Biology subjects

Frost, S.

Publications and source records attributed to Frost, S..

11 recordsLinked to original sources

bioRxiv2026

Simultaneous broad protection against Ebola Sudan, Marburg and Lassa viruses conferred by a DNA primed MVA-vectored multivalent vaccine

Sub-Saharan Africa continues to experience recurrent outbreaks of zoonotic viral diseases that spill over unpredictably from animal reservoirs into human populations. In many regions, mpox co-circulates with viral hemorrhagic fevers (VHFs) caused by Ebola Sudan virus (SUDV), Marburg virus (MARV), and Lassa fever virus (LASV). Overlapping clinical syndromes that these VHF cause challenge surveillance, diagnostics and timely deployment of effective countermeasures. A single vaccine capable of protecting against these biologically and genetically distinct pathogens would markedly reduce the cost and complexity of outbreak response, lessen dependence on emergency international aid, and strengthen long-term health system resilience. Here, we report on the development of an MVA-based mpox vaccine engineered to express computationally designed, broad-coverage antigens targeting SUDV, MARV and LASV. In preclinical challenge studies, this multivalent vaccine elicited robust immune responses and conferred significant protection against lethal infection from all three pathogens in parallel challenge experiments. These findings establish preclinical proof-of-concept for a single, broadly protective VHF vaccine and support its clinical development for deployment across diverse settings in Sub-Saharan Africa. SignificanceOutbreak control in Sub-Saharan Africa is challenged by the co-circulation of different high consequence human infections such as mpox and diverse viral hemorrhagic fevers (VHF) such as SUDV, MARV, and LASV pathogens. These VHFs have overlapping early clinical syndromes, complicating triage and delaying effective targeted interventions. We developed a single MVA-based vaccine encoding computationally designed, conserved antigens from all three VHFs encoded within the MVA vector analogous to the licensed mpox vaccine. In simultaneous challenge models, this multivalent vaccine elicited robust humoral and cellular responses and conferred significant protection against lethal infection by each hemorrhagic fever pathogen. This work provides preclinical proof-of-concept for a unified, broadly protective countermeasure compatible with existing MVA-mpox vaccine manufacturing and deployment experience. By reducing dependence on rapid differential diagnostics and streamlining logistics relative to maintaining multiple pathogen-specific vaccine stockpiles, this approach can lower costs, accelerate response, and increase equity of access during syndromic outbreaks. The platforms engineered antigen breadth and human safety profile of MVA together support a pragmatic translational pathway toward clinical evaluation and regional readiness for zoonotic spillover events that are intensifying with human and environmental changes.

immunology↗

bioRxiv2025

DNA methylation signatures of frailty beyond age: a longitudinal study of female and male mice

Frailty is an age-related geriatric syndrome with largely unknown mechanisms. We conducted a longitudinal study of aging C57BL/6JNIA mice (females; n = 40, male; n = 49), measured frailty index and derived DNA methylation data from PBMCs. We selected frailty-related differentially methylated CpGs and determined differentially methylated regions (DMRs), focusing on both age-independent and -dependent frailty, and using both mixed-sex and sex-stratified subgroups. We propose a joint set of 925 frailty-related DMRs, perform an association study with frailty outcomes, build epigenetic frailty clocks and validate in mice with interventions. Notably, age-independent frailty DMRs are enriched in nervous and endocrine pathways, distinct from signaling and lipid metabolism pathways identified from age-dependent DMRs. We observe hypermethylation in signaling pathways and hypomethylation in lipid metabolism and cytochrome P450 pathways with frailty progression. 36 DMRs show consistent associations in validation. These findings highlight distinct epigenetic signatures underlying frailty and aging, with potential sex-specific mechanisms.

molecular biology↗

bioRxiv2025

Immunogenicity and Efficacy of Digitally Immune Optimised H1N1 Vaccine Candidates in Swine and Murine Animal Models

