Biology subjects

Richardson, A.

Publications and source records attributed to Richardson, A..

At least 19 recordsLinked to original sources

bioRxiv2026

mTOR disrupts cerebrovascular RNA regulatory networks in Alzheimers disease

Cerebrovascular dysfunction is increasingly recognized as a central contributor to the initiation and progression of Alzheimer's disease (AD). The mammalian/mechanistic target of rapamycin (mTOR) pathway has emerged as a key driver of AD-related vascular dysfunction. Consistent with this role, attenuation of mTOR signaling restores multiple aspects of cerebrovascular function in AD models, including vascular density, cerebral blood flow, vascular reactivity, and neurovascular coupling. However, the molecular mechanisms linking mTOR dysregulation to cerebrovascular dysfunction in AD remain poorly understood we assessed cerebrovascular levels of RNA-regulatory proteins in hAPP(J20) mice treated with rapamycin from 6 to 12 months of age. Rapamycin partially restored disease-suppressed heterogeneous nuclear ribonucleoprotein (hnRNP) family members, including hnRNP D1 (AUF1) and hnRNP E1 (PCBP1). Rapamycin-mediated restoration of hnRNP extended to the cerebrovasculature of PS19 (P301S) tauopathy mice, indicating that mTOR-dependent hnRNP suppression is shared across amyloid- and tau-driven models of AD. Consistent with these findings, hnRNP E1 and hnRNP L each showed a nominally significant inverse relationship with Braak stage in AD patient brains, with a similar but non-significant trend for hnRNP R and hnRNP M; The coordinated pattern of decline suggests network-level disruption of RNA-binding protein homeostasis in AD. Together, our studies uncover a previously unrecognized link between mTOR signaling and the regulation of RNA-regulatory proteins and identify a previously unrecognized, reversible mTOR-dependent RNA regulatory program in the cerebrovasculature that may contribute to neurovascular dysfunction in AD and reveal new targets for therapeutic intervention.

neuroscience↗

bioRxiv2026

Spondweni virus infection in pregnant rhesus macaques causes placental pathology without apparent fetal harm

The 2015-2016 Zika virus (ZIKV) epidemic revealed the potential of flaviviruses to emerge rapidly, cause severe disease, and affect pregnancy outcomes. In 2016, Spondweni virus (SPOV), the closest known relative of ZIKV, was detected in mosquitoes in Haiti, suggesting it may also have the potential to emerge in the Western Hemisphere. The risks that close relatives of ZIKV pose to pregnant individuals are not well understood. Previously, we showed that SPOV can cause fetal demise, placental pathology, and vertical transmission in a mouse model. Here we report SPOVs pathogenic potential in pregnant rhesus macaques. We inoculated four macaques with SPOV at gestational day 30 (early first trimester) and compared their viral loads and fetal outcomes with those of macaques infected in the first trimester with either African-lineage ZIKV (ZIKV-DAK) or an Asian-lineage ZIKV isolate from Puerto Rico (ZIKV-PR) in previous studies. Plasma viremia persisted 10-31 days in SPOV-inoculated dams, whereas viremia resolved within 10-17 days for ZIKV-DAK and 5-52 days for ZIKV-PR. Cesarean deliveries near term (gestational day 152-157) revealed no demise, premature birth, or gross abnormalities in fetuses of dams inoculated with SPOV or ZIKV-PR. In contrast, under near-identical conditions, all ZIKV-DAK-inoculated dams experienced fetal demise between 12 and 20 days post-inoculation. At cesarean section, we did not detect SPOV RNA above the limit of detection in maternal (e.g., spleen, liver), placental, or fetal tissues, in contrast to previous findings with ZIKV-PR. Histological analysis revealed mononuclear/lymphohistiocytic villitis in all placentas of SPOV-exposed macaques, along with other pathological changes in individual placentas. Our findings suggest that SPOV infection of macaques in early pregnancy may result in placental pathology without overt fetal harm. Our results suggest that flaviviruses in the Spondweni serocomplex, which includes ZIKV and SPOV, may vary in their pathogenic potential during pregnancy. Author SummaryZika virus (ZIKV) can cause fetal harm. Does this risk extend to its closest known relative, Spondweni virus (SPOV)? Should SPOV circulate in humans, what risks would it pose in pregnancy? SPOV can injure fetuses in immunocompromised mice, but the physiology of pregnancy in mice differs greatly from that of humans. We therefore infected pregnant rhesus macaques with SPOV during early gestation and compared maternal viremia, placental pathology, and fetal outcomes with macaques infected with African- or Asian-lineage ZIKVs at the same gestational age. All fetuses survived to near-term pregnancy, fetal tissues were negative for SPOV RNA, and fetal growth tracked within expected ranges. Nonetheless, all SPOV-exposed pregnancies showed placental injury, including mononuclear/lymphohistiocytic villitis and maternal vascular malperfusion. Despite the absence of detectable SPOV RNA in fetal tissues, SPOV RNA persisted at term in maternal-fetal interface tissues in two of four animals. These data indicate placental injury without detectable vertical transmission in this translational model. Our results suggest that SPOV and ZIKV display a wide range of risks to the developing fetus. Identifying viral and host factors that increase the potential for fetal harm will be important for assessing risks posed by emerging viruses in this family.

