Biology subjects

Fisher, K.

Publications and source records attributed to Fisher, K..

14 recordsLinked to original sources

bioRxiv2026

Nutrient-responsive and DAF-16/FoxO target H1 histone HIL-1 promotes resistance to starvation and bacterial pathogens in Caenorhabditis elegans

Insulin/IGF-1 signaling (IIS) mediates metabolic and developmental acclimation to stressful conditions including starvation. The transcription factor DAF-16/FoxO actuates many of the physiological effects of reduced IIS, yet the specific contributions of DAF-16 target genes to stress resistance remain poorly understood. We explore the function of C. elegans H1 linker histone HIL-1/H1.0, a DAF-16 target that is upregulated during starvation. The HIL-1 sequence is divergent from the other eight annotated C. elegans H1 variants, and the others are not so highly responsive to nutrient availability and DAF-16 activity, suggesting distinct function. Using knock-in reporters, we find that HIL-1 is broadly expressed in nuclei of L1 and dauer larvae during starvation, but that expression is largely undetectable in fed larvae. Disrupting hil-1 activity through mutation or auxin-inducible degradation led to reduced growth after extended L1 starvation, revealing reduced starvation resistance. RNA-seq of hil-1 mutants suggested that HIL-1 activates genes involved in the innate immune response, and hil-1 mutants display compromised survival upon exposure to Pseudomonas aeruginosa under reduced IIS. Together these results suggest that DAF-16/FoxO activates transcription of hil-1 during starvation to promote resistance to starvation and pathogens. We demonstrate conditional regulation of an H1 histone, and we reveal a novel mechanism for how IIS promotes stress resistance by identifying a histone variant that connects nutrient sensing to immunity. ARTICLE SUMMARYH1 histones promote condensation of chromatin. Like many other organisms, the roundworm Caenorhabditis elegans has several H1 histones, but their regulation and function is unclear. We were intrigued by hil-1/H1.0 because it is dramatically up-regulated during starvation in daf-16/FoxO-dependent fashion. Insulin/IGF signaling regulates DAF-16, and DAF-16 is critical to starvation resistance. We used genome editing to create alleles to interrogate hil-1 expression and function. We show HIL-1 is expressed throughout the animal during starvation, it activates expression of immunity genes, and it promotes resistance to starvation and a bacterial pathogen. This work demonstrates a connection between nutrient sensing and immunity.

genetics↗

bioRxiv2026

KIF18A Maintains Kinetochore-Microtubule Attachments in CIN Cells by Limiting Microtubule Polymerization

Chromosomal instability (CIN) generates vulnerabilities that can be therapeutically exploited, including sensitivity to inhibition of the kinesin motor KIF18A. However, the mechanistic basis for why a subset of CIN tumor cells depend on KIF18A remains unclear. Here, we compare mitotic phenotypes across KIF18A-sensitive and -insensitive cell models. In sensitive CIN cells, KIF18A inhibition leads to formation of polar chromosomes with unattached kinetochores, recruitment of spindle assembly checkpoint proteins, and prolonged mitotic arrest. Although KIF18A loss reduces kinetochore-microtubule stability in all cell lines, sensitive cells exhibit lower baseline attachment stability and heightened microtubule polymerization rates, predisposing them to attachment failure. Acute KIF18A inhibition disrupts maintenance of attachments after metaphase alignment, while reducing microtubule polymerization suppresses mitotic defects. These findings support a model in which CIN tumor cells rely on KIF18A to restrain excessive microtubule dynamics and maintain attachment.

cancer biology↗

bioRxiv2026

Lipid-rich ascites reprograms T cell lipid metabolic transcriptome to drive dysfunction

