Biology subjects

Armstrong, A.

Publications and source records attributed to Armstrong, A..

17 recordsLinked to original sources

bioRxiv2026

Sex-Dependent Microbiome-Metabolome Remodeling Associated with Bacteroides acidifaciens Modulation of Acute Respiratory Distress Syndrome

Acute respiratory distress syndrome (ARDS) is a severe lung disorder influenced by the interplay between the intestinal microbiome, host metabolism, and immune function. We previously found that Bacteroides acidifaciens (BA) has opposing effects on staphylococcal enterotoxin B (SEB)-induced ARDS, worsening the condition in female mice while alleviating it in males. This study aimed to examine whether these outcomes are linked to sex-dependent changes in the intestinal microbiome and gut-lung metabolome. C3H/HeJ mice of both sexes were orally colonized with Bacteroides acidifaciens before SEB exposure. Stool and bronchoalveolar lavage fluid (BALF) were collected for analysis using 16S rRNA sequencing and untargeted liquid chromatography mass spectrometry metabolomics. Our findings revealed distinct sex-dependent metabolic and microbial responses. In females, disease exacerbation correlated with elevated lipid mediators (leukotriene B4, 13-oxoODE, and 13S-HODE) alongside shifts in bile acid and redox metabolism. The intestinal microbiome showed changes in Bacteroides, Akkermansia, and Lachnospiraceae. Conversely, males showed a protective phenotype characterized by increased butyrate and alterations in sphingolipid, amino acid, redox, and nucleotide pathways. Integrated analyses identified sex-associated microbial communities and metabolomic profiles, highlighting distinct patterns of lipid and redox associations in females versus sphingolipid and short-chain fatty acid patterns in males. These results suggest that host sex influences how a commensal bacterium affects inflammatory lung injury and point to pathways for future research.

microbiology↗

bioRxiv2026

Discovery of Covalent Wild-Type Isocitrate Dehydrogenase 1 (IDH1) Inhibitors Targeting Cys269

Isocitrate dehydrogenase 1 (IDH1) catalyses the interconversion of isocitrate and -ketoglutarate and is overexpressed in several cancers, supporting tumour survival and treatment resistance. Inhibitors targeting the oncogenic mutant forms of IDH1 also inhibit the wild-type (WT) protein, but lose substantial potency due to greater competition with native substrates (isocitrate and Mg2+). We hypothesised that a covalent inhibitor may be more effective at overcoming the higher substrate affinity of wild-type IDH1. Here, a covalent fragment-based approach was used to develop IDH1-C269 selective inhibitors which prevent the key regulatory segment from forming an -helix required for catalytic competency. Following the identification of C269-selective fragments, we used X-ray crystallography to characterise IDH1-fragment bound complexes and guide structure-based design efforts. Inspired by the unexpected detection of bound isocitrate molecule in an X-ray crystal structure, fragment expansion yielded a series of compounds exploiting both an adjacent site and a unique water-mediated hydrogen bonding network. This series achieved strong potency (reaching IC50 = 47.5 nM, a 155-fold improvement in potency relative to the original fragment), retained activity in the presence of competing Mg2+, showed selectivity against IDH2 and reduced NADPH concentrations in a relevant PDAC cell model. Together, these findings present a mechanistic rationale for the covalent targeting of wild-type IDH1 and provide structurally validated inhibitors for further development.

cancer biology↗

bioRxiv2026

Discovery of stereoselective targeted covalent inhibitors of the RAB27-effector protein-protein interaction

