Biology subjects

Evans, P.

Publications and source records attributed to Evans, P..

14 recordsLinked to original sources

bioRxiv2024

A rational approach for the targeted discovery and characterisation of microbiome-derived therapeutics

The human gut microbiome is intrinsically involved in health and disease, representing a wealth of untapped therapeutic potential. Here, we demonstrate the utility and potential of a metagenome guided, large cohort-based approach for the rational selection of live biotherapeutics from the human gut. We applied this approach to Inflammatory Bowel Disease (IBD), identifying several lead candidates that were significantly depleted in individuals with IBD compared to healthy controls. Their therapeutic potential was assessed in preclinical models of IBD where they improved markers of disease pathology by reducing inflammation and promoting mucosal healing and wound repair. All leads had excellent safety profiles in silico and in vitro, and several additionally presented favourable manufacturing properties, supporting their progression into clinical trials. We believe that this rational approach will be generalisable to any disease state with underlying microbiome aetiology and will expedite the development of novel microbiome-derived therapeutics to improve human health.

microbiology↗

bioRxiv2023

APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites

Computational modelling of microbiome metabolism has proved instrumental to catalyse our understanding of diet-host-microbiome-disease interactions through the interrogation of mechanistic, strain- and molecule-resolved metabolic models. We present APOLLO, a resource of 247,092 human microbial genome-scale metabolic reconstructions spanning 19 phyla and accounting for microbial genomes from 34 countries, all age groups, and five body sites. We explored the metabolic potential of the reconstructed strains and developed a machine learning classifier able to predict with high accuracy the taxonomic strain assignments. We also built 14,451 sample-specific microbial community models, which could be stratified by body site, age, and disease states. Finally, we predicted faecal metabolites enriched or depleted in gut microbiomes of people with Crohns disease, Parkinson disease, and undernourished children. APOLLO is compatible with the human whole-body models, and thus, provide unprecedented opportunities for systems-level modelling of personalised host-microbiome co-metabolism. APOLLO will be freely available under https://www.vmh.life/.

systems biology↗

bioRxiv2023

A model of sediment retention by vegetation for Great Britain: new methodologies & validation

Soil erosion is an substantial environmental concern worldwide. It has been historically and is of increasingly concern currently. Next to natural processes, over 2 million hectares of soil are at risk of erosion through intensifying agriculture in the Great Britain (England, Wales, Scotland and their territorial islands). Predictive soil erosion models, in the form of Ecosystem Service tools, aid in helping to identify areas that are vulnerable to soil erosion. Yet, no predictions for erosion or sediment retention by vegetation based on local data have been developed for Great Britain or the United Kingdom as a whole. Here we develop an erosion retention model using the InVEST platform, which is based on the RUSLE mathematical framework. We parameterise the model, as far as feasible, with GB specific input data. The developed model estimations are validated against suspended solids concentrations (sediments) in throughout England and Wales. Next to presenting the first GB wide estimate of erosion and erosion retention using the InVEST SDR module, we test three approaches here that differ from more widely applicable RUSLE model inputs, such as created for Europe as a whole. Here, we incorporate (1) periodicity to allow erosion to potentially fluctuate within years; (2) GB-specific cover periodic management factors estimates, including a range of crop types, based on observed satellite NDVI values (3) soil erosivity under heavy rainfall following GB estimates for 2000-2019. We conclude that both the GB created erosivity layer as the added periodicity do not seem to be provide substantial improvement over non-periodic estimated created with more widely available data, when validated against this set of suspended solids in rivers. In contrast, the observed cover management factors calculated from NDVI are a good improvement affecting the ranking order among catchments. Therefore, the generating of cover management factors using NDVI data could be promoted as method for InVEST SDR model development and in more general for developing RUSLE-based erosion estimates worldwide.

bioinformatics↗

bioRxiv2023

Polymer biodegradation by Halanaerobium promotes reservoir souring during hydraulic fracturing.

