Biology subjects

Cooper, E.

Publications and source records attributed to Cooper, E..

16 recordsLinked to original sources

bioRxiv2026

Calcium signals at cytoneme contacts amplify Wnt/β-catenin signalling

Wnt signalling controls morphogenesis, patterning and homeostasis across tissues. Because Wnt ligands are lipid-modified, their movement between cells cannot rely on simple diffusion and instead requires specialised transport mechanisms. Signalling filopodia, also known as cytonemes, have emerged as a key mediator of contact-dependent morphogen delivery. The mechanisms that stabilise signalling interfaces between Wnt ligand-bearing and receptor-bearing membranes at the cytoneme contact sites, a prerequisite for efficient Wnt ligand-receptor complex assembly and downstream pathway activation, remain poorly understood. Here, we show that HeLa cell cytonemes carry canonical Wnt components and form contact sites marked by focal Ca2+ transients. At these contacts, local Wnt and Ca2+ signals act in a positive feedback loop to promote longer-lasting interactions between neighbouring cells. Mechanistically, we find that E-cadherin/Cadherin 1 (CDH1) co-accumulates at these cytoneme contact sites in a Ca2+ - and Wnt-dependent manner, suggesting that contact stabilisation can be mediated by local adhesion. Consistent with this, presentation of Wnt ligands and CDH1 at cytoneme tips, together with Ca2+ availability, enhances Wnt signalosome formation at contact sites and, consequently, nuclear beta-catenin accumulation in the target cells. Our data support a model in which local Ca2+ transients stabilise cytoneme contacts and facilitate efficient Wnt ligand transfer to the receiving membrane, thereby enhancing canonical Wnt/beta-catenin signalling. We propose that focal Ca2+ signalling can serve as a contact-authentication step for morphogen signalling, converting transient cytoneme encounters into effective activators of the signal transduction cascade.

cell biology↗

bioRxiv2026

Dnmt3a-mutant Leukemia Stem Cells evade chemotherapy through enforced quiescence in Npm1c-Flt3ITD Acute Myeloid Leukemia

Concurrent mutations in DNMT3A, NPM1, and FLT3 define a high-risk subtype of acute myeloid leukemia (AML) associated with increased relapse risk and inferior survival following standard chemotherapy. However, the mechanisms by which DNMT3A mutations promote treatment resistance in NPM1c-FLT3ITD AML remain unclear. Using genetically engineered murine models of Npm1c-Flt3ITD AML with or without Dnmt3aR878H (homologous to human DNMT3AR882H), we demonstrate that Dnmt3aR878H promotes chemotherapy resistance through epigenetic regulation of leukemia stem cell (LSC) quiescence. Integrated transcriptomic and epigenetic profiling revealed coordinated remodeling of DNA methylation and chromatin accessibility in LSC-enriched populations, characterized by preferential hypomethylation and increased accessibility at loci associated with stemness and quiescence programs. These data were confirmed in human DNMT3AR882H-NPM1c-FLT3ITD AML datasets with enrichment of quiescence-associated and stem cell enriched transcriptional programs. Conversely, Dnmt3a-mutant LSCs retained sensitivity to the cell-cycle independent regimen venetoclax plus azacitidine, but residual LSCs exhibited transcriptional plasticity and reversion to a de-differentiated state. We have identified LSC heterogeneity spanning primitive hematopoietic stem cell (HSC)-and progenitor-like states and our data demonstrate preferential maintenance of a quiescent HSC-like LSC subpopulation in Dnmt3aR878H-mutant AML following chemotherapy treatment. Pharmacologic induction of cell-cycle entry using pegylated interferon (pegIFN) disrupted the quiescent LSC state and restored chemotherapy sensitivity, identifying quiescence as a reversible and therapeutically actionable mechanism of resistance. These findings identify DNMT3A-mediated epigenetic regulation of LSC quiescence as a conserved mechanism of standard chemotherapy resistance and position therapeutic reactivation of quiescent LSCs as a promising strategy to overcome chemotherapy resistance and improve outcomes in high-risk DNMT3A-mutant AML.

