Biology subjects

Parkes, M.

Publications and source records attributed to Parkes, M..

7 recordsLinked to original sources

bioRxiv2024

Central Presynapses Regulate Spontaneous Synaptic Vesicle Exocytosis Rate by Constraining Recycling Pool Density

Synapses represent a fundamental unit of information transfer during cognition. They accomplish this via presynaptic vesicle exocytosis, which can occur either spontaneously or by an action potential leading to evoked release. It has been well established that evoked release is probabilistic in nature, but it has been less clear what mechanisms mediate spontaneous release. Understanding spontaneous release is important because it is an essential maintenance mechanism for synaptic connections. We propose a mechanistic framework and model of spontaneous release based on immobile vesicles in the reserve pool geometrically constraining mobile vesicles in the recycling pool, which provides a force leading to a spontaneous release rate. We experimentally support this framework using a combination of Scanning Electron Microscopy (SEM), high-resolution fluorescence microscopy techniques using pHluorin-VGlut1 and a single vesicle SGC5 reporter, and a computational model. We observe that the spontaneous release rate increases linearly with the number of vesicles but is constant in the absence of presynaptic actin. We then use an acute agent, Forskolin, to further constrain the volume of the recycling pool, leading to an increased spontaneous release rate. We show that our framework predicts the increasing spontaneous release rate experimentally observed. These results suggest that synapses constrain the density of the recycling pool to mediate spontaneous release rate via the entropic force.

neuroscience↗

bioRxiv2021

Two microbiota subtypes identified in Irritable Bowel Syndrome with distinct responses to the low-FODMAP diet

ObjectiveReducing FODMAPs can be clinically beneficial in IBS but the mechanism is poorly understood. We aimed to detect microbial signatures that might predict response to the low FODMAP diet and assess whether microbiota compositional and functional shifts could provide insights into its mode of action. DesignWe used metagenomics to determine high-resolution taxonomic and functional profiles of the stool microbiota from IBS cases and household controls (n=56 pairs) on their usual diet. Clinical response and microbiota changes were studied in 41 pairs after 4 weeks on a low FODMAP diet. ResultsUnsupervised analysis of baseline IBS cases pre-diet identified two distinct microbiota profiles, which we refer to as IBSP (pathogenic-like) and IBSH (health-like) subtypes. IBSP microbiomes were enriched in Firmicutes and genes for amino acid and carbohydrate metabolism, but depleted in Bacteroidetes species. IBSH microbiomes were similar to controls. On the low FODMAP diet IBSH and control microbiota were unaffected, but the IBSP signature shifted towards a health-associated microbiome with an increase in Bacteroidetes (p=0.009), a decrease in Firmicutes species (p=0.004) and normalization of primary metabolic genes. The clinical response to the low FODMAP diet was greater in IBSP subjects compared to IBSH (p = 0.02). Conclusion50% of IBS cases manifested a pathogenic gut microbial signature. This shifted towards the healthy profile on the low FODMAP diet; and IBSP cases showed an enhanced clinical responsiveness to the dietary therapy. The effectiveness of FODMAP exclusion in IBSP may result from the alterations in gut microbiota and metabolites produced. Microbiota signatures could be useful as biomarkers to guide IBS treatment; and investigating IBSP species and metabolic pathways might yield insights regarding IBS pathogenic mechanisms. O_TEXTBOXSignificance of this studyO_ST_ABSWhat is already known on this subject?C_ST_ABSO_LIIBS subjects often respond to a low FODMAP diet. C_LIO_LIThe gut microbiota has been implicated in IBS. C_LIO_LIThe microbiota in IBS subjects may change with diet. C_LI What are the new findings?O_LIWe were able to stratify patients with IBS according to their gut microbiota species and metabolic gene signatures. C_LIO_LIWe identified a distinct gut microbiota subtype with an enhanced clinical response to a low FODMAP diet compared to other IBS subjects. C_LI How might it impact on clinical practice in the foreseeable future?O_LIThe potential development of a microbiota signature as a biomarker to manage IBS cases with a low FODMAP diet recommendation. C_LIO_LIIf the bacteria represented in the IBSP subtype are shown to play a pathogenic role in IBS, perhaps through the metabolic activity this provides a target for new therapies and an intermediate phenotype by which to assess them. C_LI C_TEXTBOX

microbiology↗

bioRxiv2020

Vesicle Navigation of Microtubule Ends Distinguished by A Single Rate-Constant Model