Hydraulically fractured shale reservoirs have facilitated studies of unexplored niches in the continental deep biosphere. Members of the genus Halanaerobium are ubiquitous in these environments. Polymers like guar gum used as gelling agents in hydraulic fracturing fluids are known to be fermentable substrates, but metabolic pathways encoding these processes have not been characterized. To explore this, produced water samples from the Permian Basin were incubated at 30{degrees}C to simulate above-ground storage conditions, and at 60{degrees}C to simulate subsurface reservoir conditions. Guar metabolism coincided with Halanaerobium enrichment only at 30{degrees}C, revealing genes for polymer biodegradation through the mixed-acid fermentation pathway in different metagenome-assembled genomes (MAGs). Whereas thiosulfate reduction to sulfide is often invoked to explain the dominance of Halanaerobium in these settings, Halanaerobium genomes did not uncover genes for this metabolism. Sulfide production was observed in 60{degrees}C incubations, with corresponding enrichment of Desulfohalobium and Desulfovibrionaceae that possess complete pathways for coupling mannose and acetate oxidation to sulfate reduction. These findings outline how production of fermentation intermediates (mannose, acetate) by Halanaerobium in topside settings can result in reservoir souring when these metabolites are introduced into the subsurface through produced water re-use. ImportanceHydraulically fractured shale oil reservoirs are ideal for studying extremophiles such as thermohalophiles. During hydraulic fracturing, reservoir production water is stored in surface ponds prior to re-use. Microorganisms in these systems therefore need to withstand various environmental changes such as the swing between warm downhole oil reservoir temperatures and cooler surface conditions. This study follows this water cycle during fracking and the associated microbial metabolic potential. Of particular interest are members of the genus Halanaerobium, that have been reported to reduce thiosulfate contributing to souring of oil reservoirs. Here, we show that some Halanaerobium strains were unable to grow under oil reservoir temperatures and do not possess genes for thiosulfate reduction. Rather, it is likely that these organisms metabolize complex organics in fracking fluids at lower temperatures, thereby generating substrates that support reservoir souring by thermophilic sulfate-reducing bacteria at higher temperatures.

microbiology↗

bioRxiv2021

Epigenetic regulator genes direct lineage switching in MLL-AF4 leukaemia

The fusion gene MLL-AF4 defines a high-risk subtype of pro-B acute lymphoblastic leukaemia. However, relapse can be associated with a switch from acute lymphoblastic to acute myeloid leukaemia. Here we show that these myeloid relapses share oncogene fusion breakpoints with their matched lymphoid presentations and can originate in either early, multipotent progenitors or committed B-cell precursors. Lineage switching is linked to substantial changes in chromatin accessibility and rewiring of transcriptional programmes indicating that the execution and maintenance of lymphoid lineage differentiation is impaired. We show that this subversion is recurrently associated with the dysregulation of repressive chromatin modifiers, notably the nucleosome remodelling and deacetylation complex, NuRD. In addition to mutations, we show differential expression or alternative splicing of NuRD members and other genes is able to reprogram the B lymphoid into a myeloid gene regulatory network. Lineage switching in MLL-AF4 leukaemia is therefore driven and maintained by defunct epigenetic regulation. Statement of SignificanceWe demonstrate diverse cellular origins of lineage switched relapse within MLL-AF4 pro-B acute leukaemia. Irrespective of the developmental origin of relapse, dysregulation of NuRD and/or other epigenetic machinery underpins fundamental lineage reprogramming with profound implications for the increasing use of epitope directed therapies in this high-risk leukaemia.

cancer biology↗

bioRxiv2020

Analysis of Genetically Determined Gene Expression Suggests Role of Inflammatory Processes in Exfoliation Syndrome

Exfoliation syndrome (XFS) is an age-related systemic disorder characterized by excessive production and progressive accumulation of abnormal extracellular material, with pathognomonic ocular manifestations. It is the most common cause of secondary glaucoma, resulting in widespread global blindness. We performed Transcriptomic Wide Association Studies (TWAS) using PrediXcan models trained in 48 GTEx tissues to identify genetically- determined gene expression changes associated with XFS risk, leveraging on results from a global GWAS that included 123,457 individuals from 24 countries. We observed twenty-eight genes in a three-Megabase chr15q22-25 region that showed statistically significant associations, which were further whittled down to ten genes after additional statistical validations. In experimental analysist of these ten genes, mRNA transcript levels for ARID3B, CD276, LOXL1, NEO1, SCAMP2, and UBL7 were significantly decreased in iris tissues from XFS patients compared to control samples. Genes with genetically determined expression changes in XFS were significantly enriched for genes associated with inflammatory conditions. We further explored the health consequences of high susceptibility to XFS using a large electronic health record and observed a higher incidence of XFS comorbidity with inflammatory and connective tissue diseases. Our results implicate a role for connective tissues and inflammation in the etiology of XFS. Targeting the inflammatory pathway may be a potential therapeutic option to reduce progression in XFS.

