Biology subjects

Reynolds, R.

Publications and source records attributed to Reynolds, R..

16 recordsLinked to original sources

bioRxiv2026

E3 Ligase Ligandalyzer: A Structure-First, Ligand-Centric Platform for E3 Ligase Recruiter Selection

Here, we present E3 Ligase Ligandalyzer Version 1.0, a freely accessible, recruiter-centric web platform for comparative exploration of experimentally resolved E3 ligase-recruiter complexes. The locked Version 1.0 dataset spans 35 E3 ligases, 604 reconciled recruiter entities, and 1,372 active structure-specific recruiter instances across 685 experimentally resolved PDB structures. Recruiters are linked to normalized chemical representations and analyzed using cheminformatics and structure-based workflows to compute physicochemical descriptors, scaffold relationships, aligned binding-pocket views, and solvent-accessible surface area patterns relevant to linker attachment. The platform integrates recruiter-entity, recruiter-instance, scaffold, and ligase views, allowing users to compare experimentally grounded chemical and structural observations without imposing predictive rankings. The platform supports direct transition into downstream degrader-design workflows, including integration with PROTAC Builder (protacbuilder.com). E3 Ligase Ligandalyzer is freely available at https://e3ligandalyzer.com, and the associated code and dataset-generation scripts are available at https://github.com/schurerlab/E3-Ligandalyzer-Scripts.

bioinformatics↗

bioRxiv2026

Parabens Impair Mouse Antral Follicle Growth and Alter Ovarian Hormone and Gene Expression Similar to Phthalates

Benzyl paraben (BzP) and butyl paraben (BuP) are used as preservatives and antimicrobial agents in cosmetics, pharmaceuticals, and foods. BzP and BuP have been detected in urine, placental tissue, and ovarian follicular fluid and are understudied with regards to their endocrine activity, raising concerns on their impact to the reproductive system. We tested the hypothesis that BzP and BuP are toxic to the ovary and behave similarly to other structurally similar endocrine disrupting chemicals, such as phthalates and terephthalates, by altering hormone levels and impacting cell growth and gene expression in vitro. Untreated mouse antral follicles were exposed to vehicle, 0.1, 1, 10, or 100 g/mL BzP, BuP, or the BuP analog monobutyl terephthalate (MBuTP) for 96 hours. The highest dose of BzP and BuP were cytotoxic to follicles, suggesting that medium chain length hydroxybenzoates are more cytotoxic to the ovary than corresponding terephthalic acids. BzP significantly increased levels of estradiol and testosterone compared to control. BuP decreased follicle growth and disrupted expression of cell cycle regulators, similar to phthalates. The peroxisome proliferator-activated receptor gamma (PPARg)-transcriptionally controlled gene Fabp4 was significantly upregulated by both BzP and BuP, whereas MBuTP upregulated all four PPAR target genes and decreased follicle growth. Overall, BzP, BuP, and MBuTP disrupted hormone levels, follicle growth, and cell cycle progression, suggesting similarities in toxicity to phthalates and potential endocrine disruption. Further study should be done on the reproductive toxicity and endocrine disrupting effects of chemicals similar in structure to phthalates to reduce exposure to endocrine disruptors and inform design of safer replacements.

pharmacology and toxicology↗

bioRxiv2026

Polystyrene Nanoplastics Disrupt Mouse Placenta Development in a Sex-Dependent Manner

