Biology subjects

Edwards, A.

Publications and source records attributed to Edwards, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Acquisition of daptomycin resistance in patients results in decreased virulence in Drosophila

Staphylococcus aureus can acquire antimicrobial resistance which in turn may affect its pathogenic potential. Using a panel of paired clinical isolates collected before and after daptomycin resistance acquisition, most frequently through single mprF mutation, we show a relationship between increasing daptomycin minimum inhibitory concentration and reduced virulence in a Drosophila systemic infection model. Analysing toxin production, in vitro bacterial growth characteristics, and cell surface properties, we failed to link daptomycin resistance-related attenuated virulence to either reduced virulence factor production, reduced fitness or to any of the cell surface characteristics investigated. Competition assays in Drosophila also did not support any altered ability in immune evasion. Instead, using a panel of mutant flies defective for various immune components, we show that this daptomycin resistance-related attenuated virulence is mostly explained by greater susceptibility to activity of Drosophila prophenoloxidase, a tyrosinase involved in melanization, but not to antimicrobial peptides or to Bomanin antimicrobial effectors. Further investigation could not link daptomycin resistance-related attenuation of virulence to a differential susceptibility to reactive oxygen species or to quinones prominently associated with phenoloxidase bacterial-killing activity. Taken together, it appears that daptomycin resistance attenuates Staphylococcus aureus virulence through an enhanced sensitivity to phenoloxidase based on a complex mechanism. Our study provides new insights in the understanding of the crosstalk between antimicrobial resistance, escape from immune killing, and virulence. Author summaryAcquiring antimicrobial resistance can increase or decrease bacterial virulence. However, the mechanisms causing these resistance-virulence linked effects are unclear. Here, we bring new insights on the crosstalk between antimicrobial resistance and virulence. We characterized a panel of Staphylococcus aureus strains isolated from patients before and after resistance acquisition to the antibiotic daptomycin. Relative to the parental strain, resistant isolates most often varied by one single mutation, in a gene involved in the composition of the bacterial membrane, and these strains were much less virulent when fruit-flies were infected. Our results indicate that the difference of virulence is unrelated to changes in bacterial toxin production, bacterial growth, immune evasion or cell surface properties. Instead, resistant strains were more vulnerable to a host proenzyme involved in the antibacterial melanization response, an important response deployed throughout the arthropods. We predict that daptomycin resistance forces staphylococci to alter the composition of their cell surface. This alteration causes the bacteria to become more vulnerable to killing by melanization. Our results contribute to our understanding of the link between antimicrobial resistance and pathogenicity.

microbiology↗

bioRxiv2024

Mosaic integration of spatial multi-omics with SpaMosaic

With the advent of spatial multi-omics, mosaic integration of diverse datasets with partially overlapping modalities enables construction of comprehensive multi-modal spatial atlases from heterogeneous sources. Here, we present SpaMosaic, a tool that employs contrastive learning and graph neural networks to build a modality-agnostic and batch-corrected latent space for spatial domain identification and missing modality imputation. We systematically benchmarked SpaMosaic against existing integration methods using simulated data and experimentally acquired datasets spanning RNA and protein abundance, chromatin accessibility, and histone modifications from brain, embryo, tonsil, and lymph node tissues. SpaMosaic consistently outperformed other methods in identifying coherent spatial domains by reducing noise and mitigating batch effects across diverse technologies and developmental stages. Computationally, SpaMosaic is highly scalable, capable of integrating over 100 sections and processing a single section with more than 800,000 spots. Beyond robust integration, the unified latent space generated by SpaMosaic enables accurate imputation of missing modalities. In a mosaic mouse brain dataset, the imputed histone modifications not only recapitulated expected transcriptome-epigenome correlations but also uncovered more region-specific regulatory links compared to the measured chromatin accessibility data, demonstrating the ability to infer relationships between modalities without co-profiling. In summary, SpaMosaic provides a versatile framework for unifying the rapidly accumulating heterogeneous spatial omics data into comprehensive biological atlases.

bioinformatics↗

bioRxiv2024

CACHE Challenge #1: targeting the WDR domain of LRRK2, a Parkinson's Disease associated protein.