genetics↗

bioRxiv2020

The effect of absent blood flow on the zebrafish cerebral and trunk vasculature

The role of blood flow is complex and context-dependent. In this study, we quantify the effect of the lack of blood flow on vascular development and compare its impact in two vascular beds, namely the cerebral and trunk vasculature, using zebrafish as preclinical model. We performed this by analysing vascular topology, endothelial cell number, apoptosis, and inflammatory response in animals with normal blood flow or absent blood flow. We find that absent blood flow reduced vascular area and endothelial cell number significantly in both examined vascular beds, but the effect is more severe in the cerebral vasculature. Similarly, while stereotypic vascular patterning in the trunk is maintained, intra-cerebral vessels show altered patterning. Absent blood flow lead to an increase in non-EC-specific apoptosis without increasing tissue inflammation, as quantified by cerebral immune cell numbers and nitric oxide. In conclusion, blood flow is essential for cellular survival in both the trunk and cerebral vasculature, but particularly intra-cerebral vessels are affected by the lack of blood flow, suggesting that responses to blood flow differ between these two vascular beds. Key pointsO_LIWe here use zebrafish as a model to quantitatively assess the impact of the lack of blood flow in development and compare its impact in two vascular beds, namely the cerebral to trunk vasculature. C_LIO_LIIn both vascular beds, vascular growth and endothelial cell number are reduced by lack of blood flow, with increasing effect size from 2-5 days post fertilisation. C_LIO_LIExamination of vascular patterning shows that while stereotypic patterning in the trunk is preserved, the intra-cerebral vasculature patterning is altered. C_LIO_LIWe found non-EC-specific cell death to be increased in both vascular beds, with a larger effect size in the brain, but that this cell death occurs without triggering tissue inflammation. C_LI

developmental biology↗

bioRxiv2020

JAG1-NOTCH4 MECHANOSENSING DRIVES ATHEROSCLEROSIS

Endothelial cell (EC) sensing of fluid shear stress regulates atherosclerosis, a disease of arteries that causes heart attack and stroke. Atherosclerosis preferentially develops at regions of arteries exposed to low oscillatory shear stress (LOSS), whereas high shear regions are protected. We show using inducible EC-specific genetic deletion in hyperlipidaemic mice that the Notch ligands JAG1 and DLL4 have opposing roles in atherosclerosis. While endothelial Jag1 promoted atherosclerosis at sites of LOSS, endothelial Dll4 was atheroprotective. Analysis of porcine and murine arteries and cultured human coronary artery EC exposed to experimental flow revealed that JAG1 and its receptor NOTCH4 are strongly upregulated by LOSS. Functional studies in cultured cells and in mice with EC-specific deletion of Jag1 show that JAG1-NOTCH4 signalling drives vascular dysfunction by repressing endothelial repair. These data demonstrate a fundamental role for JAG1-NOTCH4 in sensing LOSS during disease, and suggest therapeutic targeting of this pathway to treat atherosclerosis.Competing Interest StatementThe authors have declared no competing interest.View Full Text

pathology↗

bioRxiv2019

β1 integrin is a sensor of blood flow direction

The ability of endothelial cells (EC) to sense blood flow direction is a critical determinant of vascular health and disease. Unidirectional flow induces EC alignment and vascular homeostasis, whereas bidirectional flow has pathophysiological effects. EC express several mechanoreceptors that can respond to fluid flow (shear stress) but the mechanism for sensing the direction of shearing force is poorly understood. We observed using in vitro flow systems and magnetic tweezers that {beta}1 integrin is a key sensor of force direction because it is activated by unidirectional but not bidirectional shearing forces. Consistently, {beta}1 integrin was essential for Ca2+ signalling and cell alignment in response to unidirectional but not bidirectional shear stress. {beta}1 integrin activation by unidirectional force was amplified in EC that were pre-sheared in the same direction, indicating that alignment and {beta}1 integrin activity has a feedforward interaction which is a hallmark of system stability. En face staining and EC-specific genetic deletion studies of the murine aorta revealed that {beta}1 integrin is activated and is essential for EC alignment at sites of unidirectional flow but is not activated at sites of bidirectional flow. In summary, {beta}1 integrin sensing of unidirectional force is a key mechanism for decoding blood flow mechanics to promote vascular homeostasis.\n\nSUMMARY STATEMENTWe demonstrate using flow systems, magnetic tweezers and knockout mice that {beta}1 integrin is a sensor of shear stress direction in endothelial cells. {beta}1 integrin is activated by unidirectional hemodynamic shear force leading to calcium signalling and cell alignment, but it is not activated by bidirectional force.

cell biology↗

bioRxiv2018

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane and potentially propane. The number of archaeal clades encoding the MCR complex continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; rG16) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Candidatus Bathyarchaeota and Candidatus Syntrophoarchaeum MAGs. rG16 is basal to members of the class Archaeoglobi, and encodes the genes for {beta}-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. rG16 also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. As the first Archaeoglobi with the MCR complex, rG16 extends our understanding of the evolution and distribution of novel MCR encoding lineages among the Archaea.

microbiology↗

bioRxiv2018

Genetic variant pathogenicity prediction trained using large-scale disease specific clinical sequencing datasets