microbiology↗

bioRxiv2026

Hyaluronan and CD44 targeting reverses early matrix changes, proinflammatory signals and fibrosis in primary sclerosing cholangitis

Primary sclerosing cholangitis (PSC) is a rare, progressive liver disease characterized by biliary inflammation and bile duct strictures and no approved medical therapy. Despite its clinical severity, the pathological mechanisms underlying PSC remain poorly understood, largely due to early diagnostic challenges. Here we provide complementary evidence in human PSC samples, transcriptomic data, mouse models, and 3D cholangiocyte cultures that underscore the importance of hyaluronic acid (HA) and its cognate receptor CD44 in PSC pathogenesis. HA is a glycosaminoglycan abundant in the extracellular matrix in inflammatory disorders, yet its role in PSC has not been well characterized. We demonstrate that in early-stage PSC, cholangiocytes aberrantly produce high molecular weight HA that accumulates in the peribiliary matrix, increasing local tissue stiffness. This mechanical signal is transduced by a CD44/Integrin {beta}1 receptor complex in cholangiocytes, driving cell proliferation, YAP mechanosignaling, pro-inflammatory cytokine production with a transition to a ductular reactive phenotype. CD44 knockdown in cholangiocyte cell lines and mouse models significantly lowered stiffness, and attenuated inflammation. Together, these findings reveal a mechano-inflammatory axis in which HA-driven matrix stiffening perpetuates biliary inflammation and disease progression, identifying HA targeting and CD44 as promising therapeutic strategies. One Sentence SummaryHyaluronan and CD44 mediate matrix changes and progressive fibrosis in primary sclerosing cholangitis.

pathology↗

bioRxiv2026

Physioxia Reprograms Glioblastoma Cells Enhancing Migration and Altering Therapeutic Sensitivity

Background/ObjectivesGlioblastoma is an aggressive primary brain tumor that develops within a chronically low-oxygen microenvironment, yet most preclinical studies are performed under atmospheric oxygen conditions that poorly reflect in vivo physiology. This study investigated how sustained culture under physiological oxygen tension (physioxia; 5% O{square}) influences glioblastoma cell behavior, signaling, and therapeutic response. MethodsMultiple patient-derived glioblastoma models were cultured under normoxia (21% O{square}) or sustained physioxia (5% O{square}) for at least seven days before experimentation. Cell migration, proliferation, cell cycle distribution, expression of the epithelial-to-mesenchymal transition-associated transcription factor Slug (SNAI2), PDGFR{beta}-associated signaling, and sensitivity to 5-fluorouracil were evaluated using transwell migration assays, cell counting, flow cytometry, RT-qPCR, immunoblotting, and BrdU incorporation assays. Additional patient-derived cultures established and maintained continuously under physioxia were used to examine the effects of oxygen history. ResultsSustained physioxia consistently increased migration across all glioblastoma models while reducing proliferation in normoxia-adapted cell lines through increased G0/G1 cell cycle arrest. Physioxia significantly increased Slug expression in all models and enhanced PDGFR{beta}, AKT, and ERK phosphorylation in a cell line-dependent manner. Therapeutic sensitivity to 5-fluorouracil was also altered, with physioxia conferring increased resistance in selected glioblastoma models but not universally. Patient-derived cultures maintained continuously under physioxia retained enhanced migratory capacity and exhibited increased proliferation compared with normoxia, indicating that prior oxygen exposure influences proliferative responses while the pro-migratory phenotype remains conserved. ConclusionsPhysiological oxygen tension is a major regulator of glioblastoma cell behavior, influencing migration, proliferation, signaling, and therapeutic response. These findings demonstrate that conventional normoxic culture conditions can obscure biologically relevant phenotypes and support incorporating physioxia into experimental design to improve the physiological and translational relevance of preclinical glioblastoma research.