RAB27A and RAB27B are homologous small GTPases that regulate intracellular vesicle trafficking, orchestrating endocytic and exocytic processes that affect cellular communication, immune responses, and dynamics of the cellular microenvironment. Through their interactions with effector proteins, RAB27A/B play roles in tumor metastasis and chronic inflammation. However, pharmacological modulation of their activity faces challenges typical of small GTPases, including a lack of well-defined pockets outside the conserved GTP binding site, and large RAB27-effector protein-protein interaction (PPI) surfaces. Here, we present the discovery and development of the first cell-active, rationally designed covalent inhibitors of the RAB27-effector interaction, targeting a non-conserved cysteine residue flanking the PPI interface. An electrophile-first biochemical screen led to a novel class of acrylamide covalent inhibitors, and X-ray crystallography structure-guided design led to optimized inhibitors and probes that enantioselectively target RAB27A/B-Cys123 in cells. Potency and selectivity were confirmed through biochemical and cellular assays, including chemical proteomics and phenotype recapitulation in melanocytes alongside a matched inactive enantioprobe control. In contrast, a previously reported compound, Nexinhib-20, was found to be toxic and to exert its activity through non-selective reactivity. This work provides the first toolbox of cell-active chemical probes for RAB27 which can be used in future studies to shed light on the function of this protein and its potential as a therapeutic target.

biochemistry↗

bioRxiv2026

Foundation cell segmentation models performance on live microscopy and spatial-omics data

Accurate cell segmentation is an essential step for quantitative analysis of biological imaging data. Recent advances in deep learning have led to the development of generalist segmentation models that perform robustly across multiple imaging modalities, including label-free phase contrast, fluorescence cell culture, and multiplexed fluorescence tissue imaging. However, systematic comparisons of these models at the level of downstream biological analysis remain limited. To address this gap, we evaluated several recent segmentation models, including Cellpose cyto3, Cellpose-SAM, {micro}SAM, and CellSAM, on phase contrast and fluorescence cell culture images. In addition, Mesmer and InstanSeg were included for benchmarking on multiplexed fluorescence tissue images generated using CO-Detection by IndEXing (CODEX). We found that Cellpose-SAM achieved strong performance on phase contrast images, while SAM-based models consistently performed well on fluorescence cell culture data. In contrast, no single model consistently outperformed others on CODEX datasets. Instead, each model exhibited distinct strengths and limitations, which led to differences in downstream analyses, including clustering and cell type identification. Together, our study emphasizes the importance of selecting segmentation models based on dataset characteristics and analytical goals, rather than relying on a single universal approach.

bioinformatics↗

bioRxiv2025

A memory-driven model of phenotypic adaptation for anticipating the emergence of enzalutamide resistance in prostate cancer

While contemporary cancer treatment strategies have significantly prolonged the lives of patients, therapeutic resistance remains a predominant cause of disease progression and cancerrelated deaths. Cancer therapy often induces gene regulatory responses that promote cell survival in the face of this therapy. Herein, we sought to develop a stochastic model of the response to repeat therapeutic challenge. This model integrates reinforcement learning to account for environmental history-dependent cellular transitions and growth dynamics. When applied to prostate cancer, this memory-driven adaptive model successfully captures the experimentally-observed dynamics of drugsensitive and drug-resistant LNCaP cells under varying dosing schedules of androgen receptor blockade with enzalutamide (enza), significantly outperforming traditional transition models that lack history dependence. This performance is especially evident in the ability of our approach to robustly predict stochastic fluctuations in cancer cell population sizes across the entire disease trajectory, including subtle, later-emerging responses following initial therapy. The model was further evaluated by predicting the control of resistant cells in an enza environment by modeling inhibition of the p38/MAPK pro-survival stress axis, which was then validated experimentally. Lastly, we developed and applied a patient-calibrated model using prostate-specific antigen (PSA) data from clinical patient cohorts undergoing intermittent androgen deprivation therapy. Our model accurately predicts the PSA dynamics under repeated treatment cycles and effectively distinguishing between patients who respond and those who do not respond to treatment, thereby providing quantitative insight into prostate cancer progression. We anticipate that such adaptive modeling frameworks will be broadly useful for predicting cancer treatment outcomes and developing optimized adaptive therapeutic strategies tailored to patient-specific disease dynamics in additional cancer contexts.

evolutionary biology↗

bioRxiv2025

A benchtop bioreactor to impart coarctation-induced deformation and assess mechanisms of endothelial dysfunction