Plastic production has been increasing exponentially. Throughout their lifespan, plastics degrade into smaller particles that accumulate in our bodies and the environment. Recent studies found these plastic particles can cross the placental barrier and reach the fetus. However, the impact of plastic particles on placental function is still unknown. We hypothesized that nanoplastics would disrupt placental growth and function, specifically focusing on transforming growth factor beta (TGF{beta}) signaling. To understand the impact of plastic particles on the placenta, we orally exposed pregnant CD-1 mice to 50 nm or 200 nm polystyrene plastic particles from gestation day 8 to day 15 at a human-relevant concentration of 5 mg/kg/day. After euthanization on day 15, placenta and fetus weights were recorded, and tissues were prepared for histomorphology and gene expression analysis. We observed a statistically significant decrease in the area of the decidua in the placentas for the 200 nm treatment group and a borderline significant decrease in decidua area for the 50 nm treatment group compared to control. However, when we separated by sex, only the male decidua were significantly decreased in the 200 nm group. Gene expression analysis of key signaling factors in the TGF{beta} pathway identified increased expression of Smad2 and Smad3, which may be suppressing prolactin and estrogen receptor signaling. Overall, both particle sizes disrupted placenta structure and signaling in a sex-dependent manner and may be acting as endocrine disruptors.

pharmacology and toxicology↗

bioRxiv2025

TP53 and RB1 are predictive genetic biomarkers for sensitivity to cytarabine in gliomas

Therapeutic progress in glioma, one of the most lethal human cancers, has been limited by molecular heterogeneity and lack of biomarker-driven drug deployment. Here we used a proprietary large-scale CRISPRi screening in primary patient-derived glioma tumorspheres to identify genetic vulnerabilities and nominate pharmacologically tractable targets. DNA polymerase-linked dependencies emerged as top-ranked hits, which we validated through orthogonal viability assays. Network-based integration of dependency data with drug-target relationships nominated cytarabine, a nucleoside analogue already approved for intrathecal use, as a candidate agent targeting this axis. Dose-response profiling across molecularly diverse glioma models revealed substantial heterogeneity in cytarabine sensitivity (IC50 range: 0.04-9.8 {micro}M). Machine learning analysis of whole-genome sequencing data identified TP53 wild-type and RB1-wild-type status as dominant predictors of response, with double wild-type lines showing three standard deviations (3 s.d.) increased sensitivity compared to altered models. Prospective validation in an independent cohort confirmed that TP53/RB1 genotype stratifies cytarabine activity. These findings establish a mechanistically anchored, biomarker-restricted repurposing opportunity for cytarabine in leptomeningeal glioma, enabling rational prioritisation of an accessible therapy in a molecularly defined patient subset.

cancer biology↗

bioRxiv2025

Polystyrene and polyethylene terephthalate nanoplastics differentially impact mouse ovarian follicle function

Exposure to micro- and nanoplastics is unavoidable. Foods and beverages contain plastic particles from environmental contamination and processing and packaging materials, which are frequently made of polyethylene terephthalate (PET). Micro- and nanoplastics have been detected in human tissues such as the brain, liver, and placenta, as well as in ovarian follicular fluid, but little is known about the effects nanoplastics have on the female reproductive system. In addition, few studies on the health impacts of nanoplastics have been performed using environmentally relevant plastic types and concentrations. Thus, this research tested the hypothesis that nanoplastics made of spherical polystyrene (PS), a common model nanoplastic, would have different effects on cultured mouse ovarian follicles compared to secondary PET nanoplastics at environmentally relevant doses. The ovary is a highly sensitive reproductive organ responsible for the development of follicles, which contain the oocyte, and production of steroid hormones. Follicles were harvested from adult mouse ovaries and cultured for 96 h with vehicle, spherical commercially available 200 nm PS nanoplastics (1-100 {micro}g/mL), or lab-generated 240 nm PET nanoplastics (0.1-10 {micro}g/mL). PS and PET nanoplastic exposure inhibited follicle growth and altered expression of genes related to steroid synthesis, cell cycle, and oxidative stress. PET nanoplastics increased levels of pregnenolone and decreased expression of Cyp17a1. Overall, both plastic types altered ovarian function, but they impacted different genes in similar pathways. These findings suggest that nanoplastic exposure at environmentally relevant concentrations may pose a risk to female reproductive health by disrupting hormonal and molecular pathways. In addition, environmentally relevant plastic types and doses are necessary for studying health impacts of nanoplastics. HighlightsO_LINanoplastics disrupted ovarian function in vitro C_LIO_LISecondary PET and virgin PS differently inhibited follicle growth and ovarian gene expression C_LIO_LIPET exposure increased pregnenolone, impacting steroid hormone pathways C_LIO_LIEnvironmentally relevant plastics can harm female reproductive health C_LI

pharmacology and toxicology↗

bioRxiv2025

Detecting cell-level transcriptomic changes of Perturb-seq using Contrastive Fine-tuning of Single-Cell Foundation Models