cancer biology↗

bioRxiv2026

Maternal Obesity Decreases Offspring Lifespan

Data in mice, nonhuman primates, and in humans demonstrate that exposure to maternal obesity increases the risk of multiple diseases in offspring. However, little is known about the aging effects of maternal obesity on the offspring. This study shows that maternal obesity significantly reduced the lifespan of both male and female mice born to obese dams despite being weaned onto a healthy diet at three weeks of age. This reduction in longevity was linked to an increase in age-related fibrotic pathology across multiple organs, e.g., liver, heart, and kidney. Gompertz analysis of the lifespan data showed that maternal obesity offspring have reduced lifespan due to detrimental changes established early during development rather than factors that modify aging later-in-life. These findings are translationally significant as they demonstrate that the growing prevalence of MO may lead to a decrease in overall lifespan and increase in age-related diseases in the next generation.

physiology↗

bioRxiv2025

3-Mercaptopyruvate Sulfurtransferase (MPST) Regulates Mitochondrial Metabolism and Epithelial Differentiation in Neonatal Patient-derived Airway Cells

Early-life airway epithelial development relies on tightly coordinated mitochondrial metabolic programs, yet the pathways that govern normal epithelial maturation during this vulnerable developmental window remain poorly defined. Hyperoxia disrupts airway epithelial maturation, contributing to lung injury and airway remodeling in infants with bronchopulmonary dysplasia (BPD), underscoring the need to identify mitochondrial pathways that regulate early epithelial differentiation. 3-Mercaptopyruvate sulfurtransferase (MPST), a mitochondrial sulfur metabolism enzyme, supports mitochondrial metabolic and bioenergetic function, but its role in human airway epithelial development is unknown. In this study, we used neonatal patient-derived tracheal airway epithelial cells (nTAECs) in a three-dimensional air-liquid interface (ALI) model to show that hyperoxia reduces MPST protein abundance. To determine how MPST loss alters early epithelial differentiation and metabolic homeostasis we used RNAi to knock down MPST during ALI differentiation. MPST loss in nTAECs induced early (ALI day 3) transcriptomic shifts involving mitochondrial metabolic pathways, epithelial differentiation programs, and stress-response signature corresponding with decreased ciliated cell numbers during mid-differentiation phase (ALI day 7). Metabolic flux analysis revealed significantly reduced mitochondrial respiration without compensatory increase in glycolysis, indicative of disrupted metabolic flexibility. Together, these data show that MPST is essential for maintaining mitochondrial metabolic integrity necessary for normal airway epithelial development. Loss of MPST creates a developmental vulnerability that may contribute to hyperoxia-induced airway injury in neonates. Targeting MPST-dependent pathways could represent a new strategy to preserve airway health in infants at risk for BPD airway remodeling. NEW & NOTEWORTHYThis study identifies MPST as a previously unrecognized regulator of neonatal airway epithelial development. In our neonatal patient-derived three-dimensional organotypic model, hyperoxia reduces MPST, and MPST loss alters mitochondrial metabolism and epithelial differentiation programs. These findings indicate that MPST deficiency contributes to mitochondrial dysfunction under hyperoxic conditions and highlight MPST-linked pathways as potential therapeutic targets to mitigate early-life airway injury and remodeling relevant to infants with bronchopulmonary dysplasia.