Influenza A virus (IAV) zoonotic transmission and constant evolution in multiple species heightens the risk of emerging novel strains at the human-animal interface. Composite antigens including hemagglutinin (HA), neuraminidase (NA), and matrix-2 (M2) proteins were computationally designed to maximize the breadth of the immune response elicited to human seasonal, pandemic, and zoonotic H1N1 IAVs. Mouse hyperimmune serum raised against these antigens demonstrated broad H1 neutralization and N1 inhibition activity. To enhance immunogenicity, the antigens were combined as a single DNA expression construct (DVX-H1N1). Studies in the well-recognized swine model for human influenza demonstrated that DVX-H1N1 immunization induced broad, neutralizing antibody responses and markedly reduced nasal shedding of viral RNA following challenge with 1A.3.3.2 subclade strain A/swine/England/1353/2009 (H1N1). An effective immune response and reduction in virus shedding was observed in pigs immunized with a whole inactivated virus (WIV) vaccine homologous to the challenge strain but not with a human-origin seasonal WIV vaccine. Overall, we demonstrated broad immunogenicity and efficacy of the DVX-H1N1 vaccine candidate, benchmarked against relevant IAV H1N1 strains in vitro and in vivo in mice and pigs. IMPORTANCEThe zoonotic potential of swine-origin IAVs is a recognized global health threat. Vaccination remains the most effective intervention against influenza; protecting at the population level by preventing nasal shedding and transmission, but also in individuals by limiting clinical disease, particularly by reducing the severity of lung infection. The World Health Organization (WHO) spearheads biannual surveillance efforts to review evolving virus strains and vaccine antigens at Vaccine Candidate Meetings (VCM) to recommend strain updates for the human seasonal influenza vaccine and for pandemic preparedness purposes. However, the strain selection approach is complex and efficaciousness of seasonal influenza vaccines still varies significantly based on the accurate matching of the predicted strains in circulation with the manufactured vaccine antigens. This emphasizes the need for next-generation influenza vaccines that improve the breadth and longevity of immunity. We describe a computationally optimized DNA vaccine with broad immunogenicity and robust efficacy in the pig model.

immunology↗

bioRxiv2025

An epigenomic investigation of atrial fibrillation in a matched left and right atrial human cohort

As the most prevalent cardiac arrythmia, atrial fibrillation is an important contributor to cardiovascular morbidity and mortality. Human population findings increasingly support its complex genetic architecture, with most genetic association signals for atrial fibrillation found in the non-coding genome. In this study, we integrated genome-wide histone modification, gene expression and DNA methylation levels in a paired left and right atrial cohort comprising permanent atrial fibrillation patients and sinus rhythm controls. First, we first identified epigenomic regions enriched in histone H3 lysine 27 acetylation (H3K27ac) across left and right atria from patients and controls, and associated them with differentially expressed genes to derive a set of dysregulated candidate loci - including NPPB and SCX. Second, by incorporating an independent replication cohort, we were able to validate gene expression and epigenomic differences for a subset of these candidate loci. Third, we profiled base-resolution DNA methylation levels and identified differentially-methylated regions (DMRs) between atrial fibrillation and sinus rhythm samples. Integration of these data with histone modification levels and gene expression allowed us to propose epigenetic mechanisms underlying transcriptomic and epigenomic changes across dysregulated loci, such as disruption of transcription factor binding by DNA methylation at the LRRC4B locus. The data and analyses we report constitute a systematic investigation of gene regulatory alterations across the left and right atria in permanent atrial fibrillation.

genomics↗

bioRxiv2025

Mammalian epigenomic conservation of promoters and enhancers in the heart associates with trait-associated variation and impacts cardiomyocyte phenotypes

Interindividual genetic variation associated with cardiovascular traits and disease is commonly found in the non-coding genome, suggesting regulatory changes underlie many genetic association signals. Mammalian gene regulation is controlled by promoters and enhancers with rapidly divergent activities. However, the interplay between human non- coding genetic variation and regulatory evolution remains largely unexplored. Here, we investigated promoter and enhancer evolution in the mammalian heart using genome-wide epigenomic profiling, intersected these elements with genetic variants associated with cardiovascular traits, and experimentally tested candidate regions in human cardiomyocytes derived from pluripotent stem cells. First, we applied a comparative genomics approach to identify epigenomically-conserved promoters and enhancers in the heart, as well as elements with primate-specific or human-only epigenomic signals. Second, we evaluated the association of common genetic variation and signatures of cell-type specific gene regulation with mammalian epigenomic conservation. We report an enrichment of common genetic variants in epigenomically-conserved promoters and enhancers, which also associate with regulatory pleiotropy across cardiac cell types, and promoter-enhancer contacts in cardiomyocytes. Based on these findings, we selected candidate epigenomically-conserved elements across three cardiovascular genetics loci (KCNH2, CPEB4 and PRKCE), and investigated gene expression and cellular outcomes upon CRISPR/Cas9-mediated deletion of each region in human cardiomyocytes. These analyses inform how mammalian epigenomic conservation associates with specific gene expression contributions and downstream cellular responses, such as cardiomyocyte hypertrophy and sensitivity to hypoxia/reoxygenation. Moreover, the comparative analyses we present here contribute to ongoing efforts to prioritise and functionally characterise cardiovascular association signals from human population genetics.

