policy changes leading to more widespread recreational use, and the therapeutic potential of Cannabis and phytocannabinoids. Rodents have been the primary preclinical model of focus due to their relative low cost, short gestational period, genetic manipulation strategies, and gold-standard behavioral tests. However, the potential for lack of clinical translation to non-human primates and humans is high as cross-species comparisons of the endocannabinoid system has not been evaluated. To bridge this gap in knowledge, we evaluate the relative gene expression of 14 canonical and extended endocannabinoid receptors in seven peripheral organs of C57/BL6 mice, Sprague-Dawley rats, and non-human primate rhesus macaques. Notably, we identify species- and organ-specific heterogeneity in endocannabinoid receptor distribution where there is surprisingly limited overlap among the preclinical models. Importantly, we determined there were only five receptors (CB2, GPR18, GPR55, TRPV2, and FAAH) that had identical expression patterns in mice, rats, and rhesus macaques. Our findings demonstrate a critical, yet previously unappreciated, contributor to challenges of rigor and reproducibility in the cannabinoid field, which has profound implications in hampering progress in understanding the complexity of the endocannabinoid system and development of cannabinoid-based therapies.

molecular biology↗

bioRxiv2022

Antiretroviral Therapy Does Not Restore Brain Lipids During SIV Infection: Regional Analysis of Metabolic Homeostasis and Depletion

Human immunodeficiency virus (HIV) infection continues to promote neurocognitive impairment, mood disorders, and brain atrophy even in the modern era of viral suppression. Brain lipids are vulnerable to HIV-associated energetic strain and contribute to HIV-associated neurologic dysfunction due to alterations in lipid breakdown and structural lipid composition. HIV neuropathology is region dependent, yet there has not been comprehensive characterization of the spatial heterogeneity of brain lipids during infection that may impact neurologic function. To address this gap, we evaluated the spatial lipid distribution using matrix laser desorption/ionization imaging mass spectrometry (MALDI-IMS) across four brain regions (parietal cortex, midbrain, thalamus, and temporal cortex), as well as kidney for a peripheral tissue control, in a virally suppressed simian immunodeficiency virus (SIV)-infected rhesus macaque. We assessed lipids indicative of fat breakdown [acylcarnitines (CARs)] and critical structural lipids [phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs)] across fatty acid chain lengths and degrees of unsaturation. CARs with very long-chain, polyunsaturated fatty acids (PUFAs) were more abundant across all brain regions than shorter chain, saturated or monounsaturated species. We observed distinct brain lipid distribution patterns for CARs and PCs. However, no clear expression patterns emerged for PEs. Surprisingly, kidney was nearly devoid of ions corresponding to PUFAs common in brain. PEs and PCs with PUFAs had little intensity and less density than other species and, only one CAR species was observed in kidney at high intensity. Overall, our study provides substantial evidence for persistent bioenergetic changes to the brain despite viral suppression, including region-dependent mobilization of CARs for oxidation and disparities in the presence of key phospholipids necessary for maintaining proper brain structure and function. These data indicate that region-specific interventions to restore proper lipid metabolism are essential for treating HIV neurologic disease in the era of antiretroviral therapy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/508302v3_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@598d53org.highwire.dtl.DTLVardef@14d5cf1org.highwire.dtl.DTLVardef@10f6c9org.highwire.dtl.DTLVardef@1ba1aab_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

pathology↗

bioRxiv2021

Single-cell atlas of human oral mucosa reveals a stromal-neutrophil axis regulating tissue immunity in health and inflammatory disease

The oral mucosa remains an understudied barrier tissue rich in exposure to antigens, commensals and pathogens. Moreover, it is the tissue where one of the most prevalent human microbe-triggered inflammatory diseases, periodontitis, occurs. To understand this complex environment at the cellular level, we assemble herein a human single-cell transcriptome atlas of oral mucosal tissues in health and periodontitis. Our work reveals transcriptional diversity of stromal and immune cell populations, predicts intercellular communication and uncovers an altered immune responsiveness of stromal cells participating in tissue homeostasis and disease at the gingival mucosa. In health, we define unique populations of CXCL1,2,8-expressing epithelial cells and fibroblasts mediating immune homeostasis primarily through the recruitment of neutrophils. In disease, we further observe stromal, particularly fibroblast hyper-responsiveness linked to recruitment of leukocytes and neutrophil populations. Ultimately, a stromal-neutrophil axis emerges as a key regulator of mucosal immunity. Pursuant to these findings, most Mendelian forms of periodontitis were shown to be linked to genetic mutations in neutrophil and select fibroblast-expressed genes. Moreover, we document previously unappreciated expression of known pattern- and damage-recognition receptors on stromal cell populations in the setting of periodontitis, suggesting avenues for triggering stromal responses. This comprehensive atlas offers an important reference for in-depth understanding of oral mucosal homeostasis and inflammation and reveals unique stromal-immune interactions implicated in tissue immunity.

