Biology subjects

Marshall, S.

Publications and source records attributed to Marshall, S..

12 recordsLinked to original sources

bioRxiv2026

Deep Learning-Based Structure Modeling of the Treponema pallidum Proteome: Insights into Pathogenesis and Syphilis Vaccine Development

Treponema pallidum ssp. pallidum, the causative agent of syphilis, has a small proteome and encompasses numerous strains. Knowledge gaps remain in understanding the molecular mechanisms of pathogenesis of this bacterium, as well as the structure and function of the full complement of proteins encoded by T. pallidum. Here, an AI-based structure-to-function modeling workflow was used to investigate the complement of proteins encoded by T. pallidum. High-confidence structure models were generated for 976 T. pallidum proteins, covering 99% of the proteome. Analysis of the generated models using the protein structure comparison server DALI enabled high-confidence, structure-based functional annotation of 877 T. pallidum proteins, including 240 of the 323 proteins of unknown function encoded by this pathogen. Additionally, 63 putative pathogenesis related proteins (PPRPs) and seven treponemal proteins with previously uncharacterized similarity to outer membrane proteins (OMPs) from Gram-negative bacteria were identified. A workflow for B cell epitope (BCE) prediction identified 1133 surface-exposed, host-facing potential epitopes in known and predicted T. pallidum OMPs, of which 92 were prioritized based on bioinformatic analyses, biophysical properties, amino acid sequence conservation, and previous protein expression data. This work provides insight into T. pallidum pathogenesis through structure modeling-based functional annotation, including characterization of proteins of unknown function. This study also informs syphilis vaccine design by identifying new potential T. pallidum OMPs, as well as host-facing regions of T. pallidum OMPs that have conserved amino acid sequences in globally circulating strains. Statement of importance/impactThis study presents the first AI-based global structure modeling-to-function analysis of the proteome of Treponema pallidum, the bacterium that causes syphilis. Structure-based functional predictions of previously uncharacterized proteins, including proteins potentially involved in virulence, provide novel insight into mechanisms of pathogenesis. The work also informs syphilis vaccine development by the identification and structural characterization of new candidate vaccine proteins in globally circulating strains of T. pallidum.

microbiology↗

bioRxiv2025

The Lipid Hydrolase ABHD6 is a Therapeutic Target in Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD)-Related Hepatocellular Carcinoma

Primary liver cancer accounts for approximately 700,000 deaths worldwide annually ranking third in cancer-related mortality, with hepatocellular carcinoma (HCC) comprising the majority of these tumors. Metabolic dysfunction-associated steatotic liver disease (MASLD) is currently a leading cause of HCC in the United States. We previously identified the lipid hydrolase alpha/beta hydrolase domain 6 (ABHD6) as a key mediator of the development of metabolic syndrome and intimately involved in cell signaling, making it a prime target for investigation in MASLD-related HCC. ABHD6 displays higher expression within HCC tumor cores when compared to adjacent non-tumor liver tissue in human subjects. Using an in vivo antisense oligonucleotide (ASO)-driven knockdown approach, we have shown the inhibition of ABHD6 prevents the development and progression of HCC in an obesity/MASLD-driven mouse model. Additionally, a xenograft model using the human Huh7 cell line displayed reduced tumor engraftment and growth with ABHD6 genetic deletion and small molecule inhibition. ABHD6 knockout cells demonstrated increased levels of bis(monoacylglycerol)phosphates (BMPs), lipids relevant to high fat diet-induced lysosomal dysfunction, and knockout cells also demonstrated altered autophagy and lysosomal activity using in vitro model of saturated fatty acid-induced lipotoxicity. These studies reveal novel lipid signaling mechanisms by which MASLD progresses towards HCC and provide support for ABHD6 as a therapeutic target in HCC. SignificanceWe have identified that alpha/beta hydrolase domain 6 (ABHD6) plays a role in lysosomal membrane lipid remodeling pathways that are relevant in obesity/MASLD-driven HCC. Inhibitors targeting ABHD6 reorganize lysosomal lipid homeostasis to improve outcomes in HCC.

cancer biology↗

bioRxiv2024

In-Depth Mapping of DNA-PKcs Signaling Uncovers Conserved Features of Its Kinase Specificity