PurposeBispecific T cell engagers (BiTEs) have recently been approved as a locoregional immunotherapy for malignant ascites. Although ascites is recognised as a lipid-rich, immunosuppressive environment, the mechanisms by which ascites, particularly its lipid components, suppress antitumour immunity remain poorly understood. Here, we investigated the impact of ascites-associated lipids on T cell immunosuppression and assessed whether lipid modulation could enhance the efficacy of BiTE therapy. Experimental DesignTranscriptomic profiling was performed on T cells treated with acellular ascites fluid to identify gene expression signatures associated with ascites exposure. Functional assays were conducted to evaluate the effects of ascites-associated lipids on T cell activation and cytotoxicity. In parallel, T cells were cocultured with ovarian cancer cells and EpCAM-targeting BiTEs in the presence or absence of a lipid-removal agent to assess how lipid depletion affected BiTE efficacy. ResultsT cells exposed to acellular ascites fluid exhibited an enriched transcriptomic signature associated with cholesterol efflux and incomplete fatty acid oxidation, which are metabolic features often found in exhausted T cells. These alterations converged on a metabolically imbalanced state linked to impaired plasma membrane signalling. Lipid removal from ascites selectively rescued CD137 expression but not CD25, and restored BiTE-mediated cytotoxicity, suggesting a differential impact of lipid metabolism on TCR complex-dependent versus cytokine-driven activation pathways. ConclusionsThese findings identified lipid as a driver for T cell dysfunction in ovarian cancer ascites. Removal of ascites lipids restored T cell activation and augmented BiTE-mediated cytotoxicity, supporting a combination approach to potentiate BiTE therapy in malignant ascites. Translational RelevanceMalignant ascites represents a lipid-rich, immunosuppressive tumour microenvironment that is increasingly targeted by emerging T cell-based therapies. Although EpCAM-targeting bispecific T cell engagers (BiTEs) have recently been approved for malignant ascites and multiple similar BiTEs are in clinical development, the mechanisms by which ascites impairs T cell function and potentially limits therapeutic efficacy remain poorly understood. Using patient-derived ascites throughout, this study demonstrated that lipid metabolic reprogramming, rather than immune checkpoint upregulation, was a driver of T cell dysfunction. Importantly, we demonstrated that lipid removal from ascites rescued T cell function and restored BiTE efficacy, identifying a targetable metabolic barrier to immunotherapy. While EpCAM was used as a proof-of-concept target, we anticipate the metabolic insights and therapeutic strategies identified here will be equally applicable to other BiTE and CAR-T platforms, supporting a new combination approach for the treatment of malignant ascites.

cancer biology↗

bioRxiv2025

Machine perfusion and single-cell spatial transcriptome mapping identifies novel immune escape mechanisms in colorectal cancer liver metastasis

Liver metastasis is the terminal stage of colorectal cancer. Immune checkpoint blockade (ICB) has heralded remarkable clinical success across a range of cancer types, but with limited efficacy in replacement-type colorectal liver metastasis (CRLM), the most common and lethal histological subtype. Using a novel human normothermic perfusion model, we demonstrate for the first time, that T-cells preferentially extravasate within the peri-tumoural liver rather than the CRLM. We use single-cell spatial transcriptomics and multiplexed immunofluorescence to validate CRLM T-cell exclusion and show that CRLM endothelia are anergic, lacking key receptors required for T-cell extravasation. CD4 T-cells that extravasate within the peri-tumoural liver are TCR-reactive, yet exhausted, whilst CD4 T-cells within the CRLM demonstrate a stress response, impaired cytokine expression and lack of TCR reactivity. We identify the spatial cellular and molecular interactions underlying these observations, providing novel targets for future attempts to sensitise to immunotherapeutics and a justification for failed ICB efficacy in CRLM.

cancer biology↗

bioRxiv2025

The tuberculosis-associated microenvironment promotes HIV-1 persistence by impairing CD8+ T cell-mediated viral control

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is the most common coinfection in people living with HIV-1 (PLWH). This coinfection is associated with accelerated HIV-1 disease progression and reduced survival. However, the immunological and virological mechanisms driving this progression are incompletely understood. To address this knowledge gap, using pleural effusion samples from PLWH and TB, we investigated the HIV-1 genetic landscape and the anti-HIV-1 immune response impacted by a TB-associated microenvironment. Our results revealed an enrichment of genetically intact HIV-1 and impaired CD8+ T cell-mediated antiviral response at the site of HIV-1/Mtb coinfection. These findings indicate that the TB-associated microenvironment promotes the persistence of cells infected with replication-competent HIV-1 by creating a niche of reduced antiviral immune pressure, potentially contributing to the worsened clinical outcomes observed in PLWH and TB.

immunology↗

bioRxiv2023

Sphingosine induction of the Pseudomonas aeruginosa hemolytic phospholipase C/sphingomyelinase, PlcH