systems biology↗

bioRxiv2021

Proapoptotic RHG genes and mitochondria play a key non-apoptotic role in remodelling the Drosophila sensory system

Caspases are best known for their role in programmed cell death but have also been found to be important in several non-apoptotic phenomena such as cell fate specification, cell migration and terminal differentiation. The dynamics of such sub-lethal caspase events and the molecular mechanisms regulating them are still largely unknown. As more tools for visualizing and manipulating caspase activation in vivo become available, greater insights into this biology are being made. Using a new and sensitive in vivo effector caspase probe, called SR4VH, we demonstrate that effector caspases are activated in pruning sensory neurons earlier than previously thought and that the level of caspase activation in these neurons is consistently lower than in neurons undergoing cell death. We reveal that Grim and Reaper, two of the four pro-apoptotic RHG proteins, are required for sensory neuron pruning and that disrupting the dynamics of the mitochondrial network prevents effector caspase activation in both pruning and dying sensory neurons. Overall, our findings demonstrate that a sublethal deployment of the apoptotic machinery is critical for remodelling dendrites and also reveal a direct link between mitochondria and sensory neuron cell death in vivo.

developmental biology↗

bioRxiv2019

Patterned cell death sculpts functional and adaptive neural networks in flies

Changes to the structure and function of neural networks are thought to underlie the evolutionary adaptation of animal behaviours. Among the many developmental phenomena that generate change programmed cell death appears to play a key role. We show that cell death occurs continuously throughout insect neurogenesis and happens soon after neurons are born. Focusing on two dipterans which have lost flight during evolution we reveal that reductions in populations of flight interneurons are likely caused by increased cell death during development. Mimicking an evolutionary role for increasing cell numbers, we artificially block programmed cell death in the medial neuroblast lineage in Drosophila melanogaster, which results in the production of undead neurons with complex arborisations and distinct neurotransmitter identities. Activation of these undead neurons and recordings of neural activity in behaving animals demonstrate that they are functional. Our findings suggest that the evolutionary modulation of death-based patterning could generate novel network configurations.

neuroscience↗

bioRxiv2019

What drives phenotypic divergence among coral clonemates?

Evolutionary rescue of populations depends on their ability to produce phenotypic variation that is heritable and adaptive. DNA mutations are the best understood mechanisms to create phenotypic variation, but other, less well-studied mechanisms exist. Marine benthic foundation species provide opportunities to study these mechanisms because many are dominated by isogenic stands produced through asexual reproduction. For example, Caribbean acroporid corals are long lived and reproduce asexually via breakage of branches. Fragmentation is often the dominant mode of local population maintenance. Thus, large genets with many ramets (colonies) are common. Here, we observed phenotypic variation in stress response within genets following the coral bleaching events in 2014-and 2015 caused by high water temperatures. This was not due to genetic variation in their symbiotic dinoflagellates (Symbiodinium fitti) because each genet of this coral species typically harbors a single strain of S. fitti. Characterization of the microbiome via 16S tag sequencing did not provide evidence for a central role of microbiome variation in determining bleaching response. Instead, epigenetic changes were significantly correlated with the hosts genetic background, the position of the sampled polyps within the colonies (e.g. branch versus base of colony), and differences in the colonies condition during the bleaching event. We conclude that microenvironmental differences in growing conditions led to long-term changes in the way the ramets methylated their genomes contributing to, but not fully explaining, the differential bleaching response. This research provides novel data to understanding intra-genet variability in stress phenotypes of sessile marine species.

evolutionary biology↗

bioRxiv2017

Neurexin and Neuroligin-based adhesion complexes drive axonal arborisation growth independent of synaptic activity

Building arborisations of the right size and shape is fundamental for neural network function. Live imaging studies in vertebrate brains strongly suggest that nascent synapses are critical for branch growth during the development of axonal and dendritic arborisations. The molecular mechanisms underlying such synaptotropic events are largely unknown.\n\nHere we present a novel system in Drosophila for studying the development of complex axonal arborisations live, in vivo during metamorphosis. In these growing axonal arborisations we see a relationship between the punctate localisations of presynaptic components and branch dynamics that is very similar to synaptotropic growth described in fish and frogs. These presynaptic components however do not appear to represent functional presynaptic release sites and are not paired with clusters of neurotransmitter receptors. Pharmacological and genetic knockdowns of evoked and spontaneous neurotransmission do not impact the outgrowth of these neurons. Instead, we find that axonal branch growth is regulated by the dynamic focal localisations of synaptic adhesion proteins Neurexin and Neuroligin. These adhesion complexes provide selective stability for filopodia by a stick and grow-based mechanism wholly independent of synaptic activity.

neuroscience↗