Biology subjects

Hughes, B.

Publications and source records attributed to Hughes, B..

14 recordsLinked to original sources

bioRxiv2025

Oxidation of ΔFOSB at Cys172 Controls Hippocampal Gene Targets and Learning

Imbalance of reduction/oxidation (redox) in the brain is associated with numerous diseases including Alzheimers disease (AD), substance abuse disorders, and stroke. Moreover, cognitive decline can be caused by neuronal dysfunction that precedes cell death, and this dysfunction is in part produced by altered gene expression. However, the mechanisms by which redox state controls gene expression in neurons are not well understood. {Delta}FOSB is a neuronally enriched transcription factor critical for orchestrating gene expression underlying memory, mood, and motivated behaviors. It is dysregulated in many conditions including AD. We showed recently that {Delta}FOSB forms a redox-sensitive disulfide bond between cysteine 172 (C172) of {Delta}FOSB and C279 of its preferred binding partner JUND. This bond works as a redox switch to control DNA-binding, based on studies of recombinant proteins in vitro. Here, we show that this redox control of {Delta}FOSB function in vitro is conserved in vivo. We show that {Delta}FOSB C172 forms a redox-sensitive disulfide bond with JUND that regulates the stability of this AP1-transcription factor complex and its binding to DNA in cells. We also validate the formation of {Delta}FOSB-containing complexes held together via disulfide bonds in mouse brain in vivo. We show that exogenous oxidative stress reduces {Delta}FOSB binding to gene targets in mouse brain and that Fosb C172S knock-in mice, which lack a functional {Delta}FOSB redox switch, are insensitive to this oxidation-dependent reduction in target gene binding, demonstrating that {Delta}FOSB is regulated by a redox switch that modulates binding to target genes in the hippocampus. Finally, we demonstrate that FosB C172S knock-in mice are less sensitive to cognitive dysfunction induced by oxidative stress. This evidence supports {Delta}FOSB as an important mediator of oxidative stress-driven changes in gene expression and cognition and implicates {Delta}FOSB as a possible therapeutic target for diseases associated with oxidative stress in the brain, including AD.

neuroscience↗

bioRxiv2025

A novel chimeric coronavirus spike vaccine combining SARS-CoV-2 RBD and scaffold domains from HKU-1 elicits potent neutralising antibody responses

The receptor binding domain (RBD) of the SARS-CoV-2 spike is the major target for neutralising antibodies elicited by current vaccines. Using small domains such as the RBD as vaccine immunogens, however, may constrain the availability of CD4 T follicular helper (TFH) cells and impact immunogenicity. We engineered a novel chimeric trimeric RBD (CTR) glycoprotein, replacing the RBD of human coronavirus HKU-1 spike with SARS-CoV-2 RBD of either ancestral (WT) or Omicron BA.2 strains. This strategy maintains a native trimeric conformation of the RBD, while providing additional sources of CD4 T cell help via the HKU-1 spike scaffold. In C57BL/6 mice, CTR-BA.2 prime-boost vaccination elicited high anti-BA.2-RBD IgG and neutralising titres, matching responses in animals immunised with native SARS-CoV-2 spike proteins. GC B cells elicited by CTR-BA.2 were predominantly WT+/BA.2+ cross- reactive, and TFH cells predominantly recognised HKU-1 epitopes, demonstrating scaffold-directed T cell help. Macaques prime-boost immunised with CTR-WT similarly elicited high anti-RBD IgG, anti-spike IgG and neutralising responses, comparable to native spike-vaccinated animals. In draining lymph nodes of CTR-WT vaccinated macaques, RBD-specific GC B cells were present at elevated levels. In contrast to the murine studies, lymph node-draining TFH responses in macaques were broadly elicited against RBD, NTD/S2 or HKU-1-derived peptides. Although native SARS- CoV-2 spike was also highly immunogenic in animal models, our findings establish the chimeric glycoprotein design as a strategy to overcome the poor immunogenicity of the SARS-CoV-2 RBD by engaging CD4 TFH cells, while maintaining the ability to elicit protective neutralising responses. One sentence summaryA chimeric glycoprotein design preserves SARS-CoV-2 RBD antigenic conformation enabling elicitation of neutralising responses, while allowing recruitment of HKU-1 scaffold-directed CD4 helper responses to support the humoral response.