The hemolytic phospholipase C, PlcH, is an important virulence factor for Pseudomonas aeruginosa. PlcH preferentially hydrolyzes sphingomyelin and phosphatidylcholine and this hydrolysis activity can drives tissue damage, inflammation, and interferes with the oxidative burst of immune cells. Among other contributors, transcription of plcH was previously shown to be induced by phosphate starvation via PhoB and by the choline metabolite, glycine betaine, via GbdR. Here, we show that sphingosine can induce plcH transcription and resultant secreted PlcH enzyme activity. This induction is dependent on the sphingosine-sensing transcription regulator SphR. The SphR induction of plcH occurs from the promoter for the gene upstream of plcH that encodes the neutral ceramidase, CerN, and transcriptional read-through of the cerN transcription terminator. Evidence for these conclusions come from mutation of the SphR binding site in the cerN promoter, mutation of the cerN terminator, enhancement of cerN termination by adding the rrnB terminator, and RT-PCR showing that the intergenic region between cerN and plcH is made as RNA during sphingosine, but not choline, induction. We also observe that, like glycine betaine induction, sphingosine induction of plcH is under catabolite repression control, which likely explains why such induction was not seen in other studies using sphingosine in rich media. The addition of sphingosine as a novel inducer for PlcH points to regulation of plcH transcription as a site for integration of multiple host-derived signals.

microbiology↗

bioRxiv2023

Identification of the KIF18A alpha-4 helix as a therapeutic target for chromosomally unstable tumor cells

The mitotic kinesin, KIF18A, is required for proliferation of cancer cells that exhibit chromosome instability (CIN), implicating it as a promising target for treatment of a subset of aggressive tumor types. Determining regions of the KIF18A protein to target for inhibition will be important for the design and optimization of effective small molecule inhibitors. In this study, we investigated the effects of mutating S284 within the alpha-4 helix of KIF18A, which was previously identified as a phosphorylated residue. Mutations in S284 cause relocalization of KIF18A from the plus-ends of spindle microtubules to the spindle poles. Furthermore, KIF18A S284 mutants display loss of KIF18A function and fail to support proliferation in CIN tumor cells. Interestingly, similar effects on KIF18A localization and function were seen after treatment of CIN cells with KIF18A inhibitory compounds that are predicted to interact with residues within the alpha-4 helix. These data implicate the KIF18A alpha-4 helix as an effective target for inhibition and demonstrate that small molecules targeting KIF18A selectively limit CIN tumor cell proliferation and result in phenotypically similar effects on mitosis at the single cell level compared to genetic perturbations.

cancer biology↗

bioRxiv2023

Degradation and bioconversion of complex municipal solid waste streams into human biotherapeutics and biopolymers

The use of biomass and organic waste as a feedstock for the production of fuels, chemicals and materials offers great potential to support the transition to net-zero and circular economic models. However, such renewable feedstocks are often complex, highly heterogeneous, and subject to geographical and seasonal variability, creating supply-chain inconsistency that impedes adoption. Towards addressing these challenges, the development of engineered microorganisms equipped with the ability to flexibly utilise complex, heterogenous substrate compositions for growth and bio-production would be greatly enabling. Here we show through careful strain selection and metabolic engineering, that Pseudomonas putida can be employed to permit efficient co-utilisation of highly heterogeneous substrate compositions derived from hydrolysed mixed municipal-like waste fractions, with remarkable resilience to compositional variability. To further illustrate this, one pot enzymatic pre-treatments of the five most abundant, hydrolytically labile, mixed waste feedstocks was performed - including food, plastic, organic, paper and cardboard, and textiles - for growth and synthesis of exemplar bio-products by engineered P. putida. Finally, prospective life cycle assessment and life cycle costing illustrated the climate change and economic advantage, respectively, of using the waste-derived feedstock for biomanufacturing compared to conventional waste treatment options. This work demonstrates the potential for expanding the treatment strategies for mixed municipal waste to include engineered microbial bio-production platforms that can accommodate variability in feedstock inputs to synthesise a range of chemical and material outputs.