Hypertension (HTN) is common with coarctation of the aorta (CoA), a common congenital cardiovascular defect. Coarctation-induced mechanical stimuli can drive remodeling in the proximal aorta, resulting in stiffening and HTN. Natriuretic peptide receptor C (NPRC) expression is downregulated in proximal aortas of hypertensive CoA patients, and preclinical models show endothelial NPRC decreases with increasing coarctation severity. The function of NPRC is regulated by actin cytoskeleton organization. AHNAK potentiates arachidonic acid calcium mobilization in this process, but its role in CoA is unknown. Mechanistic study of NPRC in CoA is hampered by limited, heterogenous patients and lengthy, expensive preclinical models. We developed an in vitro system using human aortic endothelial cells (HAECs) to mimic NPRC and endothelial dysfunction results from CoA and study mechanisms (e.g. AHNAK) regulating NPRC membrane expression. Physiologic (12%) and pathologic (17%) strain conditions derived from preclinical control and CoA aortic measurements were applied to HAECs using a tension bioreactor. Two-photon imaging of the strain-conditioned HAECs response to CNP (agonist) revealed those exposed to pathologic strain had significantly less intracellular calcium [Ca2+]i mobilization than with physiologic strain, consistent with results from intact CoA tissue. Protein expression of NPRC and AHNAK were disrupted in actin cytoskeleton fractions from sucrose density gradient ultracentrifugation studies using lysates of HAEC exposed to pathologic conditions. These results indicate our HAECs straining system mimics the in vivo effects CoA-induced mechanical stimuli have on aortic tissue and can be used can used to conduct studies confirming and/or extending associated mechanisms.

physiology↗

bioRxiv2025

Neural correlates of perceptual decision making in primary somatosensory cortex

The brain is thought to produce decisions by gradual accumulation of sensory evidence through a hierarchically organized feedforward cascade of neuronal activities that transforms early stimulus representations in the primary somatosensory cortex (S1) to a perceptual decision processed in pre-motor areas. Recently, this prevailing view has been challenged by observation of choice- correlated neural activity as early in the hierarchy as S1. Here, to reconcile these seemingly controversial observations, we employ ethological whisker-guided navigation of mice in a tactile virtual reality paradigm combined with dense electrophysiological recordings in whisker-related wS1. Leaving only a pair of C2 whiskers for mice to navigate with, we effectively designed an information bottleneck for sensory input to decision making. We show that neural activity during sensory evidence accumulation exhibits dramatic collapse of the high-dimensional spiking activity to just a single latent variable followed by a slower and almost synchronous ramping up across the whole cortical column. We show that this variable is consistent with models of gradual accumulation of noisy sensory evidence to a decision bound. These observations indicate that S1 may directly participate in a categorical coding of all-or-none decision variable via cortico-cortical feedback loops through which sensory information reverberates to be transformed into perception and action. Significance StatementBy employing ethological whisker-guided navigation of mice in a tactile virtual reality paradigm combined with dense electrophysiological recordings in whisker-related wS1, we show that neural activity during sensory evidence accumulation exhibits dramatic collapse of the high-dimensional spiking activity to just a single latent variable followed by a slower and almost synchronous ramping up across the whole cortical column. We show that this variable is consistent with models of gradual accumulation of noisy sensory evidence to a decision bound. These observations indicate that wS1 may directly participate in a categorical coding of all-or-none decision variable. Naturalistic perceptual decisions during active whisker-guided navigation High-dimensional activity in S1 collapses to a single variable prior to decision This ramping spiking activity is consistent with drift-diffusion decision models Indicates direct involvement of S1 in evidence accumulation

neuroscience↗

bioRxiv2025

Gut microbiota phospholipids regulate intestinal gene expression and can counteract the effects of antibiotic treatment

The gut microbiome influences immune and metabolic homeostasis. Our research using non-obese diabetic (NOD) mice revealed that early-life antibiotic exposure remodels the gut microbiome affecting metabolism and accelerating type 1 diabetes (T1D) incidence, with cecal material transplant (CMT) mitigating the damage. Now examining murine intestinal lipidomic profiles, we identified 747 compounds. Comparing the lipidomic profiles of cecal contents of conventional and germ-free mice and their diets, we identified 87 microbially-produced lipids reduced by antibiotic exposure but CMT-restored. Parallel analysis of human fecal lipid profiles after azithromycin-exposure showed significant alterations with substantial overlap with mice. In vitro co-culture with mouse macrophages or small intestinal epithelial cells and human colonic epithelial cells identified phospholipids that repress inflammation through the NF{kappa}B pathway. Oral administration of these phospholipids to antibiotic-treated NOD mice reduced expression of ileal genes involved in early stages of T1D pathogenesis. These findings indicate potential therapeutic anti-inflammatory roles of microbially-produced lipids.