DNA-PKcs is a DNA damage sensor kinase with established roles in DNA double-strand break repair via non-homologous end joining. Recent studies have revealed additional roles of DNA-PKcs in the regulation of transcription, translation and DNA replication. However, the substrates through which DNA-PKcs regulates these processes remain largely undefined. Here we utilized quantitative phosphoproteomics to generate a high coverage map of DNA-PKcs signaling in response to ionizing radiation and mapped its interplay with the ATM kinase. Beyond the detection of the canonical S/T-Q phosphorylation motif, we uncovered a non-canonical mode of DNA-PKcs signaling targeting S/T-{psi}-D/E motifs. Cross-species analysis in mouse pre-B and human HCT116 cell lines revealed splicing factors and transcriptional regulators phosphorylated at this novel motif, several of which contain SAP domains. These findings expand the list of DNA-PKcs and ATM substrates and establish a novel preferential phosphorylation motif for DNA-PKcs that connects it to proteins involved in nucleotide processes and interactions.

biochemistry↗

bioRxiv2023

Methylome-wide association studies of traumatic physical injury identifies differential DNA methylation of synaptic plasticity and GABAergic-signalling.

Traumatic physical injury is often associated with psychological trauma and is a risk factor for major depressive disorder (MDD). In Generation Scotland traumatic injury was significantly associated with recurrent major depression (OR = 2.10, 95% CI 1.33-3.33, PLJ=LJ0.0016). and schizotypal symptoms, particularly disorganised thought ({beta}LJ=LJ0.111, 95% CI 0.049-0.177, PLJ=LJ0.0004). We performed methylome-wide analyses of traumatic injury in individuals with MDD and controls separately to investigate the link between traumatic injury and MDD. Nominally significant differences in differential DNA methylation between MDD and control groups were identified at 40 003 CpG sites (p < 0.05). Individuals with recurrent MDD showed significantly higher levels of DNA methylation associated with traumatic injury at CpG sites at the first exon and lower levels at exon boundaries, this was significant different to the association pattern at these sites in controls (mean difference in M-value = 0.0083, P = 21.1x10-10, and -0.0125, P = 2.1x10-174, respectively). Analyses at the level of CpG site, genes and gene ontologies implicated dysregulation of processes related to synaptic plasticity, including dendrite development, excitatory synapse and GABAergic signalling (normalised enrichment values > 2, FDR q-values < 0.01). Enrichment analyses for regional brain-expression in the recurrent MDD group highlight the limbic lobe and supraoptic nuclei (recurrent MDD FWER = 0.028 and 0.034, respectively). These results suggest that traumatic injury is associated with patterns of DNA methylation differentially in individuals with MDD compared to controls, highlighting the need for novel analysis approaches.

genomics↗

bioRxiv2022

Characterisation and Genetic Architecture of Major Depressive Disorder Subgroups Defined by Weight and Sleep Changes

Major depressive disorder, MDD, is highly heterogeneous and thus subgroups with different underlying aetiologies have been postulated. The aim of this work is to further characterise depression subgroups defined using sleep and weight changes. Probable lifetime MDD cases (n = 26,662) from the UK Biobank were stratified into three subgroups defined by self-reported weight and sleep changes during worst episode: (i) increased weight and sleep ({uparrow}WS), (ii) decreased weight and sleep ({downarrow}WS) and (iii) the remaining uncategorised individuals. Analyses compared the depression characteristics, mental health scores, neurological and inflammatory comorbidities and genetic architecture between subgroups and with 50,147 controls from UK Biobank. In contrast to {uparrow}WS depression, {downarrow}WS depression had a higher age of onset and lower proportion reporting countless or continuous episodes compared to uncategorised individuals. The {downarrow}WS depression also had a higher wellbeing score than the other subgroups. Analyses of subgroup comorbidities identified a novel association between {uparrow}WS depression and epilepsy. Subgroup-specific GWAS identified three genome-wide significant loci associated with {uparrow}WS in genes previously associated with immunometabolic traits and response to anticonvulsants. The effect of BMI adjustment in the genetic analyses of the subgroups and using broader weight-only definitions were also examined. The findings provide further evidence for differences in the characteristics and genetic architecture of depression subgroups defined by sleep and weight change and highlight the importance of dividing non-{uparrow}WS individuals into {downarrow}WS and uncategorised subgroups in analyses, as {downarrow}WS symptoms may identify a more acute depression subgroup.

genomics↗

bioRxiv2021

A video-based behavioural intervention associated with improved HPV knowledge and intention to vaccinate