developmental biology↗

bioRxiv2025

NDNF+ interneurons have a privileged role in regulating cortical excitability

Cortical processing depends critically on the precise modulation of excitatory activity by a diverse population of GABAergic interneurons. Among these, neuron-derived neurotrophic factor-expressing (NDNF+) interneurons have been proposed to be "master regulators" of cortical microcircuits. While their role in coordinating physiological cortical activity is beginning to be understood, their contribution to restraining hyperexcitability during epileptiform activity remains unexplored. To address this, we employed calcium imaging, optogenetics, and chemogenetics in an NDNF-Cre mouse line to investigate how NDNF+ interneurons influence cortical hyperactivity and spontaneous seizures. Our results demonstrate that NDNF+ interneurons are actively recruited during interictal spikes and focal seizures, although more slowly than parvalbumin-positive interneurons. Optogenetic hyperpolarization of NDNF+ interneurons exacerbates epileptic discharges, whereas their depolarization suppresses focal seizures, even when the optogenetic stimulus is delayed by several seconds from seizure onset. This effect is largely mediated by GABAB receptor signalling. Additionally, chemogenetic depolarization of NDNF+ interneurons has robust antiepileptic effects both ex vivo and in vivo. Collectively, these findings establish NDNF+ neurons as key regulators of cortical excitability and identify them as promising cellular targets for the development of anti-epileptic therapies.

neuroscience↗

bioRxiv2025

Interplay of synaptic and backpropagating signals in neurogliaform dendrites

Inhibitory interneurons are conventionally thought to support precise timing of neural activity and regulation of circuit excitability, whilst principal neurons are the main locus of synaptic plasticity. Recent evidence for long-term potentiation (LTP) at glutamatergic synapses on GABAergic interneurons calls for close attention to the sub-cellular phenomena that underlie the induction of plasticity in aspiny dendrites. Neurogliaform interneurons, in particular, exhibit large NMDA receptor-mediated currents, robust Hebbian LTP and pronounced supralinear summation of glutamatergic signals converging on dendritic compartments. Unlike pyramidal neurons, however, dendritic supralinearity in interneurons operates independently of sodium channels. Here we investigate the principles governing supralinear synaptic integration and how it interacts with backpropagating action potentials in the context of synaptic plasticity. We developed a biophysically realistic, multi-compartmental model of a murine hippocampal neurogliaform interneuron, with dendritic architecture and ion channel densities tuned to match ex vivo recordings. The interaction of synaptic inputs and action potential were validated with patch-clamp electrophysiology and two-photon imaging of dendritic calcium-dependent fluorescence transients. We show that, whether simulated glutamatergic excitatory postsynaptic potentials are clustered on a dendritic fragment or dispersed across the entire arbor, they summate supralinearly as assessed from the calculated somatic voltage response. Clustered inputs however induce more pronounced local depolarizations and calcium transients than dispersed inputs. Action potentials generated at the soma backpropagate throughout the dendritic arbor but are attenuated at branch points. Coincident synaptic input and backpropagating action potentials relieve this attenuation, further enhance dendritic depolarizations, and greatly potentiate calcium influx via NMDA receptors. Despite differences in dendritic anatomy and in the roles of sodium channels, the interplay of orthodromic and antidromic voltage propagation and resultant calcium signal amplification exhibits remarkable similarities between neurogliaform interneurons and principal cells. Author summaryLearning and memory are believed to rely in large part on the brains ability to strengthen excitatory connections among principal cells. Potentiation of excitation must however be balanced by inhibition. Our study focuses on a key player in this balancing act: the neurogliaform interneuron, which exerts a powerful inhibition of the apical dendrites of principal neurons in the cortex and hippocampus. Recent work has revealed that both principal neurons and neurogliaform interneurons amplify coincident excitatory signals in their extensively branching dendrites. Key to the induction of synaptic potentiation is the coincidence of orthodromic depolarization arising from synapses and action potentials generated at or near the cell body. We asked how these electrical signals interact, using a blend of computer simulations and experimental manipulations. Unlike principal neurons, neurogliaform interneurons are devoid of dendritic spines, and voltage-gated sodium channels are dispensable for boosting of synaptic depolarization. Nevertheless, the core principle that coincident orthodromic and antidromic signals leads to widespread depolarization spreading throughout the dendritic arbor is conserved between these neurons. The conclusions of this work shed light not only on healthy brain function but also on common disorders such as epilepsy and schizophrenia, which abnormal dendritic function has been implicated.

neuroscience↗

bioRxiv2025

Quantitative Proteomics Links Mitochondrial Dysfunction to Metabolic Changes and Epithelial Differentiation Defects in Hyperoxia-Exposed Neonatal Airway Cells