microbiology↗

bioRxiv2024

Host-derived Interleukin 1α induces an immunosuppressive tumor microenvironment via regulating monocyte-to-macrophage differentiation

Tumor-associated macrophages exhibit high heterogeneity and contribute to the establishment of an immunosuppressive tumor microenvironment (TME). Although numerous studies have demonstrated that extracellular factors promote macrophage proliferation and polarization, the regulatory mechanisms governing the differentiation process to generate phenotypically, and functionally diverse macrophage subpopulations remain largely unexplored. In this study, we examined the influence of interleukin 1 (IL-1) on the development of an immunosuppressive TME using orthotopic transplantation murine models of breast cancer. Deletion of host Il1 led to the rejection of inoculated congenic tumors. Single-cell sequencing analysis revealed that CX3CR1+ macrophage cells were the primary sources of IL-1 in the TME. The absence of IL-1 reprogrammed the monocyte-to-macrophage differentiation process within the TME, characterized by a notable decrease in the subset of CX3CR+ ductal-like macrophages and an increase in iNOS-expressing inflammatory cells. Comparative analysis of gene signatures in both human and mouse macrophage subsets suggested that IL-1 deficiency shifted the macrophage polarization from M2 to M1 phenotypes, leading to enhanced cytotoxic T lymphocyte activity in the TME. Importantly, elevated levels of IL-1 in human cancers were associated with worse prognosis following immunotherapy. These findings underscore the pivotal role of IL-1 in shaping an immune-suppressive TME through the regulation of macrophage differentiation and activity, highlighting IL-1 as a potential target for breast cancer treatment. TeaserInterleukin 1 dictates macrophage behavior, influencing an immunosuppressive microenvironment in breast cancer, suggesting it as a treatment target.

cancer biology↗

bioRxiv2024

Pavlovian cue-evoked alcohol seeking is disrupted by ventral pallidal inhibition

Cues paired with alcohol can be potent drivers of craving, alcohol-seeking, consumption, and relapse. While the ventral pallidum is implicated in appetitive and consummatory responses across several reward classes and types of behaviors, its role in behavioral responses to Pavlovian alcohol cues has not previously been established. Here, we tested the impact of optogenetic inhibition of ventral pallidum on Pavlovian-conditioned alcohol-seeking in male Long Evans rats. Rats underwent Pavlovian conditioning with an auditory cue predicting alcohol delivery to a reward port and a control cue predicting no alcohol delivery, until they consistently entered the reward port more during the alcohol cue than the control cue. We then tested the within-session effects of optogenetic inhibition during 50% of cue presentations. We found that optogenetic inhibition of ventral pallidum during the alcohol cue reduced port entry likelihood and time spent in the port, and increased port entry latency. Overall, these results suggest that normal ventral pallidum activity is necessary for Pavlovian alcohol-seeking.

neuroscience↗

bioRxiv2023

Comparative population genomics of manta rays has global implications for management

Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays (Mobula birostris) display significantly higher heterozygosity than reef manta rays (Mobula alfredi) and that M. birostris populations display higher connectivity worldwide. Through inferring modes of colonisation, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for population management. Our findings highlight the potential for fisheries to disrupt population dynamics at both local and global scales and therefore have direct relevance for international conservation of marine species.