Axonal motor driven cargo utilizes the microtubule cytoskeleton in order to direct cargo, such as presynaptic vesicle precursors, to where they are needed. This transport requires vesicles to travel up to microns in distance. It has recently been observed that finite microtubule lengths can act as roadblocks inhibiting vesicles and increasing the time required for transport. Vesicles reach the end of a microtubule and pause until they can navigate to a neighboring microtubule in order to continue transport. The mechanism by which axonal vesicles navigate the end of a microtubule in order to continue mobility is unknown. In this manuscript we model experimentally observed vesicle pausing at microtubule ends in C. elegans. We show that a single rate-constant model reproduces the time vesicles pause at MT-ends. This model is based on the time a vesicle must detach from its current microtubule and re-attach to a neighboring microtubule. We show that vesicle pause times are different for anterograde and retrograde motion, suggesting that vesicles utilize different proteins at plus and minus end sites. Last, we show that vesicles do not likely utilize a tug-of-war like mechanism and reverse direction in order to navigate microtubule ends.

biophysics↗

bioRxiv2019

The mutational profile and clonal landscape of the inflammatory bowel disease affected colon

Summary paragraphInflammatory bowel disease (IBD) is a chronic inflammatory disease associated with increased risk of gastrointestinal cancers. Here, we whole-genome sequenced 447 colonic crypts from 46 IBD patients, and compared these to 412 crypts from 41 non-IBD controls. The average mutation rate of affected colonic epithelial cells is 2.4-fold that of healthy colon and this increase is mostly driven by acceleration of mutational processes ubiquitously observed in normal colon. In contrast to the normal colon, where clonal expansions outside the confines of the crypt are rare, we observed widespread millimeter-scale clonal expansions. We discovered non-synonymous mutations in ARID1A, FBXW7, PIGR and ZC3H12A, and genes in the interleukin 17 and Toll-like receptor pathways, under positive selection in IBD. These results suggest distinct selection mechanisms in the colitis-affected colon and that somatic mutations potentially play a causal role in IBD pathogenesis.

genetics↗

bioRxiv2019

A systems genomics approach to uncover patient-specific pathogenic pathways in a complex disease

We describe a novel precision medicine workflow, the integrated single nucleotide polymorphism network platform (iSNP), designed to identify the exact mechanisms of how SNPs affect cellular regulatory networks, and how SNP co-occurrences contribute to disease pathogenesis in ulcerative colitis (UC). Using SNP profiles of 377 UC patients, we mapped the regulatory effects of the SNPs to a human signalling network containing protein-protein, miRNA-mRNA and transcription factor binding interactions. Unsupervised clustering algorithms grouped these patient-specific networks into four distinct clusters based on two large disease hubs, NFKB1 and PKCB. Pathway analysis identified the epigenetic modification as common and the T-cell specific responses as differing signalling pathways in the clusters. By integrating individual transcriptomes in active and quiescent disease setting to the patient networks, we validated the impact of non-coding SNPs. The iSNP approach identified regulatory effects of disease-associated non-coding SNPs, and identified how pathogenesis pathways are activated via different genetic modifications.