Recent advances in DNA sequencing technologies have expanded our understanding of the molecular underpinnings for several genetic disorders, and increased the utilization of genomic tests by clinicians. Given the paucity of evidence to assess each variant, and the difficulty of experimentally evaluating a variants clinical significance, many of the thousand variants that can be generated by clinical tests are reported as variants of unknown clinical significance. However, the creation of population-scale variant databases can significantly improve clinical variant interpretation. Specifically, pathogenicity prediction for novel missense variants can now utilize features describing regional variant constraint. Constrained genomic regions are those that have an unusually low variant count in the general population. Several computational methods have been introduced to capture these regions and incorporate them into pathogenicity classifiers, but these methods have yet to be compared on an independent clinical variant dataset. Here we introduce one variant dataset derived from clinical sequencing panels, and use it to compare the ability of different genomic constraint metrics to determine missense variant pathogenicity. This dataset is compiled from 17,071 patients surveyed with clinical genomic sequencing for cardiomyopathy, epilepsy, or RASopathies. We further utilize this dataset to demonstrate the necessity of disease-specific classifiers, and to train PathoPredictor, a disease-specific ensemble classifier of pathogenicity based on regional constraint and variant level features. PathoPredictor achieves an average precision greater than 90% for variants from all 99 tested disease genes while approaching 100% accuracy for some genes. Accumulation of larger clinical variant datasets and their utilization to train existing pathogenicity metrics can significantly enhance their performance in a disease and gene-specific manner.

genomics↗

bioRxiv2018

Neutrophil microvesicles drive atherosclerosis by delivering miR-155 to atheroprone endothelium.

Neutrophils have been implicated in the pathogenesis of atherosclerosis, a lipid-driven disease of arteries, but they are seldom found in atherosclerotic plaques. To resolve this longstanding paradox, we investigated whether neutrophil-derived microvesicles may influence arterial pathophysiology. Clinical and pre-clinical studies revealed that levels of circulating neutrophil microvesicles were enhanced by exposure to a high fat diet, a known risk factor for atherosclerosis. Neutrophil microvesicles accumulated at disease-prone regions of arteries that are exposed to complex flow patterns, and they promoted vascular inflammation and atherosclerosis in a murine model. Using cultured endothelial cells exposed to disturbed flow, it was demonstrated that neutrophil microvesicles promoted inflammatory gene expression by delivering a microRNA (miR-155) that enhanced NF-{kappa}B activation. Similary, neutrophil microvesicles increased miR-155 and enhanced NF-{kappa}B at disease-prone sites of disturbed flow in arteries of mice. We conclude that delivery of microvesicles carrying miR-155 to disease-prone regions of arteries provides a novel mechanism by which neutrophils contribute to vascular inflammation and atherogenesis.

cell biology↗

bioRxiv2018

ExomeSlicer: a resource for the development and validation of exome-based clinical panels

Exome-based panels (exome slices) are becoming the preferred diagnostic strategy in clinical laboratories, especially for genetically heterogeneous disorders. The advantages of this approach include enabling frequent updates to gene content without the need for re-designing, reflexing to exome analysis bioinformatically without requiring additional sequencing, and streamlining laboratory operation by using established exome kits and protocols. Despite their increasing use, there are currently no guidelines or appropriate resources to support their clinical implementation. Here, we highlight principles and important considerations for the clinical development and validation of exome-based panels, guided by clinical data from a diagnostic epilepsy panel using this approach. We also present a novel, publically accessible web-based resource, ExomeSlicer, and demonstrate its clinical utility in predicting gene-specific and exome-wide technically challenging regions that are not amenable to Next Generation Sequencing (NGS), and that might significantly lead to increased post hoc Sanger fill in burden. Using this tool, we also characterize > 2000 low complexity, GC-rich and/or high homology, regions across the exome that can be a source of false positive or false negative variant calls thus potentially leading to misdiagnoses in tested patients.

genomics↗

bioRxiv2017

RNA-Seq 2G: Online Analysis Of Differential Gene Expression With Comprehensive Options Of Statistical Methods

RNA-seq has become the most prevalent technology for measuring genome-wide gene expression, but the best practices for processing and analysing RNA-seq data are still an open question. Many statistical methods have been developed to identify genes differentially expressed between sample groups from RNA-seq data. These methods differ by their data distribution assumptions, choice of statistical test, and computational resource requirements. Over 25 methods of differential expression detection were validated and made available through a user-friendly web portal, RNA-seq 2G. All methods are suitable for analysing differential gene expression between two groups of samples. They commonly use a read count matrix derived from RNA-seq data as input and statistically compare groups for each gene. The web portal uses a Shiny app front-end and is hosted by a cloud-based server provided by Amazon Web Service. The comparison of methods showed that the data distribution assumption is the major determinant of differences between methods. Most methods are more likely to find that longer genes are differentially expressed, which substantially impacts downstream gene set-level analysis. Combining results from multiple methods can potentially diminish this bias. RNA-seq 2G makes the analysis of RNA-seq data more accessible and efficient, and is freely available at http://rnaseq2g.awsomics.org.

bioinformatics↗