The CACHE challenges are a series of prospective benchmarking exercises meant to evaluate progress in the field of computational hit-finding. Here we report the results of the inaugural CACHE #1 challenge in which 23 computational teams each selected up to 100 commercially available compounds that they predicted would bind to the WDR domain of the Parkinsons disease target LRRK2, a domain with no known ligand and only an apo structure in the PDB. The lack of known binding data and presumably low druggability of the target is a challenge to computational hit finding methods. Seventy-three of the 1955 procured molecules bound LRRK2 in an SPR assay with KD lower than 150 M and were advanced to a hit expansion phase where computational teams each selected up to 50 analogs each. Binding was observed in two orthogonal assays with affinities ranging from 18 to 140 M for seven chemically diverse series. The seven successful computational workflows varied in their screening strategies and techniques. Three used molecular dynamics to produce a conformational ensemble of the targeted site, three included a fragment docking step, three implemented a generative design strategy and five used one or more deep learning steps. CACHE #1 reflects a highly exploratory phase in computational drug design where participants sometimes adopted strikingly diverging screening strategies. Machine-learning accelerated methods achieved similar results to brute force (e.g. exhaustive) docking. First-in-class, experimentally confirmed compounds were rare and weakly potent, indicating that recent advances are not sufficient to effectively address challenging targets.

biochemistry↗

bioRxiv2024

HR3/RORα-mediated cholesterol sensing regulates TOR signaling

Cells and organisms adjust their growth based on the availability of cholesterol, which is essential for cellular functions. However, the mechanisms by which cells sense cholesterol levels and translate these into growth signals are not fully understood. We report that cholesterol rapidly activates the master growth-regulatory TOR pathway in Drosophila tissues. We identify the nuclear receptor HR3, an ortholog of mammalian ROR, as an essential factor in cholesterol-induced TOR activation. We demonstrate that HR3 binds cholesterol and promotes TOR pathway activation through a non-genomic mechanism acting upstream of the Rag GTPases. Similarly, we find that ROR is necessary for cholesterol-mediated TOR activation in human cells, suggesting that HR3/ROR represents a conserved mechanism for cholesterol sensing that couples cholesterol availability to TOR-pathway activity. These findings advance our understanding of how cholesterol influences cell growth, with implications for cholesterol-related diseases and cancer. HighlightsO_LICholesterol leads to dynamic TOR pathway activation, driving systemic growth C_LIO_LIHR3 in Drosophila binds cholesterol and couples its availability to TOR activation C_LIO_LIHR3 acts upstream of Rag GTPases to activate TOR in response to lysosomal cholesterol C_LIO_LIMammalian HR3 ortholog ROR is required for cholesterol-induced TOR activation C_LI

cell biology↗

bioRxiv2024

A frosty genetic screen unmasks a major regulatory role for SHORT VEGETATIVE PHASE of flowering in response to a cold snap

The control of flowering in plants is intricately governed by a combination of internal and environmental signals, with temperature playing a critical role. Thus, Arabidopsis thaliana plants display temperature-dependent variations in flowering time. As unexpected periods of cold temperatures can occur at any time, plants have evolved mechanisms to detect such cold snaps and to respond by delaying flowering. Plants are more tolerant to cold temperatures in the vegetative stage, while flowers are more sensitive and have reduced reproductive success due to damage to floral structures and gametes. At the molecular level, delayed flowering can be caused by repressing the FLOWERING LOCUS T (FT) gene, and several MADS box transcription factors have been shown to repress FT expression in response to cold and in this way prevent flowering. Here, we employed a forward genetic screen aimed at understanding the effect of a cold snap on the transition to flowering. We germinated a population of A. thaliana EMS M2 plants at 20{degrees}C and then gradually lowered the temperature to 10{degrees}C and selected early flowering mutants. Using whole-genome sequencing, we identified seven mutant alleles of the SHORT VEGETATIVE PHASE (SVP) gene. This finding establishes a central role for SVP in repressing flowering in response to a cold snap and provides novel alleles, several of which affect splice junctions. Our research thus presents valuable insights into the nuanced molecular mechanisms governing temperature-responsive flowering in Arabidopsis and sheds light on the dynamic interplay between SVP and environmental cues.