immunology↗

bioRxiv2025

Effects of a Cancer-Associated Mutation and Multiple SerinePhosphorylation on Poly(ADP-Ribose) Polymerase 2

Poly [ADP-ribose] polymerase 2 (PARP2) plays a crucial role in DNA repair. A common single-nucleotide polymorphism (SNP) in the PARP2 gene, rs3093921, has been associated with pancreatic cancer and marginal zone lymphoma (MZL). This SNP results in a missense mutation, D235G, in the PARP2 protein. PARP2 is also reported to undergo post-translational modifications (PTMs), particularly phosphorylation at serine residues 226, 232, and 353. The C-terminal region of PARP2 includes the Trp-Gly-Arg (WGR) and ADP-ribosyl transferase (ART) domains, and the helical subdomain (HD). The latter two, spanning residues 220 to 583, comprise the catalytic region of PARP2. The DNA-induced enzymatic activation of PARP2 is regulated by local destabilization of the HD domain. We used molecular dynamics (MD) simulations to investigate the impact of these three PTMs on both the wild-type (WT) and the mutant (D235G) forms of PARP2. Our simulations suggest that, while neither the cancer-associated mutation nor PTMs on their own significantly alter the overall flexibility of residues within the HD domain, they cause notably greater deviations in the backbone structure of the HD domain compared to the WT. In addition, PTMs in the context of the mutation show reduced interactions between the mutation site and other protein regions, likely due to structural stabilization induced by the PTMs. Importantly, PTMs mitigate the structural disruption caused by the mutation, helping the mutant protein retain a WT-like conformation. Additionally, the HD domain contributes to maintaining PARP2 in its inactive state through its connection with the ART domain. However, the D235G mutation weakens this connection. While PTMs alone do not have a significant impact on this connection, the simultaneous presence of both the mutation and PTMs partially alleviates the disruptive effect of the mutation and leads to partial restoration of the connection between the HD and ART domains.

biophysics↗

bioRxiv2025

Fucoidans are senotherapeutics that enhance SIRT6-dependent DNA repair

Aging is marked by the accumulation of senescent cells (SnCs), which contribute to tissue dysfunction and age-related diseases. Senotherapeutics, including senolytics which specifically induce lysis of SnCs and senomorphics, which suppress the senescence phenotype, represent promising therapeutic interventions for mitigating age-related pathologies and extending healthspan. Using a phenotypic-based senescent cell screening assay, we identified fucoidans, a class of sulfated polysaccharides derived from brown algae and seaweed, as novel senotherapeutics. In particular, fucoidan from Fucus vesiculosus (Fucoidan-FV) displayed potent senomorphic activity in different types of SnCs, reduced senescence in multiple tissues in aged mice, and extended healthspan in a mouse model of accelerated aging. Fucoidan-FV also enhanced the deacetylation and mono-ADP-ribosylation (mADPr) activity of SIRT6 and improved DNA repair and reduced senescence, in part, through SIRT6-dependent pathways. In addition, Fucoidan-FV downregulated genes associated with inflammation, Wnt signaling, and ECM remodeling pathways in SnCs and increased expression of genes involved with DNA repair. These findings support the translational potential of fucoidans as novel senotherapeutics that also are able to improve SIRT6-mediated DNA repair.

cell biology↗

bioRxiv2024

Development of novel flavonoid senolytics through phenotypic drug screening and drug design

Accumulation of senescent cells drives aging and age-related diseases. Senolytics, which selectively kill senescent cells, offer a promising approach for treating many age-related diseases. Using a senescent cell-based phenotypic drug discovery approach that combines drug screening and drug design, we developed two novel flavonoid senolytics, SR29384 and SR31133, derived from the senolytic fisetin. These compounds demonstrated enhanced senolytic activities, effectively eliminating multiple senescent cell types, reducing tissue senescence in vivo, and extending healthspan in a mouse model of accelerated aging. Mechanistic studies utilizing RNA-Seq, machine learning, network pharmacology, and computational simulation suggest that these novel flavonoid senolytics target PARP1, BCL-xL, and CDK2 to induce selective senescent cell death. This phenotype-based discovery of novel flavonoid senolytics, coupled with mechanistic insights, represents a key advancement in developing next-generation senolyticss with potential clinical applications in treating aging and age-related diseases.

