Biology subjects

Barnes, C.

Publications and source records attributed to Barnes, C..

14 recordsLinked to original sources

bioRxiv2026

Biomarker-driven and gene-enhanced viral therapy for malignant peripheral nerve sheath tumor

Background: High-grade malignant peripheral nerve sheath tumors (MPNST) frequently lose Polycomb Repressive Complex 2 (PRC2), reducing the repressive histone mark, H3K27me3. We hypothesized that H3K27me3 loss sensitizes MPNST to oncolytic HSV due to impaired transcriptional resistance. HSV replication is also restricted by the integrated stress response, normally countered by HSV ICP34.5, representing an additional resistance pathway to ICP34.5-attenuated HSV. Methods: PRC2 loss-of-function was evaluated as a biomarker of HSV G47{Delta} ({Delta}ICP34.5) susceptibility in MPNST using isogenic, pharmacologic inhibition, and genetic rescue models. CUT&RUN and RNA-sequencing defined PRC2-dependent viral and host responses. We engineered a G47{Delta}-derived vector (G47{Delta}2) with tumor-regulated ICP34.5 expression [G47{Delta}2,ins(BIRC5>ICP34.5)] and evaluated efficacy in MPNST xenografts. Results: H3K27me3 deficiency increased G47{Delta} sensitivity and viral spread in vitro. CUT&RUN demonstrated PRC2-dependent H3K27me3 accumulation on the viral genome, explaining G47{Delta} activity in H3K27me3-deficient MPNST. RNA sequencing of G47{Delta} infected MPNST cells revealed heightened integrated stress response activity and blunted induction of translation-associated programs in the PRC2-deficient state (both p<0.001), consistent with compensatory resistance at the level of viral protein translation. Accordingly, tumor-regulated ICP34.5 HSV limited daily tumor-volume growth to 0.6% (95% CI, -2.9-4.2%), improving upon both G47{Delta}2 (8.3%; 4.5-12.2%) and controls (22.5%; 17.4-27.8%). A murine gastrointestinal toxicity phenotype reduced all-cause event-free survival, indicating vector and dosing optimizations are needed to widen the therapeutic window. Conclusions: H3K27me3 loss creates a paradoxical antiviral state that tumor-selective ICP34.5 overcomes to rescue HSV anti-tumor activity, supporting biomarker-driven viral engineering to exploit the permissive transcriptional state of H3K27me3-deficient MPNSTs.

cancer biology↗

bioRxiv2026

Trypanosoma brucei infection remodels the uterine immune environment and drives neuroendocrine dysfunction

Human African Trypanosomiasis (HAT) or sleeping sickness is a systemic parasitic infection caused by the protozoan parasite Trypanosoma brucei. HAT is associated with substantial immunological, metabolic, and neurological pathology. Although reproductive dysfunction has previously been recognised in both human and experimental T. brucei infection, whether parasites can directly infiltrate the female reproductive tract (FRT), and how infection may reshape the FRT immune landscape remains poorly understood. Using a murine model of T. brucei infection we reveal that parasites are localised in the uterine lining (endometrium) during both acute and chronic infection stages in mice. Chronic T. brucei infection was associated with progressive fat wasting, disruption of the reproductive (oestrous) cycle, uterine and ovarian atrophy, and extensive transcriptional dysregulation across the hypothalamic-pituitary-gonadal (HPG) axis. Acute and chronic infection induced remodelling of the uterine immune landscape, characterised by T cell infiltration, pro-inflammatory myeloid activation, alongside broader type 1 inflammatory changes across reproductive tissues and HPG components. Ovarian pathology was accompanied by follicular degeneration, a reduction in corpora lutea and alterations to steroidogenic pathways. Hormonal rescue with selective oestrogen receptor modulator, tamoxifen, restored uterine morphology and prevented oestrous cycle arrest, but did not reverse the infection-induced uterine immune remodelling, indicating that endocrine dysfunction and infection-driven inflammation are distinct processes. Taken together, these findings identify the FRT as a major target of T. brucei infection and demonstrate how chronic parasitic infection can disrupt reproductive physiology through a combination of immune, endocrine, and metabolic pathways. They also highlight the need to specifically assess the FRT in other models of systemic inflammation. Author summaryHuman and animal African trypanosomiasis, also known as sleeping sickness and nagana, are caused by the parasite, Trypanosoma brucei. These chronic infections are associated with immune changes across the body as well as changes to metabolism and neurology. In both humans and animals, infection has been linked to poor reproductive outcomes, including miscarriage, foetal growth restriction and menstrual irregularities. However, whether T. brucei can infiltrate into the uterus of infected mice and whether this presence can alter the local immune cell dynamics remains poorly understood. Using an animal model of acute and chronic T. brucei infection, we were able to detect the parasites within the uterus of infected female mice. In addition, we found that the immune cell profile from the uterus of infected females was more pro-inflammatory during T. brucei infection. During chronic infection, we found that animals showed progressive fat wastage, disruption of reproductive cycling, and marked uterine and ovarian shrinkage. When we administered an oestrogen-like compound, we found that uterine and ovarian size changes were hormone-dependent but the immune changes in the uterus were hormone-independent.