plant biology↗

bioRxiv2023

Mapping host-microbe transcriptional interactions by dual perturb-seq

Intracellular pathogens and other endosymbionts reprogram host cell transcription to suppress immune responses and recalibrate biosynthetic pathways. This reprogramming is critical in determining the outcome of infection or colonisation. Here, we combine pooled CRISPR knockout screening with dual host-microbe single-cell RNA-sequencing to identify the molecular mediators of these transcriptional interactions, a method we term dual perturb-seq. Applying dual perturb-seq to the intracellular pathogen Toxoplasma gondii, we are able to identify previously uncharacterised effector proteins and directly infer their function from the transcriptomic data. We show that TgGRA59 contributes to the export of other effector proteins from the parasite into the host cell and identify a novel effector, TgSOS1, that is necessary for sustained host STAT6 signalling and thereby contributes to parasite immune evasion and persistence. Together, this work demonstrates a novel tool that can be broadly adapted to interrogate host-microbe transcriptional interactions and reveal mechanisms of infection and immune evasion.

molecular biology↗

bioRxiv2023

Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data

In the past decade, high-dimensional single cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation which are computationally intense and difficult to evaluate and optimize. Here we present Cyclone, an analysis pipeline integrating dimensionality reduction, clustering, evaluation and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification, but also enables the unsupervised identification of lymphocytes and mononuclear phagocytes subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on variety of cytometry datasets which will further power immunology research and provide a scaffold for biological discovery.

immunology↗

bioRxiv2023

Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology

Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom designed topologies.

bioengineering↗

bioRxiv2023

Linear versus Nonlinear Muscle Networks: A Case Study to Decode Hidden Synergistic Patterns During Dynamic Lower-limb Tasks

This paper, for the first time, compares the behaviors of nonlinear versus linear muscle networks in decoding hidden peripheral synergistic neural patterns during dynamic functional tasks. In this paper, we report a case study during which one healthy subject conducts a series of four lower limb repetitive tasks. Specifically, the paper focuses on tasks that involve the right knee joint, including walking, sit-tostand, stepping, and drop-jump. Twelve muscles were recorded using the Delsys Trigno system. The linear muscle network was generated using coherence analysis, and the nonlinear network was generated using Spearmans correlation. The results show that the degree, clustering coefficient, and global efficiency of the muscle network have the highest value among tasks in the linear domain for the walking task, while a low linear synergistic network behavior for the sit-to-stand is observed. On the other hand, the results show that the nonlinear functional muscle network decodes high connectivity (degree) and clustering coefficient and efficiency for the sit-tostand when compared with other tasks. We have also developed a two-dimensional functional connectivity plane composed of linear and nonlinear features and shown that it can span the lower-limb dynamic task space. The results of this paper for the first time highlight the importance of observing both linear and nonlinear connectivity patterns, especially for complex dynamic tasks. It should also be noted that through a simultaneous EEG recording (using BrainVision System), we have shown that, indeed, cortical activity may indirectly explain highly-connected nonlinear muscle network for the sit-to-stand task, highlighting the importance of nonlinear muscle network as a neurophysiological window of observation beyond the periphery.

bioengineering↗

bioRxiv2022

Trajectory classification method for anchored molecular motor-biopolymer interactions in the C. elegans first mitosis.