cell biology↗

bioRxiv2024

Identification of lipid senolytics targeting senescent cells through ferroptosis induction

Cellular senescence is a key driver of the aging process and contributes to tissue dysfunction and age-related pathologies. Senolytics have emerged as a promising therapeutic intervention to extend healthspan and treat age-related diseases. Through a senescent cell-based phenotypic drug screen, we identified a class of conjugated polyunsaturated fatty acids, specifically -eleostearic acid and its methyl ester derivative, as novel senolytics that effectively killed a broad range of senescent cells, reduced tissue senescence, and extended healthspan in mice. Importantly, these novel lipids induced senolysis through ferroptosis, rather than apoptosis or necrosis, by exploiting elevated iron, cytosolic PUFAs and ROS levels in senescent cells. Mechanistic studies and computational analyses further revealed their key targets in the ferroptosis pathway, ACSL4, LPCAT3, and ALOX15, important for lipid-induced senolysis. This new class of ferroptosis-inducing lipid senolytics provides a novel approach to slow aging and treat age-related disease, targeting senescent cells that are primed for ferroptosis.

cell biology↗

bioRxiv2024

Sex differences and behaviour in the pace-of-life of rodents

Male and female rodents experience different selective pressures associated with reproductive costs. Thus, we may expect the expression of different Pace-of-life (POL) strategies between sexes. Further, the pace-of-life syndrome (POLS) hypothesis and anisogamy predict differences in the costs of gamete production, where variation in life history trait expression should follow a fast-slow continuum such that males and females might exist on opposite ends of the spectrum. However, males and females could express a similar POL strategy in systems where the reproductive costs are consistent between sexes or where selective pressures force a similar directionality of traits. We used standardized behavioural tests and fecal glucocorticoid metabolite (FGM) concentrations to measure potential differences in POL strategies among three rodent species in Algonquin Provincial Park. We hypothesized that differences in reproductive costs between males and females would result in differences in POL traits along the fast-slow continuum. We predicted that males would express more explorative behaviours and have a higher level FGMs than female counterparts. We found little support for the POLS hypothesis between sexes. Instead, we suggest that the species observed may express a similar directionality of selection for the observed behavioural traits, where both sexes express similar relationships in POL. Thus, some male rodents may be more explorative to accommodate the increase of energetic stress associated with mate acquisition, while females may share similar trait expressions to accommodate the increased metabolic demand for the care and development of young. Significance statementDocility and exploration are measurements of how species or individuals react to novel and sometimes risky stimuli. Further, reproduction is an energetically expensive and inherently risky process. In seasonally breeding rodents, males often invest in fast pace-of-life behaviours that accommodate an increased necessity to disperse and find a mate. Meanwhile, females often invest in metabolically expensive physiological processes, including pregnancy and lactate development, increased protection of the young and the need for self-maintenance. Using a series of behavioural tests and fecal glucocorticoid metabolites (FGMs), we measured the relationship between metabolic stress, docility and exploration in three species of rodents during the breeding season. We observed consistent relationships in behaviour and FGMs, indicating uniformity between sexes regarding these behaviours. We posit that the costs associated with mate acquisition for males and the care and development of young for females can influence similar behavioural strategies.

ecology↗

bioRxiv2024

Exploratory and risk-taking behaviours in coexisting rodents

There has been an increasing interest in modelling the influence of animal personality on species interactions within ecosystems. Animal personality traits associated with dispersal, movement within a home range and risk-taking, including docility and exploration, have been shown to influence an array of environmental variables including seed dispersal and habitat availability. Despite growing interest however, little information is available to model the effects of differences in personality phenotypes among coexisting species. Since coexisting or sympatric species often compete for resources, differences in movement patterns can help mitigate the impact of intra- and interspecific competition. We used two standardized behavioural tests with three species of coexisting rodents in Algonquin Provincial Park, Ontario, Canada to measure exploration and docility personality phenotypes. To evaluate personalities, we modelled plastic changes in behaviours within species and phenotypic variation in behavioural strategies among species. We show empirical evidence to support differences in personality phenotypes in coexisting species and consider the importance of alternative personality strategies in shaping community dynamics.