evolutionary biology↗

bioRxiv2022

Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer

Advanced prostate cancer patients initially respond to hormone therapy, be it in the form of androgen deprivation therapy or second-generation hormone therapies, such as abiraterone acetate or enzalutamide. However, most men with prostate cancer eventually develop hormone therapy resistance. This resistance emerges in several ways, such as through genetic mutations, epigenetic mechanisms, or through non-genetic pathways, such as lineage plasticity along epithelial-mesenchymal or neuroendocrine-like axes. These mechanisms of hormone therapy resistance often co-exist within a single patients tumor and can overlap within a single cell. There exists a growing need to better understand how phenotypic heterogeneity and plasticity results from emergent dynamics of the regulatory networks governing androgen independence. Here, we investigated the dynamics of a regulatory network connecting the drivers of androgen receptor (AR) splice variant-mediated androgen independence and those of epithelial-mesenchymal transition. Model simulations for this network revealed four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR) and mesenchymal-sensitive (MS), with the latter phenotype occurring rarely. We observed that well-coordinated "teams" of regulators working antagonistically within the network enable these phenotypes. These model predictions are supported by multiple transcriptomic datasets both at single-cell and bulk levels, including in vitro EMT induction models and clinical samples. Further, our simulations reveal spontaneous stochastic switching between the ES and MR states. Addition of the immune checkpoint molecule, PD-L1, to the network was able to capture the interactions between AR, PD-L1, and the mesenchymal marker SNAIL, which was also confirmed through quantitative experiments. This systems-level understanding of the driver of androgen independence and EMT could aid in understanding non-genetic transitions and progression of such cancers and help in identifying novel therapeutic strategies or targets.

cancer biology↗

bioRxiv2022

Small molecule mediated stabilization of PP2A modulates the Homologous Recombination pathway and potentiates DNA damage-induced cell death

High-Grade Serous Carcinoma (HGSC) is the most common and lethal ovarian cancer subtype. PARP-inhibitors (PARPi) have become the mainstay of HGSC targeted therapy, given that these tumors are driven by a high degree of genomic instability and Homologous Recombination (HR) defects. Nonetheless, only [~]30% of patients initially respond to treatment, ultimately relapsing with resistant disease. Thus, despite recent advances in drug development and increased understanding of genetic alterations driving HGSC progression, mortality has not declined, highlighting the need for novel therapies. Using a Small Molecule Activator of Protein Phosphatase 2A (PP2A) (SMAP-061), we investigated the mechanism by which PP2A stabilization induces apoptosis in Patient-Derived HGSC cells and Xenograft (PDX) models alone or in combination with PARPi. We uncovered that PP2A genes essential for transformation (B56,B56{gamma} and PR72) and basal phosphatase activity (PP2A-A and -C) are heterozygously lost in the majority of HGSC. Moreover, loss of these PP2A genes correlates with worse overall patient survival. We show that SMAP-061 stabilization of PP2A inhibits the HR output by targeting RAD51, leading to chronic accumulation of DNA damage and ultimately apoptosis. Furthermore, combination of SMAP-061 and PARPi leads to enhanced apoptosis in both HR-proficient and -deficient cells and in patient-derived xenograft models. Our studies identify PP2A as novel regulator of HR and introduces PP2A activators as a potential treatment for HGSC tumors. Our studies further emphasize the potential of PP2A modulators to overcome PARPi insensitivity, given that targeting RAD51 has presented benefits in overcoming PARPi-resistance driven by BRCA1/2 mutation reversions.

cancer biology↗

bioRxiv2022

Reinstatement of Pavlovian responses to alcohol cues by stress

RationaleStress may contribute to relapse to alcohol use in part by enhancing reactivity to cues previously paired with alcohol. Yet, standard models of stress-induced reinstatement generally use contingent presentations of alcohol-paired cues to reinforce instrumental behaviors, making it difficult to isolate the ability of cues to invigorate alcohol-seeking. ObjectiveHere we sought to test the impact of stress on behavioral responses to alcohol-paired cues, using a model of stress-induced reinstatement of Pavlovian conditioned approach, inspired by Nadia Chaudhris work on context-induced reinstatement. MethodsLong Evans rats were trained to associate one auditory cue with delivery of alcohol or sucrose and an alternative auditory cue with no reward. Following extinction training, rats were exposed to a stressor prior to being re-exposed to the cues under extinction conditions. We assessed the effects of yohimbine, intermittent footshock and olfactory cues paired with social defeat on responses to alcohol-paired cues, and the effects of yohimbine on responses to sucrose-paired cues. ResultsThe pharmacological stressor, yohimbine, enhanced Pavlovian responses to both alcohol and sucrose cues, but intermittent footshock and social defeat cues did not. ConclusionsWhile yohimbine elicited reinstatement of Pavlovian conditioned responses, these effects may be unrelated to activation of stress systems.