During zygotic mitosis, forces generated at the cell cortex are required for the separation and migration of paternally provided centrosomes, pronuclear migration, proper segregation of genetic material, and successful cell division. Identification of individual cortical force generating units in vivo is necessary to study the regulation of microtubule dependent force generation throughout the cell cycle, to further understanding of asymmetric cell division, and to identify the molecular mechanism of force generation. Here we present a method to determine both the location and relative number of microtubule dependent cortical force generating units using single molecule imaging of fluorescently labelled dynein. Dynein behavior is modeled to differentiate and categorize trajectories that correspond to that which is cortically bound and interacting with a microtubule, and is cortically bound and not interacting with a microtubule. The categorization strategy recapitulates well known force asymmetries in the first mitosis of the C. elegans embryo. To evaluate the robustness of categorization, we RNAi depleted the microtubule subunit TBA-2 resulting in reduction of the number of trajectories categorized as engaged with a microtubule. This technique will be a valuable tool to provide new insight to the molecular mechanisms of dynein cortical force generation and its regulation as well as other instances wherein anchored motors interact with biopolymers (eg. Actin, tubulin, DNA).

cell biology↗

bioRxiv2022

The identification of potent and selective antibodies for Serine/threonine-protein kinase TBK1, for use in immunoblot, immunofluorescence and immunoprecipitation

TBK1 is a serine-threonine kinase that has been linked to a number of diseases, including amyotrophic lateral sclerosis and frontotemporal dementia. Reproducible research on TBK1 has been hampered by the lack of well characterized antibodies. In this study, we characterized 11 commercial antibodies for immunoblot, immunofluorescence and immunoprecipitation, using a knock-out cell line as the control. For each application, we identified several potent and selective antibodies that will facilitate studies on TBK1.

biochemistry↗

bioRxiv2022

Prolonged β-Adrenergic Stimulation Disperses Ryanodine Receptor Clusters in Cardiomyocytes: Implications for Heart Failure

Ryanodine Receptors (RyRs) exhibit dynamic arrangements in cardiomyocytes, and we previously showed that "dispersion" of RyR clusters disrupts Ca2+ homeostasis during heart failure (HF) (Kolstad et al., eLife, 2018). Here, we investigated whether prolonged {beta}-adrenergic stimulation, a hallmark of HF, promotes RyR cluster dispersion, and examined the underlying mechanisms. We observed that treatment of healthy rat cardiomyocytes with isoproterenol for 1 hour triggered progressive fragmentation of RyR clusters. Pharmacological inhibition of CaMKII reversed these effects, while cluster dispersion was reproduced by specific activation of CaMKII, and in mice with constitutively active Ser2814-RyR. A similar role of protein kinase A (PKA) in promoting RyR cluster fragmentation was established by employing PKA activation or inhibition. Progressive cluster dispersion was linked to declining Ca2+ spark fidelity and magnitude, and slowed release kinetics from Ca2+ propagation between more numerous RyR clusters. In healthy cells, this served to dampen the stimulatory actions of {beta}-adrenergic stimulation over the longer term, and protect against pro-arrhythmic Ca2+ waves. However, during HF, RyR dispersion was linked to impaired Ca2+ release. Thus, RyR localization and function are intimately linked via channel phosphorylation by both CaMKII and PKA which, while finely tuned in healthy cardiomyocytes, underlies impaired cardiac function during pathology. Significance statementThe heartbeat is triggered by the release of Ca2+ from Ryanodine Receptors (RyRs) within cardiomyocytes. Recent data indicate RyR arrangement is highly malleable. However, mechanisms controlling RyR reorganisation and the subsequent impact on Ca2+ homeostasis remain unclear. Here, we show that prolonged {beta}-adrenergic stimulation causes RyR clusters to disperse, drastically altering the frequency and kinetics of Ca2+ release events called "Ca2+ sparks" in a process that is dependent on CaMKII and PKA. In healthy cells, these compensatory effects protect against arrhythmogenic Ca2+ over-activity. However, during heart failure, RyR hyper-phosphorylation and dispersion impairs Ca2+ release and cardiac performance. Thus, RyR localization and function are intimately linked via channel phosphorylation which, while finely tuned in health, underlies impaired cardiac function during pathology.