immunology↗

bioRxiv2026

Adaptive metabolic reprogramming of the brain tissue during late-stage Trypanosoma brucei infection maintains host learning and memory

Human African Trypanosomiasis (HAT) is a two-stage infection caused by Trypanosoma brucei ssp. In stage I the trypanosomes are in blood, lymph and tissue interstitial space and the infection progresses to stage II when the parasites enter the central nervous system (CNS), resulting in behavioural aberrations that proceed to coma and death. Here, we use a bioluminescent murine model of HAT to examine parasite localisation and the changes in host brain gene expression, metabolism and function, and behaviour that occur over the course of the infection. The murine HAT model reproduces the decrease in brain tryptophan seen in clinical samples, and we report for the first time an unprecedented 1.8-fold decrease in global brain glucose metabolism in stage II infection. These metabolic changes are accompanied by an 18-fold decrease in brain insulin transcripts without changes in pathways regulating the cellular responses to insulin. By contrast, genes involved in fatty acid and lipid metabolism are upregulated in the brain during stage II infection. Moreover, we show that transcriptional programmes regulating mitochondrial metabolism dynamically adapts across the time course of HAT infection, ultimately leading to a transcriptional programme that diverts host brain metabolism away from glycolysis during stage II infection. Overall, our data demonstrate a reprogramming of brain energy metabolism during stage II HAT infection that favours the utilization of fatty acids and lipids to meet the energy demands of the brain, with a reduced reliance on glucose metabolism. Despite the profound neurometabolic changes observed, host anxiety-like behaviour is unchanged and episodic learning and memory is not impaired, suggesting that brain metabolic reprogramming enables the utilisation of adipose reserves to maintain core brain functions. These finding may explain the progressive onset of neurological symptoms in HAT patients and inform the development therapeutic interventions to alleviate them. Author SummaryHuman African Trypanosomiasis is classically characterised as being a two-stage infection, stage I where the extracellular Trypanosoma brucei multiply in the blood, lymph and peripheral tissues, and stage II where parasite cross the blood-brain barrier (BBB) causing neurological symptoms and eventually death. Using a murine model of HAT we show that in stage II the key brain metabolite tryptophan is depleted and cerebral glucose utilisation is decreased, accompanied by extensive metabolic transcriptome reprogramming of the cerebral tissue during stage II infection. Despite this we see no significant change in mouse anxiety-like behaviour or learning and memory. Our data are consistent with the brain switching from glucose as the primary energy source, instead utilising the products of lipolysis to maintain essential brain functions. This new understanding of the neurometabolic changes that occur in stage II HAT may help to develop new treatments for the neurological symptoms that affect patients at this stage of the disease.

immunology↗

bioRxiv2026

Spatiotemporally dynamic noradrenergic regulation of cortical networks

Brain activity and cognition exhibit state-dependent fluctuations that may reflect the influence of neuromodulatory systems, including norepinephrine (NE). Although the activity of noradrenergic neurons is strongly coupled to sleep-wake cycles and pupil dynamics, suggesting a global arousal signal, recent evidence suggests potentially modular partitioning of these cells. In addition, it is unclear whether different neuromodulatory signals exhibit distinct spatiotemporal patterns. We performed simultaneous, dual color mesoscopic imaging of either NE and calcium or NE and acetylcholine (ACh) signals across the neocortex, along with high-density electrophysiology, to investigate the relationship between NE release and neural activity. We find that the pattern of cortical NE signaling varies with behavioral state and is associated with enhanced functional connectivity. Simultaneous imaging of NE and ACh reveals spatiotemporally dynamic coupling between signals. Finally, NE signaling and functional connectivity are disrupted by sleep deprivation. Overall, our findings demonstrate that NE provides a multimodal signal that links transitions in behavioral state to cortical network interactions.