Premature infants often require supplemental oxygen therapy, however, exposure to supraphysiological oxygen (hyperoxia) can disrupt normal lung development and contribute to bronchopulmonary dysplasia (BPD). Mitochondrial dysfunction is increasingly recognized as a contributor to hyperoxia-induced BPD. However, the effects of hyperoxia on mitochondrial function and mucociliary differentiation in the developing upper airway epithelium remain poorly understood. This study tested the hypothesis that hyperoxia impairs neonatal airway mucociliary differentiation by disrupting mitochondrial bioenergetic function. Neonatal tracheal airway epithelial cells (nTAECs) from term infants (n=5) were cultured in a 3D air-liquid interface (ALI) model and exposed to 60% O2 during the mid-phase of differentiation (ALI day 7-14). Cellular phenotype was assessed using immunofluorescence staining and gene expression analyses. Mitochondrial function was evaluated through Seahorse metabolic flux analysis, and global protein changes were characterized by quantitative proteomics. Hyperoxia exposure significantly impaired terminal epithelial differentiation, characterized by reductions in ciliated and goblet cells. Seahorse assay revealed a decrease in baseline oxygen consumption and mitochondrial ATP production, accompanied by a compensatory increase in glycolytic ATP production. Quantitative proteomics identified disruption of mitochondrial Complex I as a central feature of the hyperoxic response. Downstream proteomic pathway analyses further confirmed the metabolic shift from mitochondrial to glycolytic ATP production and demonstrated altered epithelial differentiation pathways, including NOTCH and TGF-{beta} signaling. These findings reveal that moderate hyperoxia impairs mitochondrial bioenergetics and alters metabolic programming, leading to disrupted mucociliary differentiation. Future in vivo studies should evaluate mitochondrial oxidative fitness as a therapeutic target in neonatal lung disease. NEW & NOTEWORTHYWe report that moderate hyperoxia during a critical window of mucociliary differentiation disrupts terminal maturation in neonatal airway epithelial cells cultured in a 3D model. Hyperoxia induced mitochondrial bioenergetic dysfunction and metabolic reprogramming, with proteomic analysis identifying Complex I disruption as a key driver of impaired differentiation. Overall, these findings reveal a previously underrecognized link between mitochondrial bioenergetics and airway epithelial development, positioning metabolic dysfunction as an early trigger of hyperoxia-induced neonatal airway injury.

developmental biology↗

bioRxiv2025

Ontogeny of the spinal cord dorsal horn

The dorsal horn of the mammalian spinal cord is an exquisite example of form serving function. It is comprised of diverse neuronal populations stacked into laminae, each of which receives different circuit connections and plays specialized roles in behavior. An outstanding question is how this organization emerges during development from an apparently homogeneous pool of neural progenitors. Here, we found that dorsal neurons are diversified by time, with families of related cell types born as temporal cohorts, and by a spatial-molecular gradient that specifies the full array of individual cell types. Excitatory dorsal neurons then settle in a chronotopic arrangement that transforms their progressive birthdates into anatomical order. This establishes the dorsal horn laminae, as these neurons are also required for spatial organization of inhibitory neurons and sensory axons. This work reveals essential ontogenetic principles that shape dorsal progenitors into the diverse cell types and architecture that subserve sensorimotor behavior. Highlights- Temporal cohorts of late-born dorsal neurons give rise to neuronal families - Sequentially-born excitatory neuron families form adjacent laminae - Laminar structure specifically requires excitatory (but not inhibitory or sensory) neurons - Graded expression of Zic transcription factors directs fine neuronal identity

neuroscience↗

bioRxiv2024

Age, Sex, and mitochondrial-haplotype influence gut microbiome composition and metabolites in a genetically diverse rat model.