cell biology↗

bioRxiv2021

Stabilizing selection shapes variation in phenotypic plasticity

The adaptive nature of phenotypic plasticity is widely documented in natural populations. However, little is known about the evolutionary forces that shape genetic variation in plasticity within populations. Here we empirically address this issue by testing the hypothesis that stabilizing selection shapes genetic variation in the anti-predator developmental plasticity of Daphnia pulex. The anti-predator morphological defense is characterized by pedestal and spikes that grow on the back of the Daphnia neck following exposure to predator cure. We characterized variation in this plasticity using a novel, high-throughput phenotyping method that describes the entire dorsal shape amongst >100 D. pulex strains originating from a natural population in the UK. We found low genetic diversity for morphological defenses among genetically diverse clones upon predation risk exposure. The strongest reduction in genetic variation was observed in areas of greatest phenotypic plasticity, which we interpret as evidence of stabilizing selection. By assessing among-clone variance in clonally related, field derived strains, we contrasted mutational variation (Vm) to standing variation (Vg). We found that Vg/Vm is lowest in areas of greatest plasticity. These data strongly suggest that stabilizing selection operates directly on phenotypic plasticity, providing a rare glimpse into the evolution of fitness related traits in natural populations.

evolutionary biology↗

bioRxiv2021

Active Surveillance Characterizes Human Intratumoral T Cell Exhaustion

Intratumoral T cells that might otherwise control tumors are often identified in an exhausted state, defined by specific epigenetic modifications as well as upregulation of genes such as CD38, CTLA-4 and PD-1. While the term might imply inactivity, there has been little study of this state at the phenotypic level in tumors to understand the extent of their incapacitation. Starting with the observation that T cells move more quickly through mouse tumors as residence time increases and they progress towards exhaustion, we elaborated a non-stimulatory live-biopsy method for real-time study of T cell behaviors within individual patient tumors. Using two-photon microscopy, we studied native CD8 T cells interacting with APCs and with cancer cells in different micro-niches of human tumors, finding that T cell speed was variable by region and by patient, was independent of T cell density and was inversely correlated with local tumor density. Across a range of tumor types, we found a strong relationship between CD8 T cell motility and exhausted T cell state that corresponds to observations made in mouse models where exhausted T cells move faster. While this is a small study, it demonstrates at least two types of T cell dynamic states in individual human tumors and supports the existence of an active program in exhausted T cells that extends beyond incapacitating them.

immunology↗

bioRxiv2021

A Pan-Cancer Census of Dominant Tumor Immune Archetypes

Cancers display significant heterogeneity with respect to tissue of origin, driver mutations and other features of the surrounding tissue. It is likely that persistent tumors differentially engage inherent patterns-here Archetypes-of the immune system, to both benefit from a tumor immune microenvironment (TIME) and to disengage tumor-targeting. To discover dominant immune system archetypes, the Immunoprofiler Initiative (IPI) processed 364 individual tumors across 12 cancer types using standardized protocols. Computational clustering of flow cytometry and transcriptomic data obtained from cell sub compartments uncovered archetypes that exist across indications. These Immune composition-based archetypes differentiate tumors based upon unique immune and tumor gene-expression patterns. Archetypes discovered this way also tie closely to well-established classifications of tumor biology. The IPI resource provides a template for understanding cancer immunity as a collection of dominant patterns of immune infiltration and provides a rational path forward to learn how to modulate these patterns to improve therapy. O_FIG O_LINKSMALLFIG WIDTH=182 HEIGHT=200 SRC="FIGDIR/small/441344v1_ufig1.gif" ALT="Figure 1"> View larger version (77K): org.highwire.dtl.DTLVardef@55a5ccorg.highwire.dtl.DTLVardef@f8205corg.highwire.dtl.DTLVardef@1480b8org.highwire.dtl.DTLVardef@eb94e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2020