neuroscience↗

bioRxiv2026

Dynamic control of Raf-ERK signaling modulates neuronal activity across biological scales

Neuronal activity robustly engages the extracellular signal-regulated kinase (ERK) signaling pathway through Ca2+-dependent mechanisms; however, whether ERK can acutely and causally modulates ongoing neuronal activity remains unsolved due to complex upstream regulation and diverse subcellular functions. Here, we directly address this question using an optogenetic ERK activator, opto-miniRaf, that enables selective, rapid, graded, and reversible control of ERK signaling. Combining this AAV-compatible system with calcium imaging and electrophysiology, we interrogate ERK functions across biological scales, from cultured neurons, acute brain slices, and the intact brain. Acute optogenetic activation of ERK enhances synchronized network burst activity in cultured rat cortical neurons and increases calcium activity of cortical pyramidal neurons in awake and moving mice following non-invasive light stimulation. Together, these results establish ERK signaling as an acute modulator of neuronal and network activity, positioning opto-miniRaf as a generalizable platform for precise spatiotemporal control of intracellular kinase signaling in complex biological systems.

neuroscience↗

bioRxiv2024

The genomic trajectory of ovarian high grade serous carcinoma is determined in STIC lesions

Ovarian high-grade serous carcinoma (HGSC) originates in the fallopian tube, with secretory cells carrying a TP53 mutation, known as p53 signatures, identified as potential precursors. p53 signatures evolve into serous tubal intraepithelial carcinomas (STIC) lesions, which, in turn, progress into invasive HGSC that readily spread to the ovary and disseminate around the peritoneal cavity. We recently investigated the genomic landscape of early- and late-stage HGSC and found higher ploidy in late-stage (median 3.1) than early-stage (median 2.0) samples. Here, to explore whether the high ploidy and possible whole genome duplication observed in late-stage disease are determined early in the evolution of HGSC, we analysed archival formalin-fixed paraffin-embedded samples (FFPE) from five HGSC patients. p53 signatures and STIC lesions were laser-capture microdissected and sequenced using shallow whole genome sequencing (sWGS), while invasive ovarian/fallopian tube and metastatic carcinoma samples underwent macrodissection and were profiled using both sWGS and targeted next generation sequencing. Results showed highly similar patterns of global copy number change between STIC lesions and invasive carcinoma samples within each patient. Ploidy changes were evident in STIC lesions, but not p53 signatures, and there was strong correlation between ploidy in STIC lesions and invasive ovarian/fallopian tube and metastatic samples in each patient. The reconstruction of sample phylogeny for each patient from relative copy number indicated that high ploidy, when present, occurred early in the evolution of HGSC, which was further validated by copy number signatures in ovarian and metastatic tumours. These findings suggest that aberrant ploidy, suggestive of whole genome duplication, arises early in HGSC, and is detected in STIC lesions, implying that the trajectory of HGSC may be determined at the earliest stages of tumour development.

cancer biology↗

bioRxiv2023

Negative feedback control of hunger circuits by the taste of food

The rewarding taste of food is critical for motivating animals to eat, but whether taste has a parallel function in promoting meal termination is not well understood. Here we show that hunger-promoting AgRP neurons are rapidly inhibited during each bout of ingestion by a signal linked to the taste of food. Blocking these transient dips in activity via closed-loop optogenetic stimulation increases food intake by selectively delaying the onset of satiety. We show that upstream leptin receptor-expressing neurons in the dorsomedial hypothalamus (DMHLepR) are tuned to respond to sweet or fatty tastes and exhibit time-locked activation during feeding that is the mirror image of downstream AgRP cells. These findings reveal an unexpected role for taste in the negative feedback control of ingestion. They also reveal a mechanism by which AgRP neurons, which are the primary cells that drive hunger, are able to influence the moment-by-moment dynamics of food consumption.