We evaluated the impact of sex and mitochondrial-haplotype on the age-related changes in the fecal gut microbiome of the genetically heterogeneous rodent model, the OKC-HETB/W rat. Alpha-diversity, measuring richness and evenness of gut microbiome composition, did not change with age or mitochondrial-haplotype. However, beta-diversity, a measure of microbial differences among samples, was significantly modulated by age in male and female rats in both mitochondrial-haplotypes. The age-related changes in the microbiome differed markedly between male and female rats. Five microbial species changed significantly with age in male rats compared to nine microbial species in female rats. Only three of these microbes changed with age in both male and female rats. The mitochondrial-haplotype of the rats also affected how aging altered the microbiome. Interestingly, most of the microbial species that changed significantly with age were mitochondrial-haplotype and sex specific, i.e., changing in one sex and not the other. We also discovered that sex and mitochondrial-haplotype significantly affected the age-related variations in content of fecal short-chain fatty acids and plasma metabolites that influence or are regulated by the microbiome, e.g., tryptophan derived metabolites and bile acids. This study demonstrates that the hosts sex plays a significant role in how the gut microbiome evolves with age, even within a genetically diverse background. Importantly, this is the first study to show that the mitochondrial-haplotype of a host impacts the age-related changes in the microbiome and supports previous studies suggesting a bidirectional interaction between the gut microbiome and host mitochondria. HighlightsMost age-related changes in microbial species occurred in one sex but not the other Mitochondrial-haplotype altered the microbiome and was generally sex dependent Microbiome associated metabolites differed by age, sex, and mitochondria-haplotype

microbiology↗

bioRxiv2024

Broad-spectrum RNA antiviral inspired by ISG15-/- deficiency

Type I interferons (IFN-I) are cytokines with potent antiviral and inflammatory capacities. IFN-I signaling drives the expression of hundreds of IFN-I stimulated genes (ISGs), whose aggregate function results in the control of viral infection. A few of these ISGs are tasked with negatively regulating the IFN-I response to prevent overt inflammation. ISG15 is a negative regulator whose absence leads to persistent, low-grade elevation of ISG expression and concurrent, self-resolving mild autoinflammation. The limited breadth and low-grade persistence of ISGs expressed in ISG15 deficiency are sufficient to confer broad-spectrum antiviral resistance. Inspired by ISG15 deficiency, we have identified a nominal collection of 10 ISGs that recapitulate the broad antiviral potential of the IFN-I system. The expression of the 10 ISG collection in an IFN-I non-responsive cell line increased cellular resistance to Zika, Vesicular Stomatitis, Influenza A (IAV), and SARS-CoV-2 viruses. A deliverable prophylactic formulation of this syndicate of 10 ISGs significantly inhibited IAV PR8 replication in vivo in mice and protected hamsters against a lethal SARS-CoV-2 challenge, suggesting its potential as a broad-spectrum antiviral against many current and future emerging viral pathogens. One-Sentence SummaryHuman inborn error of immunity-guided discovery and development of a broad-spectrum RNA antiviral therapy

immunology↗

bioRxiv2024

Non-Necroptotic Roles of MLKL in Diet-Induced Obesity, Liver Pathology, and Insulin Sensitivity: Insights from a High Fat, High Fructose, High Cholesterol Diet Mouse Model

Chronic inflammation is a key player in metabolic dysfunction-associated fatty liver disease (MAFLD) progression. Necroptosis, an inflammatory cell death pathway, is elevated in MAFLD patients and mouse models, yet its role is unclear due to diverse mouse models and inhibition strategies. In our study, we inhibited necroptosis by targeting mixed lineage kinase domain like pseudokinase (MLKL), the terminal effector of necroptosis, in a high-fat, high-fructose, high-cholesterol (HFHFrHC) mouse model of diet-induced MAFLD mouse model. Despite HFHFrHC diet upregulating MLKL (2.5-fold), WT mice livers showed no increase in necroptosis markers or associated proinflammatory cytokines. Surprisingly, Mlkl-/-mice experienced exacerbated liver inflammation without protection from diet-induced liver damage, steatosis, or fibrosis. In contrast, Mlkl+/- mice showed significant reduction in these parameters that was associated with elevated Ppar and Ppar{gamma} levels. Both Mlkl-/-and Mlkl+/- mice on HFHFrHC diet resisted diet-induced obesity, attributed to increased beiging, enhanced oxygen consumption and energy expenditure due to adipose tissue, and exhibited improved insulin sensitivity. These findings highlight the tissue specific effects of MLKL on the liver and adipose tissue, and suggest a dose-dependent effect of MLKL on liver pathology.

biochemistry↗

bioRxiv2023

Computational Design of Periplasmic Binding Protein Biosensors Guided by Molecular Dynamics