Genome-scale perturbation cell atlases are an exciting new resource to understand the transcriptomic and phenotypic impact of single-gene activation or knockdown. However, in terms of differentially expressed genes identified, the signal detected in these data atlases is low, leading to the exclusion of most data from downstream analyses. Recent advances in single-cell foundation models have shown promise in capturing complex biological insights. However, their application to perturbation analysis, especially in predicting perturbed single-cell transcriptomes, remains limited. In this paper, we focus on learning representations of single-cell transcriptomes that capture subtle, yet important, transcriptome-wide changes, and we propose a novel fine-tuning strategy using contrastive learning to leverage single-cell foundation models for this task. We pre-train a single-cell foundation model and fine-tune on a genome-scale perturbation dataset using a contrastive loss, which minimises the distance between cell embeddings from unperturbed cells while maximising the distance between perturbed and unperturbed cells. We validate and test the model on unseen perturbations, demonstrating its ability to identify global biologically meaningful transcriptional changes not captured by traditional differential expression methods. Our approach provides a novel framework for analysing single-cell perturbation data and offers a more effective means of identifying perturbations that drive systemic gene expression changes.

bioinformatics↗

bioRxiv2024

Emergent Metabolic Niches for Marine Heterotrophs

Ocean microbial communities are made up of thousands of diverse taxa whose metabolic demands set the rates of both biomass production and degradation. Thus, these microscopic organisms play a critical role in ecosystem dynamics, global carbon cycling, and climate. While we have frameworks for relating phytoplankton diversity to rates of carbon fixation, our knowledge of how variations in heterotrophic microbial populations drive changes in carbon cycling is in its infancy. Here, we leverage global metagenomic datasets and metabolic models to identify a set of metabolic niches with distinct growth strategies. These groupings provide a simplifying framework for describing microbial communities in different oceanographic regions and for understanding how heterotrophic microbial populations function. This framework, predicated directly on metabolic capability rather than taxonomy, enables us to tractably link heterotrophic diversity directly to biogeochemical rates in large scale ecosystem models.

ecology↗

bioRxiv2023

Defective lysosomal acidification contributes to TNFR1 mediated neuronal necroptosis in Alzheimer's disease

Background: Tumor necrosis factor (TNF) receptor 1 (TNFR1) signaling mediates neuronal necroptosis in Alzheimer's disease (AD). Interaction of TNFR1 signaling axis with autolysosomal pathway and the accumulation of necrosome molecules in impaired lysosomes have been shown to lead to necroptotic neuronal death. This has been attributed to the terminal failure of the autophagic process, primarily due to lysosomal degradation dysfunction. Being the final and determining step of the autolysosomal pathway, lysosomes with sufficient acidification as maintained by functional vacuolar (H+)-ATPase (V-ATPase) are required to achieve complete autophagic degradation of toxic cellular components. Here, we aim to investigate the role of defective lysosomal acidification in mediating TNFR1 induced neuronal necroptosis in AD. Methods: Neuropathological analysis of human post-mortem AD brains was performed to examine the correlation between TNFR1 induced neuronal necroptosis and autolysosomal dysfunction. Specifically, we probed for the level of V-ATPase subunits in AD brains to determine the extent of lysosomal acidification and function. Cell-based assays were conducted to understand the effect of TNFR1 activation in driving lysosomal acidification defect, proteolytic function, membrane integrity, autophagic impairment, mitochondrial dysfunction, and neuronal death in SH-SY5Y neuroblastoma cells. Furthermore, we applied lysosome-acidifying nanoparticles (AcNPs) to determine whether restoration of lysosomal acidification can rescue neuronal necroptosis in both TNF-treated SH-SY5Y cells and APPNL-G-F knock-in mouse model of AD. Results: We found that TNFR1 activated neuronal necroptosis correlated with autolysosomal dysfunction as characterized by downregulation of V-ATPase subunits and accumulation of autophagy receptor p62 in human AD brains. In cell culture, we showed for the first time that lysosomal acidification is only impaired in cells treated with TNF and not with other cytokines, contributing to inhibition of autophagic degradation in SH-SY5Y cells. TNF also disrupted lysosomal trafficking and membrane dynamics and induced lysosomal membrane permeabilization, followed by impaired autophagic clearance, defective mitochondrial turnover, reduced mitochondrial function, and neuronal death. Importantly, we demonstrated that AcNPs restored lysosomal, autophagic, and mitochondrial function, improved lysosomal membrane homeostasis, and rescued neuronal necroptosis in both TNF-treated SH-SY5Y cells and APPNL-G-F mice.