neuroscience↗

bioRxiv2023

VIP interneurons regulate cortical size tuning and visual perception

Local cortical circuit function is regulated by diverse populations of GABAergic interneurons with distinct properties and extensive interconnectivity. Inhibitory-to-inhibitory interactions between interneuron populations may play key roles in shaping circuit operation according to behavioral context. A specialized population of GABAergic interneurons that co-express vasoactive intestinal peptide (VIP-INs) are activated during arousal and locomotion and innervate other local interneurons and pyramidal neurons. Although modulation of VIP-IN activity by behavioral state has been extensively studied, their role in regulating information processing and selectivity is less well understood. Using a combination of cellular imaging, short and long-term manipulation, and perceptual behavior, we examined the impact of VIP-INs on their synaptic target populations in the primary visual cortex of awake behaving mice. We find that loss of VIP-IN activity alters the behavioral state-dependent modulation of somatostatin-expressing interneurons (SST-INs) but not pyramidal neurons (PNs). In contrast, reduced VIP-IN activity disrupts visual feature selectivity for stimulus size in both populations. Inhibitory-to inhibitory interactions thus directly shape the selectivity of GABAergic interneurons for sensory stimuli. Moreover, the impact of VIP-IN activity on perceptual behavior varies with visual context and is more acute for small than large visual cues. VIP-INs thus contribute to both state-dependent modulation of cortical circuit activity and sensory context-dependent perceptual performance.

neuroscience↗

bioRxiv2022

Museomic approaches to genotype historic Cinchona barks

Over the last few centuries, millions of plant specimens have been collected and stored within herbaria and biocultural collections. They therefore represent a considerable resource for a broad range of scientific uses. However, collections degrade over time, and it is therefore increasingly difficult to characterise their genetic signatures. Here, we genotyped highly degraded Cinchona barks and leaves from herbaria using two separate high-throughput sequencing methods (HtS) and compared their performance. We subsequently genotyped specimens using genome skimming, the most commonly performed high-throughput sequencing (HtS) technique. We additionally used a recently developed capture bait set (Angiosperm353) for a target enrichment approach. Specifically, phylogenomic analyses of modern leaf and historical barks of Cinchona were performed, including 23 historical barks and six fresh leaf specimens. We found that samples degraded over time, which directly reduced the quantity and quality of the data produced by both methodologies (in terms of reads mapped to the references). However, we found that both approaches generated enough data to infer phylogenetic relationships, even between highly degraded specimens that are over 230 years old. However, the target capture kit produced data for target nuclear loci and also chloroplast data, which allowed for phylogenies to be inferred from both genomes, whereas it was only possible to use chloroplast data using genome skimming. We therefore find the Angiosperms353 target capture kit a powerful alternative to genome skimming, which can be used to obtain more information from herbarium specimens, and ultimately additional cultural benefits.

genomics↗

bioRxiv2022

Building a novel nuclear-organelle genomic framework for the fever tree (Cinchona pubescens Vahl) through short and long-read DNA data assemblies

BackgroundThe Andean Fever tree (Cinchona L.; Rubiaceae) is the iconic source of bioactive quinine alkaloids, which have been vital to treating malaria for centuries. C. pubescens Vahl, in particular, has been an essential source of income for several countries within its native range in north-western South America. However, an absence of available genomic resources is essential for placing the Cinchona species within the tree of life and setting the foundation for exploring the evolution and biosynthesis of quinine alkaloids. FindingsWe address this gap by providing the first highly contiguous and annotated nuclear and organelle genome assemblies for C. pubescens. Using a combination of [~]120 Gb of long sequencing reads derived from the Oxford Nanopore PromethION platform and 142 Gb of short-read Illumina data. Our nuclear genome assembly comprises 603 scaffolds comprising a total length of 904 Mb, and the completeness represents [~]85% of the genome size (1.1 Gb/1C). This draft genome sequence was complemented by annotating 72,305 CDSs using a combination of de novo and reference-based transcriptome assemblies. Completeness analysis revealed that our assembly is moderately complete, displaying 83% of the BUSCO gene set and a small fraction of genes (4.6%) classified as fragmented. Additionally, we report C. pubescens plastome with a length of [~]157 Kb and a GC content of 37.74%. We demonstrate the utility of these novel genomic resources by placing C. pubescens in the Gentianales order using additional plastid and nuclear datasets. ConclusionsOur study provides the first genomic resource for C. pubescens, thus opening new research avenues, including the provision of crucial genetic resources for analysis of alkaloid biosynthesis in the Fever tree.