cancer biology↗

bioRxiv2025

Minimal Impact of Low Vision on Explicit Sensorimotor Adaptation

Rehabilitation from motor system dysfunction relies on learning deliberate motor corrections through practice and feedback. This is called explicit motor adaptation. One key source of feedback for this adaptation is the visual error signal between the intended movement and the achieved movement. As people age, both motor dysfunction and visual impairment become more common, potentially compromising the visual feedback signal. Previous work has shown that visual impairment can disrupt the implicit, automatic adjustments made by the sensorimotor system. But how visual impairment influences the explicit motor adaptation, a cornerstone of rehabilitation, remains unknown. To address this gap, we recruited individuals with low vision--defined as uncorrectable visual impairment resulting in functional vision loss--and age-matched controls to complete a visuomotor task designed to isolate two components of explicit motor adaptation: discovering a new deliberate sensorimotor strategy and recalling a previously learned one. Surprisingly, low vision had no measurable impact on either component. Despite reduced visual fidelity, individuals with low vision were as effective as controls in both discovering and retrieving successful explicit sensorimotor strategies. These results highlight potential mechanisms that can be leveraged in rehabilitation.

neuroscience↗

bioRxiv2025

Homozygous kinase-dead Csf1r mutation in outbred mice reveals essential and redundant functions of tissue resident macrophages

The proliferation, differentiation and survival of cells of the macrophage lineage depends on signals from the macrophage colony-stimulating factor receptor (CSF1R). On a C57BL/6J background homozygous kinase-dead Csf1r mutation (Csf1rE631K/E631K - E631Km/m) causes perinatal lethality. Here we demonstrate that E631Km/m mice on a mixed genetic background (C57 x BALB/c F2) are osteopetrotic and growth retarded but viable as adults with no other gross developmental deficits. They lack osteoclasts, microglia and most peripheral tissue resident macrophages and exhibit perturbed hematopoiesis. Although CD169+ tissue resident macrophages in bone marrow are considered an essential component of the hematopoietic niche, CD169 is undetectable in E631Km/m marrow and F4/80+ macrophages are depleted. These changes are associated with expansion of mature and immature granulocytes and reduced B cells, whereas monocytes and stem and progenitor populations are unaffected as a proportion of total cells. Erythropoiesis in bone marrow is maintained in E631Km/m mice, associated with a residual population of CSF1R-independent CD169-ve/F4/80+ macrophages. Nevertheless, splenic extramedullary hematopoiesis in E631Km/m mice indicates a degree of bone marrow insufficiency. Red pulp macrophages are retained but CD169+ marginal metallophil macrophages are absent and CD209b+ (SIGNR1) macrophages are present but disorganized. Circulating white blood cell count is unchanged in E631Km/m mice, but the proportion of neutrophils is greatly increased whilst B cells and monocytes are reduced. This novel model reveals the essential roles of CSF1R-dependent macrophages in hematopoiesis and demonstrates that many developmental and homeostatic functions attributed to murine resident tissue macrophages are redundant and/or specific to inbred mouse strains.

immunology↗

bioRxiv2024

Natural language processing charts transcriptome evolution to design combination cancer therapies

Combination treatment-the mainstay of cancer therapy-often fails because treatment interactions evoke complex resistance mechanisms that are hard to predict. Designing combination therapy to prevent treatment resistance is especially challenging for rare cancers. Here, we introduce REsistance through COntext DRift (RECODR): a computational pipeline that tracks how genes change their transcriptome context across cancer development and drug treatment conditions. By applying RECODR to a genetically modified mouse model of choroid plexus carcinoma-a rare brain tumour of young children-we identified patterns of transcriptome evolution, cellular heterogeneity and treatment targets that emerged as tumours were initiated and resisted combination treatment. This enabled the prediction of treatment resistance mechanisms and the design of highly effective therapeutic protocols that avoided treatment failure. RECODR can describe complex and dynamic changes in normal and diseased tissues that could be applied to multimodal data from a variety of settings, mitigating treatment resistance across cancers and other diseases.

cancer biology↗

bioRxiv2024

Construction of whole cell bacterial biosensors as an alternative environmental monitoring technology to detect naphthenic acids in oil sands process-affected water.

After extraction of bitumen from oil sands deposits, the oil sand process-affected water (OSPW) is stored in tailings ponds. Naphthenic acids in tailings ponds have been identified as the primary contributor to toxicity to aquatic life. As an alternative to other analytical methods, here we identify bacterial genes induced after growth in naphthenic acids and use synthetic biology approaches to construct a panel of candidate biosensors for NA detection in water. The main promoters of interest were the atuAR promoters from a naphthenic acid degradation operon and upstream TetR regulator, the marR operon which includes a MarR regulator and downstream naphthenic acid resistance genes, and a hypothetical gene with a possible role in fatty acid biology. Promoters were printed and cloned as transcriptional lux reporter plasmids that were introduced into a tailings pond-derived Pseudomonas species. All candidate biosensor strains were tested for transcriptional responses to naphthenic acid mixtures and individual compounds. The three priority promoters respond in a dose-dependent manner, which allows semi-quantitative measurements, to simple, acyclic and complex NA mixtures, and each promoter has unique NA specificities. The limits of NA detection from the various NA mixtures ranged between 1.5 - 15 mg/L. The atuA and marR promoters also detected NA in small volumes of OSPW samples and were induced by extracts of the panel of OSPW samples. While biosensors have been constructed for other hydrocarbons, here we describe a biosensor approach that could be employed in environmental monitoring of naphthenic acids in oil sands mining wastewater.