neuroscience↗

bioRxiv2023

Widespread B-vitamin auxotrophy in marine particle-associated bacteria

Microbial community assembly is governed by trophic interactions that mediate the transfer of carbon sources and biomass building blocks between species. However, central metabolism corresponds to only a small fraction of the biosynthetic potential of microbes: metabolites such as antimicrobial compounds, signaling molecules, and co-factors are underexplored forces shaping microbial communities. Here, we focus on B vitamin exchange in coastal marine bacterial communities that degrade particulate organic matter and find that natural seawater communities are vitamin limited. While almost a third of bacterial isolates from these communities are B vitamin auxotrophs, the pioneering degraders that first arrive on particles are vitamin producers that likely support auxotrophs through cross-feeding. However, combining experiments and a resource-explicit model, we show that auxotroph growth is often not restored by coculture with vitamin producers, but rather requires lysis and subsequent vitamin recycling. Our results highlight the importance of vitamin auxotrophies and lysis-mediated cross-feeding as important factors controlling microbial community assembly and succession on marine particles.

microbiology↗

bioRxiv2021

TNF-mediated neuroinflammation is linked to neuronal necroptosis in Alzheimer's disease hippocampus

The pathogenetic mechanisms underlying neuronal death and dysfunction in Alzheimers disease (AD) remain unclear. However, chronic neuroinflammation has been implicated in stimulating or exacerbating neuronal damage. The tumor necrosis factor (TNF) superfamily of cytokines are involved in many systemic chronic inflammatory and degenerative conditions and are amongst the key mediators of neuroinflammation. TNF binds to the TNFR1 and TNFR2 receptors to activate diverse cellular responses that can be either neuroprotective or neurodegenerative. In particular, TNF can induce programmed necrosis or necroptosis in an inflammatory environment. Although activation of necroptosis has recently been demonstrated in the AD brain, its significance in AD neuron loss and the role of TNF signaling is unclear. We demonstrate an increase in expression of multiple proteins in the TNF/TNF receptor-1-mediated necroptosis pathway in the AD post-mortem brain, as indicated by the phosphorylation of RIPK3 and MLKL, predominantly observed in the CA1 pyramidal neurons. The density of phosphoRIPK3+ and phosphoMLKL+ neurons correlated inversely with total neuron density and showed significant sexual dimorphism within the AD cohort. In addition, apoptotic signaling was not significantly activated in the AD brain compared to the control brain. Exposure of human iPSC-derived glutamatergic neurons to TNF increased necroptotic cell death when apoptosis was inhibited, which was significantly reversed by small molecule inhibitors of RIPK1, RIPK3, and MLKL. In the post-mortem AD brain and in human iPSC neurons to TNF, we show evidence of altered expression of proteins of the ESCRT III complex, which has been recently suggested as an antagonist of necroptosis and a possible mechanism by which cells can survive after necroptosis has been triggered. Taken together, our results suggest that neuronal loss in AD is due to TNF-mediated necroptosis rather than apoptosis, which is amenable to therapeutic intervention at several points in the signaling pathway.