neuroscience↗

bioRxiv2020

Acrylamide Fragment Inhibitors that Induce Unprecedented Conformational Distortions in Enterovirus 71 3C and SARS-CoV-2 Main Protease

RNA viruses are critically dependent upon virally encoded proteases that cleave the viral polyproteins into functional mature proteins. Many of these proteases are structurally conserved with an essential catalytic cysteine and this offers the opportunity to irreversibly inhibit these enzymes with electrophilic small molecules. Here we describe the successful application of quantitative irreversible tethering (qIT) to identify acrylamide fragments that selectively target the active site cysteine of the 3C protease (3Cpro) of Enterovirus 71, the causative agent of hand, foot and mouth disease in humans, altering the substrate binding region. Further, we effectively re-purpose these hits towards the main protease (Mpro) of SARS-CoV-2 which shares the 3C-like fold as well as similar catalytic-triad. We demonstrate that the hit fragments covalently link to the catalytic cysteine of Mpro to inhibit its activity. In addition, we provide the first demonstration that targeting the active site cysteine of Mpro can also have profound allosteric effects, distorting secondary structures required for formation of the active dimeric unit of Mpro. These new data provide novel mechanistic insights into the design of EV71 3Cpro and SARS-CoV-2 Mpro inhibitors and identify acrylamide-tagged pharmacophores for elaboration into more selective agents of therapeutic potential.

biochemistry↗

bioRxiv2020

A novel female-specific circadian clock mechanism regulating metabolism

Circadian clocks enable organisms to predict and align their behaviors and physiologies to constant daily day-night environmental cycle. Because the ubiquitin ligase Siah2 has been identified as a potential regulator of circadian clock function in cultured cells, we have used Siah2-deficient mice to examine its function in vivo. Our experiments demonstrate a striking and unexpected sexually dimorphic effect of Siah2 deficiency on the regulation of rhythmically expressed genes. The absence of Siah2 in females, but not in males, altered the expression of core circadian clock genes and drastically remodeled the rhythmic hepatic transcriptome. Siah2 loss, only in females, increased the expression of 100s of genes selectively at mid-day, resulting in a >50% increase in the number of rhythmically expressed genes, and shifted the expression of 100s of other genes from a mid-night peak, to a mid-day peak. The combined result is a near inversion of overall rhythmicity in gene expression selectively in Siah2-deficient females. This dramatic reorganization created a substantial misalignment between rhythmic liver functions and feeding/behavioral rhythms, and consequently disrupted daily patterns of lipid/lipoprotein metabolism and metabolic responses to high-fat diet. Collectively, our results suggest that Siah2 is part of a female-specific circadian mechanism important for maintaining metabolic homeostasis and may play a key role in establishing sexual dimorphisms in metabolism, and broadly reveal that circadian clocks may drive rhythms using novel sex-specific transcriptional pathways.

physiology↗

bioRxiv2020

The hearing aid dilemma: amplification, compression, and distortion of the neural code

Hearing aids are the only available treatment for mild-to-moderate sensorineural hearing loss, but often fail to improve perception in difficult listening conditions. To identify the reasons for this failure, we studied the underlying neural code using large-scale single-neuron recordings in gerbils, a common animal model of human hearing. We found that a hearing aid restored the sensitivity of neural responses, but failed to restore their selectivity. The low selectivity of aided responses was not a direct effect of hearing loss per se, but rather a consequence of the strategies used by hearing aids to restore sensitivity: compression, which decreases the spectral and temporal contrast of incoming sounds, and amplification, which produces high intensities that distort the neural code even with normal hearing. To improve future hearing aids, new processing strategies that avoid this tradeoff between neural sensitivity and selectivity must be developed.

bioengineering↗