ecology↗

bioRxiv2023

SenPred: A single-cell RNA sequencing-based machine learning pipeline to classify senescent cells for the detection of an in vivo senescent cell burden

Senescence classification is an acknowledged challenge within the field, as markers are cell-type and context dependent. Currently, multiple morphological and immunofluorescence markers are required for senescent cell identification. However, emerging scRNA-seq datasets have enabled increased understanding of the heterogeneity of senescence. Here we present SenPred, a machine-learning pipeline which can identify senescence based on single-cell transcriptomics. Using scRNA-seq of both 2D and 3D deeply senescent fibroblasts, the model predicts intra-experimental and inter-experimental fibroblast senescence to a high degree of accuracy (>99% true positives). We position this as a proof-of-concept study, with the goal of building a holistic model to detect multiple senescent subtypes. Importantly, utilising scRNA-seq datasets from deeply senescent fibroblasts grown in 3D refines our ML model leading to improved detection of senescent cells in vivo. This has allowed for detection of an in vivo senescent cell burden, which could have broader implications for the treatment of age-related morbidities.

cell biology↗

bioRxiv2023

Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis

The monocytic/macrophage system is essential for skeletal muscle homeostasis, but its dysregulation contributes to the pathogenesis of muscle degenerative disorders. Despite our increasing knowledge of the role of macrophages in degenerative disease, it still remains unclear how macrophages contribute to muscle fibrosis. Here, we used single-cell transcriptomics to determine the molecular attributes of dystrophic and healthy muscle macrophages. We identified six novel clusters. Unexpectedly, none corresponded to traditional definitions of M1 or M2 macrophage activation. Rather, the predominant macrophage signature in dystrophic muscle was characterized by high expression of fibrotic factors, galectin-3 and spp1. Spatial transcriptomics and computational inferences of intercellular communication indicated that spp1 regulates stromal progenitor and macrophage interactions during muscular dystrophy. Galectin-3+ macrophages were chronically activated in dystrophic muscle and adoptive transfer assays showed that the galectin-3+ phenotype was the dominant molecular program induced within the dystrophic milieu. Histological examination of human muscle biopsies revealed that galectin-3+ macrophages were also elevated in multiple myopathies. These studies advance our understanding of macrophages in muscular dystrophy by defining the transcriptional programs induced in muscle macrophages, and reveal spp1 as a major regulator of macrophage and stromal progenitor interactions.

immunology↗

bioRxiv2022

Comparative whole plastome and low copy number phylogenetics of the core Saccharinae and Sorghinae.

AO_SCPLOWBSTRACTC_SCPLOWDespite over 60 years worth of taxonomic efforts, the relationships between sugarcane (Saccharum hybrid cultivars), Sorghum and their closest evolutionary relatives remain largely unresolved. Even relationships between generally accepted genera such as Miscanthus and Saccharum have not been examined in any large-scale molecular detail. Genera such as Erianthus, Miscanthidium and Narenga pose even greater taxonomic contention. Erianthus is not monophyletic and Erianthus sect. Ripidium (Valdes and Scholz 2006, Lloyd Evans et al. 2019a; Welker et al. 2019) represents a distinct and separate genus, Tripidium Scholz. Miscanthidium is placed within Miscanthus by many workers, whilst the New World Erianthus species and Narenga are currently placed within Saccharum. As these species represent a significant portion of the gene pool that sugarcane breeders use for introgression into sugarcane, their taxonomic placement and relationships to Saccharum are of significant economic import. Erianthus species from the Americas have not been significantly employed in sugarcane breeding and may represent an untapped genetic resource. In an attempt to resolve the taxonomic relationships of these genera, we have assembled three novel chloroplasts, from Miscanthidium capense, Miscanthidium junceum and Narenga porphyrocoma (this latter assembled from transcriptomic and long read data). In parallel, five low copy number loci have been assembled from species within Saccharum, Miscanthus, Sarga and Sorghum. Phylogenetic analyses were performed using both low copy number genes and whole chloroplasts. The phylogenetic results were compared with karyotype data to circumscribe the genera most closely related to sugarcane. We reveal that genera Miscanthus and Saccharum are monophyletic and have never undergone polyploidization outside their own genera. Genera Erianthus, Miscanthidium and Narenga are allopolyploids, which excludes them from being members of Saccharum and Miscanthus. Moreover, all three of these genera have divergent evolutionary histories. We therefore support the use of the genera Miscanthus, Miscanthidium, Erianthus (for the New World Species) and Narenga for those species and genera most closely allied to Saccharum. Our data demonstrate that all these genera should be excluded from Saccharum sensu lato.