genomics↗

bioRxiv2023

Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits

Changes in gene regulation have long been thought to underlie most phenotypic differences between species. Subterranean rodents, and in particular the naked mole-rat, have attracted substantial attention due to their proposed phenotypic adaptations, which include hypoxia tolerance, metabolic changes and cancer resistance. However, it is largely unknown what regulatory changes may associate with these phenotypic traits, and whether these are unique to the naked mole-rat, the mole-rat clade or also present in other mammals. Here, we investigate regulatory evolution in heart and liver from two African mole-rat species and two rodent outgroups using genome-wide epigenomic profiling. First, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous regulatory elements, and identified thousands of promoter and enhancer regions with differential epigenomic activity in mole-rats. These elements associate with known mole-rat adaptation in metabolic and functional pathways, and suggest candidate genetic loci that may underlie mole-rat innovations. Second, we evaluated ancestral and species-specific regulatory changes in the study phylogeny, and report several candidate pathways experiencing stepwise remodeling during the evolution of mole-rats - such as the insulin and hypoxia response pathways. Third, we report non-orthologous regulatory elements overlap with lineage-specific repetitive elements and appear to modify metabolic pathways by rewiring of HNF4 and RAR/RXR transcription factor binding sites in mole-rats. These comparative analyses reveal how mole-rat regulatory evolution informs previously reported phenotypic adaptations. Moreover, the phylogenetic modeling framework we propose here improves upon the state-of-the-art by addressing known limitations of inter-species comparisons of epigenomic profiles, and has broad implications in the field of comparative functional genomics.

genomics↗

bioRxiv2022

Bat pluripotent stem cells reveal unique entanglement between host and viruses

Bats have evolved features unique amongst mammals, including flight, laryngeal echolocation, and certain species have been shown to have a unique immune response that may enable them to tolerate viruses such as SARS-CoVs, MERS-CoVs, Nipah, and Marburg viruses. Robust cellular models have yet to be developed for bats, hindering our ability to further understand their special biology and handling of viral pathogens. To establish bats as new model study species, we generated induced pluripotent stem cells (iPSCs) from a wild greater horseshoe bat (Rhinolophus ferrumequinum) using a modified Yamanaka protocol. Rhinolophids are amongst the longest living bat species and are asymptomatic carriers of coronaviruses, including one of the viruses most closely related to SARS-CoV-2. Bat induced pluripotent stem (BiPS) cells were stable in culture, readily differentiated into all three germ layers, and formed complex embryoid bodies, including organoids. The BiPS cells were found to have a core pluripotency gene expression program similar to that of other species, but it also resembled that of cells attacked by viruses. The BiPS cells produced a rich set of diverse endogenized viral sequences and in particular retroviruses. We further validated our protocol by developing iPS cells from an evolutionary distant bat species Myotis myotis (greater mouse-eared bat) non-lethally sampled in the wild, which exhibited similar attributes to the greater horseshoe bat iPS cells, suggesting that this unique pluripotent state evolved in the ancestral bat lineage. Although previous studies have suggested that bats have developed powerful strategies to tame their inflammatory response, our results argue that they have also evolved mechanisms to accommodate a substantial load of endogenous viral sequences and suggest that the natural history of bats and viruses is more profoundly intertwined than previously thought. Further study of bat iPS cells and their differentiated progeny should advance our understanding of the role bats play as virus hosts, provide a novel method of disease surveillance, and enable the functional studies required to ascertain the molecular basis of bats unique traits.

developmental biology↗

bioRxiv2022

Genetic perturbation of MAPK11 (p38β) promotes radiosensitivity by enhancing IR-associated senescence.