AimsThe aim of this study was to design, develop and evaluate a theory and evidence-based intervention to improve human papillomavirus (HPV) and HPV vaccine knowledge, and intention to vaccinate, among parent-daughter dyads. MethodsA theory and evidence-based online behavioural intervention, "Is the HPV vaccine for me?" was developed to improve HPV and HPV vaccine knowledge, and intention to vaccinate. The impact and feasibility of the intervention was evaluated in a prospective randomised controlled feasibility trial. ResultsA total of 49 parent-daughter dyads completed baseline knowledge assessment (n=24 control, n=25 intervention), and 35 dyads completed knowledge assessment at week 2 (n=17 control, n=18 intervention). The intervention was associated with a statistically significant increase in HPV, and HPV vaccine knowledge and intention to vaccinate. All intervention participants found the video interesting, while 96% found it useful. ConclusionsThis intervention was found to be affordable, practicable, effective (cost-effective), acceptable, safe, and equitable, in this feasibility study.

scientific communication and education↗

bioRxiv2021

Acidity and sulfur oxidation intermediate concentrations controlled by O2-driven partitioning of sulfur oxidizing bacteria in a mine tailings impoundment

Acidification of freshwater in mining impacted areas is a major global environmental problem catalyzed by sulfur-oxidizing bacteria (SOB). To date, little is known about the active bacteria in mine tailings impoundments and their environmental niches. Here, biological sulfur oxidation was investigated over four years in a mine tailings impoundment, integrating sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics. We demonstrated oxygen driven niche partitioning of SOB and their metabolic pathways that explain acidity generation and thiosulfate persistence. Four chemolithoautotrophic SOB, Halothiobacillus, Thiobacillus, Sulfuricurvum and Sediminibacterium comprised 37% to 73% of the analyzed communities. The impoundment waters alternated between the dominance of Halothiobacillus versus a Thiobacillus, Halothiobacillus, Sulfuricurvum and Sediminibacterium consortia. Halothiobacillus dominance was associated with lower pH values ([~]4.3), higher [H+]/[SO42-] and lower [S2O32-], collectively indicative of extensive sulfur oxidation. Halothiobacillus, which couple sulfur oxidation via the Sox pathway to aerobic respiration or NO2- reduction, were present throughout the depth profile, yet their expression of sox genes occurred only in upper highly oxygenated waters. Conversely, when consortia of Thiobacillus, Halothiobacillus, Sulfuricurvum and Sediminibacterium dominated, recycling/disproportionating reactions were more prevalent. Thiobacillus, which dominated deeper micro-oxic/anoxic waters, oxidized sulfur primarily through the rDSR pathway, coupled to NO3-/NO2- reduction, resulting in lower [H+]/[SO42-] and higher [S2O32-] relative to upper waters. These field results mirror the Sox/rDSR-geochemical patterns of experimental SOB enrichments and reveal opportunities for biological treatments of recalcitrant reduced sulfur compounds, as well as gene-based monitoring and in situ RNA detection to predict the onset of problematic geochemistry.

microbiology↗

bioRxiv2021

Metabolic breakdown of non-small cell lung cancers by mitochondrial HSPD1 targeting

The identification of novel targets is of paramount importance to develop more effective drugs and improve the treatment of non-small cell lung cancer (NSCLC), the leading cause of cancer-related deaths worldwide. Since cells alter their metabolic rewiring during tumorigenesis and along cancer progression, targeting key metabolic players and metabolism-associated proteins represents a valuable approach with a high therapeutic potential. Metabolic fitness relies on the functionality of heat shock proteins (HSPs), molecular chaperones that facilitate the correct folding of metabolism enzymes and their assembly in macromolecular structures. Here, we show HSPD1 (HSP60) as a survival gene ubiquitously expressed in NSCLC and associated with poor patients prognosis. HSPD1 knockdown or its chemical disruption by the small molecule KHS101 induces a drastic breakdown of oxidative phosphorylation, and suppresses cell proliferation both in vitro and in vivo. By combining drug profiling with transcriptomics and through a whole-genome CRISPR/Cas9 screen, we demonstrate that HSPD1-targeted anti-cancer effects are dependent on OXPHOS and validated molecular determinants of KHS101 sensitivity, in particular, the creatine-transporter SLC6A8 and the subunit of the cytochrome c oxidase complex COX5B. These results highlight mitochondrial metabolism as an attractive target and HSPD1 as a potential theranostic marker for developing therapies to combat NCSLC. SignificanceHSPD1 elimination or disruption interferes with NSCLC metabolic activity causing a strong OXPHOS-dependent energetic breakdown, which the cancer cells fail to overcome, highlighting HSPD1 as a potential theranostic marker for improving lung cancer therapy.

cancer biology↗

bioRxiv2020

The effect of E-liquid exposure on Caenorhabditis elegans.