evolutionary biology↗

bioRxiv2021

Using mass Spectrometry to investigate fluorescent compounds in squirrel fur

While an array of taxa are capable of producing fluorescent pigments, fluorescence in mammals is a novel and poorly understood phenomenon. We believe that a first step towards understanding the potential adaptive functions of fluorescence in mammals is to develop an understanding of fluorescent compounds, or fluorophores, that are present in fluorescent tissue. Here we use Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) of flying squirrel fur known to fluoresce under ultraviolet (UV) light to identify potentially fluorescent compounds in squirrel fur. All of the potentially fluorescent compounds we identified were either present in non-fluorescent fur or were not present in all species of fluorescent flying squirrel. Therefore, we consider that the compounds responsible for fluorescence in flying squirrels may also be present in non-fluorescent mammal fur. Some factor currently unexplained likely leads to excitation of fluorophores in flying squirrel fur. A recently suggested hypothesis that fluorescence in mammals is widely caused by porphyrins is consistent with our findings.

ecology↗

bioRxiv2020

Complete Chloroplast Genomes of Saccharum giganteum, Saccharum longisetosum, Cleistachne sorghoides, Sarga timorense, Narenga porphyrocoma and Tripsacum dactyloides. Comparisons with ITS phylogeny and Placement within Saccharum.

The first complete chloroplast and Internal Transcribed Sequence (ITS) cassette sequences for the species: Saccharum giganteum, Saccharum longisetosum, Cleistachne sorghoides, Saccharum narenga and Tripsacum dactyloides are presented. Corresponding sequences for a new isolate of Sarga timorense were assembled. Phylogenetic analyses place S. giganteum, S. longisetosum and S. narenga within the Saccharinae but distinct from Saccharum, whilst C. sorghoides emerges as a member of genus Sarga and Tripsacum datyloides as a member of the Tripsacinae. Comparison of chloroplast and ITS phylogenies reveal complex reticulate evolution within the Saccharinae, with S. giganteum, S. longisetosum and S. narenga, despite having the same base chromosome count (15) having different evolutionary origins; making them members of different genera and not members of genus Saccharum. The importance of reticulate evolution in the origins of Andropogoneae, particularly the Saccharinae and the unique positions of Saccharum and Miscanthus is discussed.

evolutionary biology↗

bioRxiv2019

Investigating on-road lane maintenance and speed regulation in post-stroke driving: a pilot case-control study

The post-stroke population is expected to rise and the cohort of post-stroke individuals who wish to return to driving is likely to rapidly increase too. Stroke can adversely affect coordination and judgement of drivers due to the executive dysfunction, which is relatively common in the post-stroke population but often undetected. Quantitatively examining vehicle control performance in post-stroke driving becomes essential to inspect whether and where post-stroke drivers are risky. To date, it is unclear as to which indicators, such as lane keeping or speed control, can differentiate driving performance of post-stroke drivers from that of normal (neurotypical) older drivers. By employing a case-control design using advanced vehicle movement tracking and analysis technology, this pilot study aimed to compare the variations in driving trajectory, lane keeping and speed control between the two groups using spatial and statistical techniques. The results showed that the mean Standard Deviation of Lane Deviation (SDLD) in post-stroke participants was higher than those of normal participants in complex driving tasks (U-turn and left turn) but almost the same in simple driving tasks (straight-line sections). No statistically significant differences were found in the speed maintenance between the post-stroke drivers and the normal adults. The findings indicate that, although older drivers can still drive as they need to after a stroke, the decline in cognitive abilities still imposes higher cognitive workload and more effort for post-stroke older drivers. Future studies can investigate post-stroke adults driving behaviour at more challenging driving scenarios, or design driving intervention program to improve their executive function in driving.

scientific communication and education↗