Background and purposeMAPKs are among the most relevant signalling pathways involved in coordinating cell responses to different stimuli. This group includes p38MAPKs, constituted by 4 different proteins with a high sequence homology: MAPK14 (p38), MAPK11 (p38{beta}), MAPK12 (p38{gamma}) and MAPK13 (p38{delta}). Despite their high similarity, each member shows unique expression patterns and even exclusive functions. Thus, analysing protein-specific functions of MAPK members is necessary to unequivocally uncover the roles of this signalling pathway. Here, we investigate the possible role of MAPK11 in the cell response to ionizing radiation (IR). Materials and methodsWe developed MAPK11/14 knockdown through shRNA and CRISPR interference gene perturbation approaches, and analysed the downstream effects on cell responses to ionizing radiation in A549, HCT-116 and MCF-7 cancer cell lines. Specifically, we assessed IR toxicity by clonogenic assays; DNA damage response activity by immunocytochemistry; apoptosis and cell cycle by flow cytometry (Annexin V and propidium iodide, respectively); DNA repair by comet assay; and senescence induction by both X-Gal staining and gene expression of senescence-associated genes by RT-qPCR. ResultsOur findings demonstrate a critical role of MAPK11 in the cellular response to IR by controlling the associated senescent phenotype, and without observable effects on DDR, apoptosis, cell cycle or DNA damage repair. ConclusionOur results highlight MAPK11 as a novel mediator of the cellular response to ionising radiation through the control exerted onto IR-associated senescence. HighlightsO_LIGenetic perturbation of MAPK11, but not MAPK14, promotes radiosensitivity in a panel of tumor cell lines. C_LIO_LIAbrogation of MAPK11 did not modify DNA damage response, proliferation, apoptosis or cell cycle in response to ionizing radiation C_LIO_LIMAPK11 controls ionizing radiation-induced senescence C_LIO_LIMAPK11 expression could be a novel target and biomarker for radiosensitivity C_LI

cancer biology↗

bioRxiv2020

The impact of second language immersion: Evidence from a bi-directional longitudinal cross-linguistic study

Brice et al. (2019) presented data from the first epoch of a longitudinal study of the neurobiological underpinnings of first-language (L1) and second-language (L2) processing. Results showed a similar network of activation for reading across L1 and L2, as well as significant convergence of print and speech processing across a network of left-hemisphere regions in both L1 and L2 with greater activation and convergence for L2 in anterior regions, and greater activation and convergence for L1 in posterior regions of the reading network. Here, we present the first look at longitudinal changes in these effects. L2 showed relatively few changes in activation, with some shifts in the weighting between ventral and dorsal processing. L1, however, showed more widespread differences in processing, suggesting that the neurobiological footprint of reading is dynamic, with both L1 and L2 impacting each other. Print/speech convergence showed very little longitudinal change, suggesting that it is a stable marker of the differences in L1 and L2 processing.

neuroscience↗

bioRxiv2019

Identification of hidden population structure in time-scaled phylogenies

Population structure influences genealogical patterns, however data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealised genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partial pol sequences. This revealed the presence of clades which had grown rapidly in the recent past, and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genome Neisseria gonorrhoeae sequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance.

evolutionary biology↗

bioRxiv2016

Biased phylodynamic inferences from analysing clusters of viral sequences

Phylogenetic methods are being increasingly used to help understand the transmission dynamics of measurably evolving viruses, including HIV. Clusters of highly similar sequences are often observed, which appear to follow a power law behaviour, with a small number of very large clusters. These clusters may help to identify subpopulations in an epidemic, and inform where intervention strategies should be implemented. However, clustering of samples does not necessarily imply the presence of a subpopulation with high transmission rates, as groups of closely related viruses can also occur due to non-epidemiological effects such as over-sampling. It is important to ensure that observed phylogenetic clustering reflects true heterogeneity in the transmitting population, and is not being driven by non-epidemiological effects.\n\nWe quantify the effect of using a falsely identified transmission cluster of sequences to estimate phylodynamic parameters including the effective population size and exponential growth rate. Our simulation studies show that taking the maximum size cluster to re-estimate parameters from trees simulated under a randomly mixing, constant population size coalescent process systematically underestimates the overall effective population size. In addition, the transmission cluster wrongly resembles an exponential or logistic growth model 95% of the time. We also illustrate the consequences of false clusters in exponentially growing coalescent and birth-death trees, where again, the growth rate is skewed upwards. This has clear implications for identifying clusters in large viral databases, where a false cluster could result in wasted intervention resources.

genetics↗