Periplasmic binding proteins (PBPs) are bacterial proteins commonly used as scaffolds for substrate-detecting biosensors. In such biosensors, effector proteins, for example circularly permuted green fluorescent protein (cpGFP), are inserted into a PBP such that the effector proteins output changes upon PBP-substate binding. The insertion site is often determined by comparison of PBP apo/holo crystal structures, but random insertion libraries have shown that this can miss the best sites. Here, we present a PBP biosensor design method based on residue contact analysis from molecular dynamics. This computational method identifies the best previously known insertion sites in the maltose binding PBP, and suggests further previously unknown sites. We experimentally characterise cpGFP insertions at these new sites, finding they too give functional biosensors. Our method is sufficiently flexible to both suggest insertion sites compatible with a variety of effector proteins and be applied to binding proteins beyond PBPs.

synthetic biology↗

bioRxiv2023

Sperm Cell Painting: A Mechanism Driven Approach for Drug Discovery in Human Spermatozoa

We have adapted the cell painting assay developed by Carpenter and colleagues on cultured U2OS cells to human spermatozoa. In Sperm Cell Painting (SCP) we assemble an image-based quantitative fingerprint of the functional state of sperm. We use this assay to gain insight into the mechanism of action of compounds that modify sperm function and as a platform for contraceptive discovery.

cell biology↗

bioRxiv2023

Sperm Toolbox - A selection of small molecules to study human spermatozoa

Male contraceptive options and infertility treatments are limited. To help overcome these limitations we established a small molecule library as a toolbox for assay development and screening campaigns using human spermatozoa. We have profiled all compounds in our automated high-throughput screening platform and provide the dataset, which allows direct side-by-side comparisons of compound effects and assays using live human spermatozoa.

pharmacology and toxicology↗

bioRxiv2022

Impact of cannabis use on immune cell populations and the viral reservoir in people with HIV on suppressive antiretroviral therapy.

HIV infection remains incurable due to the persistence of a viral reservoir during antiretroviral therapy. Cannabis (CB) use is prevalent amongst people with HIV (PWH), but the impact of CB on the latent HIV reservoir has not been investigated. Peripheral CD4 and CD8 T cells from a cohort of CB-using PWH and a matched cohort of non-users on antiretroviral therapy were evaluated for expression of maturation/activation markers, HIV-specific T cell responses, and the frequency of intact proviral DNA. CB use was associated with increased abundance of naive T cells, reduced effector T cells, and reduced expression of activation markers. CB users also exhibited reduced levels of exhausted and senescent T cells compared to non-using controls. HIV-specific CD8 T cell responses were unaffected by CB use. While the abundance of intact proviruses was not significantly affected by CB use across the whole cohort, we observed that, for participants with high frequency of NKG2A or CD16 expression in NK cells, CB use was associated with a smaller intact HIV reservoir. This analysis is consistent with the hypothesis that CB use reduces activation, exhaustion and senescence in the T cells of PWH and may influence the size of the HIV reservoir.

microbiology↗

bioRxiv2022

Expanding the HDAC druggable landscape beyond enzymatic inhibition

Enzymatic pockets such as those of histone deacetylases (HDACs) are among the most favored targets for drug development. However, enzymatic inhibitors often exhibit low selectivity and high toxicity due to targeting multiple enzyme paralogs, which are often involved in distinct multisubunit complexes. Here, we report the discovery and characterization of a non-enzymatic small molecule inhibitor of HDAC transcriptional repression functions with comparable anti-tumor activity to the enzymatic HDAC inhibitor Vorinostat, and anti-psychedelic activity of an HDAC2 knockout in vivo. We highlight that these phenotypes are achieved while modulating the expression of 20- and 80-fold fewer genes than enzymatic and genetic inhibition in the respective models. Thus, by achieving the same biological outcomes as established therapeutics while impacting a dramatically smaller number of genes, inhibitors of protein-protein interactions can offer important advantages in improving the selectivity of epigenetic modulators. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/519454v2_ufig1.gif" ALT="Figure 1"> View larger version (96K): org.highwire.dtl.DTLVardef@3a4e68org.highwire.dtl.DTLVardef@1f1be2corg.highwire.dtl.DTLVardef@1fc5e94org.highwire.dtl.DTLVardef@1a54790_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