microbiology↗

bioRxiv2024

Plural molecular and cellular mechanisms of pore domain KCNQ2 encephalopathy

KCNQ2 variants in children with neurodevelopmental impairment are difficult to assess due to their heterogeneity and unclear pathogenic mechanisms. We describe a child with neonatal-onset epilepsy, developmental impairment of intermediate severity, and KCNQ2 G256W heterozygosity. Analyzing prior KCNQ2 channel cryoelectron microscopy models revealed G256 as a node of an arch-shaped non-covalent bond network linking S5, the pore turret, and the ion path. Co-expression with G256W dominantly suppressed conduction by wild-type subunits in heterologous cells. Ezogabine partly reversed this suppression. G256W/+ mice have epilepsy leading to premature deaths. Hippocampal CA1 pyramidal cells from G256W/+ brain slices showed hyperexcitability. G256W/+ pyramidal cell KCNQ2 and KCNQ3 immunolabeling was significantly shifted from axon initial segments to neuronal somata. Despite normal mRNA levels, G256W/+ mouse KCNQ2 protein levels were reduced by about 50%. Our findings indicate that G256W pathogenicity results from multiplicative effects, including reductions in intrinsic conduction, subcellular targeting, and protein stability. These studies provide evidence for an unexpected and novel role for the KCNQ2 pore turret and introduce a valid animal model of KCNQ2 encephalopathy. Our results, spanning structure to behavior, may be broadly applicable because the majority of KCNQ2 encephalopathy patients share variants near the selectivity filter.

neuroscience↗

bioRxiv2023

Oncogenic drivers dictate immune control of acute myeloid leukemia.

Acute myeloid leukemia (AML) is a genetically heterogeneous, aggressive hematological malignancy induced by distinct oncogenic driver mutations. The effect of specific AML oncogenes on immune activation or suppression has not been investigated. Here, we examine immune responses in genetically distinct models of AML and demonstrate that specific AML oncogenes dictate immunogenicity, the quality of immune response and immune escape through immunoediting. Specifically, expression of NrasG12D alone is sufficient to drive a potent anti-leukemia response through increased MHC Class II expression that can be overcome with increased expression of Myc. These data have important implications for the design and implementation of personalized immunotherapies for patients with AML. Statement of SignificanceThe endogenous immune response against acute myeloid leukemia (AML) is determined by leukemia-specific oncogenic driver mutations. Mutant Nras drives immunological selection of AML.

cancer biology↗

bioRxiv2022

Modified MRI anonymization (de-facing) for improved MEG coregistration

Localising the sources of MEG/EEG signals often requires a structural MRI to create a head model, while ensuring reproducible scientific results requires sharing data and code. However, sharing of structural MRI data often requires removal of the face to help protect the identity of the individuals concerned. While automated de-facing methods exist, they tend to remove the whole face, which can impair methods for coregistering the MRI data with the EEG/MEG data. We show that a new, automated de-facing method that retains the nose maintains good MRI-MEG/EEG coregistration. Importantly, behavioural data show that this "face-trimming" method does not increase levels of identification relative to a standard de-facing approach, and has less effect on the automated segmentation and surface extraction sometimes used to create head models for MEG/EEG localisation. We suggest that this trimming approach could be employed for future sharing of structural MRI data, at least for those to be used in forward modelling (source reconstruction) of EEG/MEG data.

molecular biology↗

bioRxiv2021

Conjugation of palbociclib with MHI-148 has an increased cytotoxic effect for breast cancer cells and an altered mechanism of action