bioinformatics↗

bioRxiv2021

Assessment of the evolutionary consequence of putative driver mutations in colorectal cancer with spatial multiomic data

Cancer genomic medicine relies on targeting driver genes. However, current catalogues of cancer drivers are mostly based on indirect measurements of mutation frequencies, positions or types, rather than their effect on clonal expansions in vivo. Moreover, non-genetic drivers are largely unknown, as are the epigenetic and transcriptomic effects of genetic drivers. Here we perform spatial computational inference on multiomic data with matched whole-genome sequencing, ATAC-seq and RNA-seq. Using 436 samples, we directly quantify the contribution, or lack thereof, of putative driver genes to subclonal expansions in vivo in 30 colorectal carcinomas (4-33 samples per patient, median=15). Although subclonal neutral evolution was widespread (13/26 cases with sufficient data), there were cases with clear evidence of subclonal selection (6/26) in which we measured epigenetic and transcriptomic differences between subclones in vivo. In 7/26 cases we could not distinguish between neutral or selective evolution with the available data. We identified expanding subclones that were not driven by known genetic alterations, and propose candidate epigenetic drivers. We identified the distinguishing patterns of genomic heterogeneity produced in fast, exponentially growing tumours (7/26) versus neoplasms growing only at the periphery (19/26), as well as identifying clonally intermixed (16/28 cases with sufficient data) versus segregated malignancies (10/28). Our model-based approach measures genetic and non-genetic subclonal selection, or lack thereof, in space and time and allows in vivo comparisons of the emergent phenotypic properties of subclones within human tumours.

cancer biology↗

bioRxiv2021

Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies

Antibodies elicited in response to infection undergo somatic mutation in germinal centers that can result in higher affinity for the cognate antigen. To determine the effects of somatic mutation on the properties of SARS-CoV-2 spike receptor-binding domain (RBD)-specific antibodies, we analyzed six independent antibody lineages. As well as increased neutralization potency, antibody evolution changed pathways for acquisition of resistance and, in some cases, restricted the range of neutralization escape options. For some antibodies, maturation apparently imposed a requirement for multiple spike mutations to enable escape. For certain antibody lineages, maturation enabled neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.

microbiology↗

bioRxiv2020

Convergent Antibody Responses to SARS-CoV-2 Infection in Convalescent Individuals

During the COVID-19 pandemic, SARS-CoV-2 infected millions of people and claimed hundreds of thousands of lives. Virus entry into cells depends on the receptor binding domain (RBD) of the SARS-CoV-2 spike protein (S). Although there is no vaccine, it is likely that antibodies will be essential for protection. However, little is known about the human antibody response to SARS-CoV-21-5. Here we report on 149 COVID-19 convalescent individuals. Plasmas collected an average of 39 days after the onset of symptoms had variable half-maximal neutralizing titers ranging from undetectable in 33% to below 1:1000 in 79%, while only 1% showed titers >1:5000. Antibody cloning revealed expanded clones of RBD-specific memory B cells expressing closely related antibodies in different individuals. Despite low plasma titers, antibodies to three distinct epitopes on RBD neutralized at half-maximal inhibitory concentrations (IC50s) as low as single digit ng/mL. Thus, most convalescent plasmas obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.

immunology↗

bioRxiv2016

Quantification of subclonal selection in cancer from bulk sequencing data

Recent studies have identified prevalent subclonal architectures within many cancer types. However, the temporal evolutionary dynamics that produce these subclonal architectures remain unknown. Here we measure evolutionary dynamics in primary human cancers using computational modelling of clonal selection applied to high throughput sequencing data. Our approach simultaneously determines the subclonal architecture of a tumour sample, and measures the mutation rate, the selective advantage, and the time of appearance of subclones. Simulations demonstrate the accuracy of the method, and revealed the degree to which evolutionary dynamics are recorded in the genome. Application of our method to high-depth sequencing data from gastric and lung cancers revealed that detectable subclones consistently emerged early during tumour growth and had considerably large fitness advantages (>20% growth advantage). Our quantitative platform provides new insight into the evolutionary history of cancers by facilitating the measurement of fundamental evolutionary parameters in individual patients.

cancer biology↗