bioinformatics↗

bioRxiv2019

A blood-based prognostic biomarker in inflammatory bowel disease

ObjectiveWe have previously described a prognostic transcriptional signature in CD8 T cells that separates inflammatory bowel disease (IBD) patients into 2 phenotypically-distinct subgroups, which we termed IBD1 and IBD2. Here we sought to develop a blood-based prognostic test that could identify these patient subgroups without the need for cell separation, and thus be suitable for routine clinical use in Crohns disease (CD) and ulcerative colitis (UC). DesignPatients with active IBD were recruited before treatment. Transcriptomic analyses were performed on purified CD8 T cells and/or whole blood. Detailed phenotype information was collected prospectively. IBD1/IBD2 patient subgroups were identified by consensus clustering of CD8 T cell transcriptomes. In a training cohort, statistical (machine) learning was used to identify groups of genes ("classifiers") whose differential expression in whole blood re-created the IBD1/IBD2 patient subgroups. Genes from the best classifiers were qPCR-optimised, and further statistical learning was applied to the qPCR dataset to identify the optimal classifier, which was locked-down for further testing. Independent validation was sought in separate cohorts of CD (n=66) and UC patients (n=57). ResultsIn both independent validation cohorts, a 17-gene qPCR-based classifier stratified patients into two distinct subgroups. Irrespective of the underlying diagnosis, IBDhi patients (analogous to the poor prognosis IBD1 subgroup) experienced significantly more aggressive disease than IBDlo patients (analogous to IBD2), with earlier need for treatment escalation and more escalations over time. ConclusionThis is the first validated prognostic biomarker that can predict prognosis in newly-diagnosed IBD patients, and represents a step towards personalised therapy. What is already known about this subject?The course of CD and UC varies considerably between patients, but reliable prognostic markers are not available in clinical practice. This hinders disease management because treatment approaches that would be optimal for patients with indolent disease - characterised by infrequent flare-ups that can be readily controlled by first-line therapy - will inevitably undertreat those with progressive disease. Conversely, strategies that would appropriately control frequently-relapsing, progressive disease will expose patients with more quiescent disease to the risks and side effects of unnecessary treatment. We have previously described a CD8 T cell gene expression signature that corresponds to differences in T cell exhaustion, is detectable during active untreated disease (including at diagnosis), and predicts disease course in both UC and CD. However, the need for cell separation and microarray-based gene expression analysis would make this difficult to translate to clinical practice. What are the new findings?We have developed, optimised, and independently validated a whole blood qPCR-based classifier - designed to identify the IBD1 and IBD2 patient subgroups - that can reliably predict prognosis in patients with CD or UC from diagnosis without the need for cell separation. We also present a detailed phenotypic update on the disease course experienced by patients in either the IBD1/IBDhi or IBD2/IBDlo subgroups, incorporating both expanded patient cohorts and substantially longer follow-up. This affords new insights into the spectrum of therapies that are differentially required in these patient subgroups, and reinforces their association with disease prognosis. How might it impact on clinical practice in the foreseeable future?The qPCR-based classifier has performance characteristics that compare favourably to prognostic biomarkers currently in use in oncology, and should be sufficient to guide therapy from diagnosis in patients with CD or UC. This represents an important step towards personalised therapy in inflammatory bowel disease.

genomics↗

bioRxiv2018

HLA-DQA1*05 is associated with the development of antibodies to anti-TNF therapy

BackgroundAnti-tumour necrosis factor (anti-TNF) therapies are the most widely used biologic therapies for treating immune-mediated diseases. Their efficacy is significantly reduced by the development of anti-drug antibodies which can lead to treatment failure and adverse reactions. The biological mechanisms underlying antibody development are unknown but the ability to identify subjects at higher risk would have significant clinical benefits.\n\nMethodsThe PANTS cohort consists of Crohns disease patients recruited prior to first administration of anti-TNF, with serial measurements of anti-drug antibody titres. We performed a genome-wide association study across 1240 individuals from this cohort to identify genetic variants associated with anti-drug antibody development.\n\nFindingsThe Human Leukocyte Antigen allele, HLA-DQA1*05, carried by approximately 40% of Europeans, significantly increased the rate of anti-drug antibody development (hazard ratio [HR], 1.90; 95% confidence interval [CI], 1.60 to 2.25; P=5.88x10-13). This association was consistent for patients treated with adalimumab (HR, 1.89; 95% CI, 1.32 to 2.70) and infliximab (HR, 1.92; 95% CI, 1.57 to 2.33), and for patients treated with mono-(HR, 1.75; 95% CI, 1.37 to 2.22) or combination therapy with immunomodulators (HR, 2.0; 95% CI, 1.57 to 2.58).\n\nInterpretationHLA-DQA1*05 is significantly associated with an increased rate of anti-drug antibody formation in patients with Crohns disease treated with infliximab and adalimumab. Pre-treatment HLA-DQA1*05 genetic testing may help personalise the choice of anti-TNF therapy and allow the targeted use of immunomodulator therapy to minimise risk and maximise response.

genomics↗