The CDK4/6 inhibitor palbociclib, combined with endocrine therapy, has been shown to be effective in postmenopausal women with estrogen receptor positive, HER2-negative advanced or metastatic breast cancer. However, palbociclib is not as effective in the highly aggressive triple-negative breast cancer that lacks sensitivity to chemotherapy or endocrine therapy. We hypothesized that conjugation of the near-infrared dye MHI-148 with palbociclib can produce a potential theranostic in triple-negative as well as estrogen receptor positive breast cancer cells. In our study, the conjugate was found to have enhanced activity in all mammalian cell lines tested in vitro. However, the conjugate was cytotoxic and did not induce G1 cell cycle arrest in breast cancer cells suggesting the mechanism of action differed from the parent compound palbociclib. The study highlights the importance of investigating the mechanism of conjugates of near-infrared dyes to therapeutic compounds as conjugation can potentially result in a change of mechanism or target, with an enhanced cytotoxic effect in this case.

cancer biology↗

bioRxiv2020

Removal of KCNQ2 from Parvalbumin-expressing Interneurons Improves Anti-Seizure Efficacy of Retigabine

Anti-seizure drug (ASD) targets are widely expressed in both excitatory and inhibitory neurons. It remains unknown if the action of an ASD upon inhibitory neurons could counteract its beneficial effects on excitatory neurons (or vice versa), thereby reducing the efficacy of the ASD. Here, we examine whether the efficacy of the ASD retigabine (RTG) is altered after removal of the Kv7 potassium channel subunit KCNQ2, one of its drug targets, from parvalbumin-expressing interneurons (PV-INs). Parvalbumin-Cre (PV-Cre) mice were crossed with Kcnq2-floxed (Kcnq2fl/fl) mice to conditionally delete Kcnq2 from PV-INs. In these conditional knockout mice (cKO, PV-Kcnq2fl/fl), RTG (10 mg/kg, i.p.) significantly delayed the onset of either picrotoxin (PTX, 10 mg/kg, i.p)- or kainic acid (KA, 30mg/kg, i.p.)-induced convulsive seizures compared to vehicle, while RTG was not effective in wild-type littermates (WT). Immunostaining for KCNQ2 and KCNQ3 revealed that both subunits were enriched at axon initial segments (AISs) of hippocampal CA1 PV-INs, and their specific expression was selectively abolished in cKO mice. Accordingly, the M-currents recorded from CA1 PV-INs and their sensitivity to RTG were significantly reduced in cKO mice. While the ability of RTG to suppress CA1 excitatory neurons in hippocampal slices was unchanged in cKO mice, its suppressive effect on the spike activity of CA1 PV-INs was significantly reduced compared with WT mice. In addition, the RTG-induced suppression on intrinsic membrane excitability of PV-INs in WT mice was significantly reduced in cKO mice. These findings suggest that preventing RTG from suppressing PV-INs improves its anticonvulsant effect. Significance StatementOne out of three patients with epilepsy remain resistant to anti-seizure drugs (ASD). Therefore, strategies that can enhance the efficacy of current ASDs or aid in the development of novel ASDs are in high demand. Here we show that by sparing a subset of inhibitory neurons, the ASD retigabine becomes more efficacious. These findings indicate that developing the ASDs that have relatively greater effects on excitatory over inhibitory neurons may be an effective strategy to improve the efficacy of ASDs.

neuroscience↗

bioRxiv2020

Converging preganglionic axons refine without synaptic transmission when targets downstream of sympathetic nerves are active

Synaptic activity plays several roles as developing neurons make connections with their targets. It acts locally at synapses to influence the expression of genes needed to establish and maintain synaptic contacts. And, downstream it provides the necessary activity to strengthen and refine connections. Many studies have demonstrated how synaptic activity alters synaptic strength and increases synapse numbers. Much less is known, however, about the long-term consequences when a circuit develops without synaptic activity. To address this, we developed a mosaic model of sympathetic ganglia where synaptically-active and synaptically-inactive sympathetic neurons develop side-by-side in vivo. This model allowed us to address two issues. One is the relationship between activity and the refinement of converging inputs; the second is how synaptic activity contributes to a neurons gene expression profile. Our results indicate that converging presynaptic inputs to synaptically-silent neurons do not require postsynaptic activity to refine, provided these neurons share targets with synaptically-active neurons. Second, we demonstrate with single-cell RNA sequencing experiments that the expression of many genes by sympathetic neurons is independent of endogenous activity or local signals immediately downstream of excitatory postsynaptic potentials. An exception are genes required for neurotransmitter metabolism: We found that for a large sub-population of sympathetic neurons, synaptic activity increases the expression of adrenergic genes and supresses the expression of cholinergic genes. We conclude that signals generated locally at synapses do not initiate refinement of converging inputs, and that synaptic activitys influence on a neurons gene expression profiles is complex and depends on context.

neuroscience↗

bioRxiv2020

Memory deficits following hippocampal versus parahippocampal damage double-dissociate according to both process and material type