neuroscience↗

bioRxiv2021

Enrichment analysis of GWAS data in autoimmunity delineates the multiple sclerosis-Epstein Barr virus association

We exploited genetic information to assess non-genetic influences in autoimmunity. We isolated gene modules whose products physically interact with environmental exposures related to autoimmunity, and analyzed their nominal statistical evidence of association with autoimmune and non-autoimmune diseases in genome-wide association studies (GWAS) data. Epstein Barr virus (EBV) and other Herpesviruses interactomes emerged as specifically associated with multiple sclerosis (MS), possibly under common regulatory mechanisms. Analyses of MS blood and brain transcriptomes, cytofluorimetric studies of endogenous EBV-infected lymphoblastoid lines, and lesion immunohistochemistry, confirmed a dysregulation of MS-associated EBV interactors, suggesting their contribution to CD40 signaling alterations in MS. These interactors resulted enriched in modules from inherited axonopathies-causing genes, supporting a link between EBV and neurodegeneration in MS, in accord with the observed transcriptomic dysregulations in MS brains. They were also enriched with top-ranked pharmaceutical targets prioritized on a genetic basis. This study delineates a disease-specific influence of herpesviruses on MS biology.

neuroscience↗

bioRxiv2021

Lymphotoxin-alpha expression in the meninges causes lymphoid tissue formation and neurodegeneration

Lymphotoxin alpha (LT) plays an important role in lymphoid organ development and cellular cytotoxicity in the immune system. LT expression is increased in the cerebrospinal fluid of naive and progressive multiple sclerosis (MS) patients and post-mortem meningeal tissue. Here we show that persistently increased levels of LT in the cerebral meninges can give rise to lymphoid-like structures and underlying MS-like cortical pathology. Stereotaxic injections of recombinant LT into the rat meninges leads to acute meningeal inflammation and subpial demyelination that resolves after 28 days. Injection of an LT lentiviral vector induces lymphoid-like immune cell aggregates, maintained over 3 months, including T-cell rich zones containing podoplanin+ fibroblastic reticular stromal cells and B-cell rich zones with a network of follicular dendritic cells, together with expression of lymphoid chemokines and their receptors. Extensive microglial activation, subpial demyelination and marked neuronal loss occurs in the underlying cortical parenchyma. These results show that chronic LT overexpression is sufficient to induce formation of meningeal lymphoid-like structures and subsequent neurodegeneration. SummaryIncreased release of lymphotoxin-alpha contributes to the pro-inflammatory milieu of the cerebrospinal fluid of MS patients. A persistent elevated expression of this cytokine in the meninges of rats gives rise to chronic inflammation with lymphoid tissue induction and accompanying neurodegenerative and demyelinating pathology in the underlying brain tissue.

neuroscience↗

bioRxiv2020

Meningeal inflammation in multiple sclerosis induces phenotypic changes in cortical microglia that differentially associate with neurodegeneration

Meningeal inflammation strongly associates with demyelination and neuronal loss in the underlying cortex of progressive MS patients, contributing to clinical disability. However, the pathological mechanisms of meningeal inflammation-induced cortical pathology are still largely elusive. Using extensive analysis of human post-mortem tissue, we identified two distinct microglial phenotypes, termed MS1 and MS2, in the cortex of progressive MS patients. These phenotypes differed in morphology and protein expression, but both associated with inflammation of the overlying meninges. We could replicate the MS-specific microglial phenotypes in a novel in vivo rat model for progressive MS-like meningeal inflammation, with microglia present at 1 month post-induction resembling MS1 microglia whereas those at 2 months acquired an MS2-like phenotype. Interestingly, MS1 microglia were involved in presynaptic displacement and phagocytosis and associated with a relative sparing of neurons in the MS and animal cortex. In contrast, the presence of MS2 microglia coincided with substantial neuronal loss. Taken together, we uncovered that in response to meningeal inflammation, microglia acquire two distinct phenotypes that differentially associate with neurodegeneration in the progressive MS cortex. Our data suggests that these phenotypes occur sequentially and that microglia may lose their protective properties over time, contributing to neuronal loss.