Reduced activity of Adenylyl Cyclase 1 Attenuates Morphine Induced Hyperalgesia and Inflammatory Pain in Mice

Opioid tolerance and opioid-induced hyperalgesia during repeated opioid administration and chronic pain are associated with upregulation of adenylyl cyclase activity. The objective of this study was to test the hypothesis that a reduction in adenylyl cyclase 1 (AC1) activity or expression would attenuate morphine tolerance and hypersensitivity, and inflammatory pain using murine models. To investigate opioid tolerance and opioid-induced hyperalgesia, mice were subjected to twice daily treatments of saline or morphine using either a static (15 mg/kg, 5 days) or an escalating tolerance paradigm (10-40 mg/kg, 4 days). Systemic treatment with an AC1 inhibitor, ST03437 (5 mg/kg, ip), reduced morphine tolerance and morphine hyperalgesia in mice. Lumbar intrathecal administration of a vector incorporating adeno-associated virus and short-hairpin RNA against Adcy1 reduced morphine induced hypersensitivity compared to control vector treated mice. In contrast, morphine antinociception, along with baseline thermal paw withdrawal latencies, motor performance, exploration in an open field test, and burrowing behaviors were not affected by intrathecal Adcy1 knockdown. Knockdown of Adcy1 by intrathecal injection also attenuated inflammatory mechanical hyperalgesia after intraplantar administration of Complete Freunds Adjuvant (CFA) after one week post injection. This Adcy1 knockdown strategy also increased burrowing and nesting activity after CFA injection when compared to controls. Together, these data indicate targeting AC1 to mitigate opioid-induced adverse effects, or as a method to treat chronic pain, are appropriate as a clinical approach and further development into generating pharmaceuticals targeting these genes/proteins may prove beneficial in the future.

neuroscience↗

bioRxiv2020

A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume

We have sequenced the genome of grass pea (Lathyrus sativus), a resilient diploid (2n=14) legume closely related to pea (Pisum sativum). We determined the genome size of the sequenced European accession (LS007) as 6.3 Gbp. We generated two assemblies of this genome, i) EIv1 using Illumina PCR-free paired-end sequencing and assembly followed by long-mate-pair scaffolding and ii) Rbp using Oxford Nanopore Technologies long-read sequencing and assembly followed by polishing with Illumina paired-end data. EIv1 has a total length of 8.12 Gbp (including 1.9 billion Ns) and scaffold N50 59,7 kbp. Annotation has identified 33,819 high confidence genes in the assembly. Rbp has a total length of 6.2 Gbp (with no Ns) and a contig N50 of 155.7 kbp. Gene space assessment using the eukaryote BUSCO database showed completeness scores of 82.8 % and 89.8%, respectively.

genomics↗

bioRxiv2020

Directed Evolution of Adenine Base Editors with Increased Activity and Therapeutic Application

The foundational adenine base editors (e.g. ABE7.10) enable programmable C*G to T*A point mutations but editing efficiencies can be low at challenging loci in primary human cells. Here we further evolve ABE7.10 using a library of adenosine deaminase variants to create ABE8s. At NGG PAM sites, ABE8s result in [~]1.5x higher editing at protospacer positions A5-A7 and [~]3.2x higher editing at positions A3-A4 and A8-A10 compared with ABE7.10. Non-NGG PAM variants have a [~]4.2-fold overall higher on-target editing efficiency than ABE7.10. In human CD34+ cells, ABE8 can recreate a natural allele at the promoter of the {gamma}-globin genes HBG1 and HBG2, with up to 60% efficiency, causing persistence of fetal hemoglobin. In primary human T cells, ABE8s achieve 98-99% target modification which is maintained when multiplexed across three loci. Delivered as mRNA, ABE8s induce no significant levels of sgRNA-independent off-target adenine deamination in genomic DNA and very low levels of adenine deamination in cellular mRNA.

genomics↗