A central debate in the systems neuroscience of memory concerns whether different medial temporal lobe (MTL) structures support different processes or material-types in recognition memory. We tested a rare patient (Patient MH) with a perirhinal lesion that appeared to spare the hippocampus, using two recognition memory paradigms, each run separately with faces, scenes and words. Replicating reports of a previous case, Patient MH showed impaired familiarity and preserved recollection, relative to controls, with no evidence for any effect of material-type. Moreover, when compared with other amnesic patients, who had hippocampal lesions that appeared to spare the perirhinal cortex, Patient MH showed greater impairment on familiarity and less on recollection, forming a double dissociation. However, when replacing this traditional, binary categorization of patients with a parametric analysis that related memory performance to continuous measures of brain damage across all patients, we found a different pattern: while hippocampal damage predicted recollection, it was parahippocampal instead of perirhinal (or entorhinal) cortex volume that predicted familiarity. Furthermore, there was no evidence that these brain-behavior relationships were moderated by material-type, nor by laterality of damage. Thus, while our data provide the most compelling support yet for dual-process models of recognition memory, in which recollection and familiarity depend on different MTL structures, they suggest that familiarity depends more strongly upon the parahippocampal rather than perirhinal cortex. More generally, our study reinforces the need to go beyond single-case and group studies, and instead examine continuous brain-behavior relationships across larger patient groups.

neuroscience↗

bioRxiv2019

Tau pathology in early Alzheimer’s disease disrupts selective neurophysiological networks dynamics

The role of aggregation of misfolded Tau protein in the pathogenesis of Alzheimers disease is the subject of rapid biomarker development and new therapeutic strategies to slow or prevent dementia. We tested the hypothesis that Tau pathology is associated with functional organization of widespread neurophysiological networks. We used electro-magnetoencephalography (E/MEG) in combination with [18F]AV1451 PET scanning to quantify Tau-dependent network disruption. Using a graph theoretical approach to MEG connectivity, we quantified nodal measures of functional segregation, centrality and efficiency of information transfer. We correlated these metrics against the nodes uptake of [18F]AV1451. There were both regional- and frequency-specific effects of Tau levels on the efficiency of information transfer and network segregation in early AD. Tau correlated with temporal regional participation coefficient (in delta, theta, beta bands); and temporal lobar eigenvector centrality (in theta, alpha, beta bands), but greater eccentricity at higher frequencies (gamma). The results support the translational development of neurophysiological "signatures" as biomarkers of Alzheimers disease, with potential to facilitate experimental medicines studies.

neuroscience↗

bioRxiv2017

Systematic misperceptions of 3D motion explained by Bayesian inference

People make surprising but reliable perceptual errors. Here, we provide a unified explanation for errors in the perception of three-dimensional (3D) motion. To do so, we characterized the retinal motion signals produced by objects moving with arbitrary trajectories through arbitrary locations in 3D. Next, we developed a Bayesian model, treating 3D motion perception as optimal inference given sensory noise and the geometry of 3D viewing. The model predicts a wide array of systematic perceptual errors, that depend on stimulus distance, contrast, and eccentricity. We then used a virtual reality (VR) headset as well as a standard 3D display to test these predictions in both traditional psychophysical and more naturalistic settings. We found evidence that people make many of the predicted errors, including a lateral bias in the perception of motion trajectories, a dependency of this bias on stimulus contrast, viewing distance, and eccentricity, and a surprising tendency to misreport approaching motion as receding and vice versa. In sum, we developed a quantitative model that provides a parsimonious account for a range of systematic misperceptions of motion in naturalistic environments.

neuroscience↗

bioRxiv2017

No effect of hippocampal lesions on stimulus-response bindings

The hippocampus is believed to be important for rapid learning of arbitrary stimulus-response contingencies, or S-R bindings. In support of this, Schnyer et al., 2006 (Experiment 2) measured priming of reaction times (RTs) to categorise visual objects, and found that patients with medial temporal lobe damage, unlike healthy controls, failed to show evidence of reduced priming when response contingencies were reversed between initial and repeated categorisation of objects (a signature of S-R bindings). We ran a similar though extended object classification task on 6 patients who appear to have selective hippocampal lesions, together with 24 age-matched controls. Unlike Schnyer et al., 2006, we found that reversing response contingencies abolished priming in both controls and patients. Bayes Factors provided no reason to believe that response reversal had less effect on patients than controls. We therefore conclude that it is unlikely that the hippocampus is needed for S-R bindings.

neuroscience↗