neuroscience↗

bioRxiv2020

Neuroinflammation in the normal appearing white matter of multiple sclerosis brain causes abnormalities at the node of Ranvier

Changes to the structure of nodes of Ranvier in the normal-appearing white matter (NAWM) of MS brains are associated with chronic inflammation. We show that the paranodal domains in MS NAWM are longer on average than control, with Kv1.2 channels dislocated into the paranode. These pathological features are reproduced in a model of chronic meningeal inflammation generated by the injection of lentiviral vectors for the lymphotoxin- (LT) and interferon-{gamma} (IFN{gamma}) genes. We show that tumour necrosis factor (TNF), IFN{gamma} and glutamate can provoke paranodal elongation in cerebellar slice cultures, which could be reversed by an NMDA blocker. When these changes were inserted into a computational model to simulate axonal conduction, a rapid decrease in velocity was observed, reaching conduction failure in small diameter axons. We suggest that glial cells activated by proinflammatory cytokines can produce high levels of glutamate, which triggers paranodal pathology, contributing to axonal damage and conduction deficits.

neuroscience↗

bioRxiv2019

Targeted stimulation of human orbitofrontal networks disrupts outcome-guided behavior

Outcome-guided behavior requires knowledge about the current value of expected outcomes. Such behavior can be isolated in the reinforcer devaluation task, which assesses the ability to infer the current value of rewards after devaluation. Animal lesion studies demonstrate that orbitofrontal cortex (OFC) is necessary for normal behavior in this task, but a causal role for human OFC in outcome-guided behavior has not been established. Here we used sham-controlled non-invasive continuous theta-burst stimulation (cTBS) to temporarily disrupt human OFC network activity prior to devaluation of food odor rewards in a between-subjects design. Subjects in the sham group appropriately avoided Pavlovian cues associated with devalued food odors. However, subjects in the stimulation group persistently chose those cues, even though devaluation of food odors themselves was unaffected by cTBS. This behavioral impairment was mirrored in changes in resting-stated functional magnetic resonance imaging (rs-fMRI) activity, such that subjects in the stimulation group exhibited reduced global OFC network connectivity after cTBS, and the magnitude of this reduction was correlated with choices after devaluation. These findings demonstrate the feasibility of indirectly targeting the human OFC with non-invasive cTBS, and indicate that OFC is specifically required for inferring the value of expected outcomes.

neuroscience↗

bioRxiv2019

MS Atlas - A molecular map of brain lesion stages in progressive multiple sclerosis

Multiple sclerosis (MS) is a chronic inflammatory neurodegenerative disorder of the central nervous system with an untreatable late progressive phase in a high percentage of patients. Molecular maps of different stages of brain lesion evolution in patients with progressive MS (PMS) are missing but critical for understanding disease development and to identify novel targets to halt progression. We introduce the first MS brain lesion atlas (msatlas.dk), developed to address the current challenges of understanding mechanisms driving the fate of PMS on lesion basis. The MS Atlas gives means for testing research hypotheses, validating candidate biomarkers and drug targets. The MS Atlas data base comprises comprehensive high-quality transcriptomic profiles of 73 brain white matter lesions at different stages of lesion evolution from 10 PMS patients and 25 control white matter samples from five patients with non-neurological disease. The MS Atlas was assembled from next generation RNA sequencing of post mortem samples using strict, conservative preprocessing as well as advanced statistical data analysis. It comes with a user-friendly web interface, which allows for querying and interactively analyzing the PMS lesion evolution. It fosters bioinformatics methods for de novo network enrichment to extract mechanistic markers for specific lesion types and pathway-based lesion type comparison. We describe examples of how the MS Atlas can be used to extract systems medicine signatures. We also demonstrate how its interface can interactively condense and visualize the atlas content. This compendium of mechanistic PMS white matter lesion profiles is an invaluable resource to fuel future multiple sclerosis research and a new basis for treatment development.

systems biology↗