E-cigarettes are being promoted as a less harmful alternative to smoking tobacco. However, vaping is a new phenomenon and safety profiles have not been fully established. Model organisms can be used to examine the cellular processes that may be changed by exposure to the E-liquids used for vaping. Mitochondria are essential in eukaryotic cells for production of ATP, protein biogenesis, metabolic pathways, cellular signalling, stress responses and apoptosis. Mitochondrial health can be used as a proxy for many aspects of healthy cellular physiology. Mutations in the PINK1 gene can lead to mitochondria-specific autophagy deficiency. We exposed two strains of Caenorhabditis elegans, CB5600 control and CC46 pink1, with 10% concentrations of nine different flavoured E liquids. We measured lifespan, movement, body size, brood size, and we examined their mitochondrial networks to investigate the effect of the E-liquids. We show that the CC46 (pink1) strain is affected by the E-liquids, even the flavours without nicotine, and that they have reduced lifespan, movement ability and mitochondrial organisation. We found that some E-liquids can dramatically shorten lifespan in this strain. Our data emphasise a need to carefully ascertain the potential harm that may be caused by the use of E-liquids.

cell biology↗

bioRxiv2020

Maximizing Quantitative Phosphoproteomics of Kinase Signaling Expands the Mec1 and Tel1 Networks

Global phosphoproteome analysis is crucial for comprehensive and unbiased investigation of kinase-mediated signaling. However, since each phosphopeptide represents a unique entity for defining identity, site-localization, and quantitative changes, phosphoproteomics often suffers from lack of redundancy and statistical power for generating high confidence datasets. Here we developed a phosphoproteomic approach in which data consistency among experiments using reciprocal stable isotope labeling defines a central filtering rule for achieving reliability in phosphopeptide identification and quantitation. We find that most experimental error or biological variation in phosphopeptide quantitation does not revert in quantitation once light and heavy media are swapped between two experimental conditions. Exclusion of non-reverting data-points from the dataset not only reduces quantitation error and variation, but also drastically reduces false positive identifications. Application of our approach in combination with extensive fractionation of phosphopeptides by HILIC identifies new substrates of the Mec1 and Tel1 kinases, expanding our understanding of the DNA damage signaling network regulated by these kinases. Overall, the proposed quantitative phosphoproteomic approach should be generally applicable for investigating kinase signaling networks with high confidence and depth.

molecular biology↗

bioRxiv2019

Development of the mandibular curve of Spee and maxillary compensating curve: A finite element model

The curved planes of the human dentition seen in the sagittal view, the mandibular curve of Spee and the maxillary compensating curve, have clinical importance to modern dentistry and potential relevance to the craniofacial evolution of hominins. However, the mechanism providing the formation of these curved planes is poorly understood. To explore this further, we use a simplified finite element model, consisting of maxillary and mandibular \"blocks\", developed to simulate tooth eruption, and forces opposing eruption, during simplified masticatory function. We test our hypothesis that curved occlusal planes develop from interplay between tooth eruption, occlusal load, and mandibular movement.\n\nOur results indicate that our simulation of rhythmic chewing movement, tooth eruption, and tooth eruption inhibition, applied concurrently, results in a transformation of the contacting maxillary and mandibular block surfaces from flat to curved. The depth of the curvature appears to be dependent on the radius length of the rotating (chewing) movement of the mandibular block. Our results suggest mandibular function and maxillo-mandibular spatial relationship may contribute to the development of human occlusal curvature.

developmental biology↗

bioRxiv2017

Functional effects of heating and cooling gene networks

Everyday existence and survival of most organisms requires coping with temperature changes, which involves gene regulatory networks both as subjects and agents of cellular protection. Yet, how temperature affects gene network function remains unclear, partly because natural gene networks are complex and incompletely characterized. Here, we study how heating and cooling affect the function of single genes and well-characterized synthetic gene circuits in Saccharomyces cerevisiae. We found nontrivial, nonmonotone temperature-dependent gene expression trends at non-growth-optimal temperatures. In addition, heating caused unusual bimodality in the negative-feedback gene circuit expression and shifts upward the bimodal regime for the positive feedback gene circuit. Mathematical models incorporating temperature-dependent growth rates and Arrhenius scaling of reaction rates captured the effects of cooling, but not those of heating. Molecular dynamics simulations revealed that heating alters the conformational dynamics and allows DNA-binding of the TetR transcriptional repressor, fully explaining the experimental results for the negative-feedback gene circuit. Overall, we uncover how temperature shifts may corrupt gene networks, which may aid future designs of temperature-robust synthetic gene circuits.

synthetic biology↗