synthetic biology↗

bioRxiv2022

Mountains as refugia: evidence from bumble bee brain transcriptomes

As anthropogenic change continues to impact global biodiversity, the importance of rapidly identifying biodiversity refugia cannot be overstated. In this study, we employed a molecular test of the hypothesis that mountains serve as refugia for bumble bees against anthropogenic stressors. To explore this hypothesis, we compared stress-related patterns of gene expression in the brains of wild, pollen-foraging bumble bees of two species, B. vosnesenskii and B. melanopygus, collected at different elevations throughout the Sierra Nevada Mountain range in California, USA. We found evidence that the expression of several immune and detoxification genes is associated with elevational differences. This suggests that bees are experiencing differential exposure to stressors along an elevational gradient, which is an important criterion for identifying refugia across dynamic and heterogenous environments. This study thus provides evidence that mountains may serve as refugia for bumble bees in response to anthropogenic stressors, as has been detected for many other organisms.

ecology↗

bioRxiv2021

Natural variation in the irld gene family affects insulin/IGF signaling and starvation resistance

Starvation resistance is important to disease and fitness, but the genetic basis of its natural variation is unknown. We developed a synthetic-population (re)sequencing approach using molecular inversion probes (MIP-seq) to measure relative fitness during and after larval starvation in C. elegans. We applied this competitive assay to 100 genetically diverse, sequenced, wild strains, revealing natural variation in starvation resistance. We confirmed that the most starvation-resistant strains survive and recover from starvation better than the most starvation-sensitive strain, MY2147, using standard assays. We performed genome-wide association with the MIP-seq trait data and identified three quantitative trait loci (QTL) for starvation resistance. These QTL contain several members of the Insulin/EGF Receptor-L Domain (irld) family with sequence variation associated with variation in starvation resistance. We used genome editing to show that individual modification of four irld genes increases starvation resistance of MY2147. Modification of irld-39 and irld-52 together increases starvation resistance of the laboratory-reference strain N2. Increased starvation resistance of the irld-39; irld-52 double mutant depends on daf-16/FoxO, and these worms also show increased nuclear localization of DAF-16 during starvation. DAF-16/FoxO is a widely conserved transcriptional effector of insulin/IGF signaling (IIS), and these results suggest that IRLD proteins modify IIS. This work demonstrates efficacy of using MIP-seq to dissect a complex trait, identifies irld genes as natural modifiers of starvation resistance in C. elegans, and suggests that an expanded gene family affects a deeply conserved signaling pathway to alter a fitness-proximal trait.

genetics↗

bioRxiv2021

The Drosophila gene smoke alarm regulates nociceptor-epidermis interactions and thermal nociception behavior

The detection and processing of noxious sensory input depends on the proper growth and function of nociceptor sensory neurons in the peripheral nervous system. In Drosophila melanogaster, the class IV (cIV) multidendritic dendritic arborization (md-da) neurons detect noxious stimuli through their highly branched dendrites that innervate the epidermis of the larval body wall. Here, we describe requirements of a previously uncharacterized gene named smoke alarm (smal), a discoidin domain receptor, in cIV md-da dendrite morphogenesis and nociception behavior. We find that smal mutant larvae exhibit thermal hyperalgesia that is fully rescued with a BAC transgene containing smal. Consistent with this phenotype, a smal reporter gene was expressed in nociceptors and other peripheral sensory neurons. Smal::GFP protein localized to punctate structures throughout the cIV md-da neurons. We further show that smal loss-of-function results in reduced nociceptor dendrite branching. Interestingly, mammalian homologues of smal act as collagen receptors, and we find that smal mutant dendrites showed an increase in epidermal cell ensheathment relative to animals that are wild type for smal. Based on this phenotype we propose that Smal protein function is required for attachment of dendrites to the extracellular matrix (ECM) and the loss of this activity results in thermal hyperalgesia.

neuroscience↗

bioRxiv2021

Intergenerational adaptations to stress are evolutionarily conserved, stress-specific, and have deleterious trade-offs

Despite reports of parental exposure to stress promoting physiological adaptations in progeny in diverse organisms, there remains considerable debate over the significance and evolutionary conservation of such multigenerational effects. Here, we investigate four independent models of intergenerational adaptations to stress in C. elegans - bacterial infection, eukaryotic infection, osmotic stress and nutrient stress - across multiple species. We found that all four intergenerational physiological adaptations are conserved in at least one other species, that they are stress-specific, and that they have deleterious trade-offs in mismatched environments. By profiling the effects of parental bacterial infection and osmotic stress exposure on progeny gene expression across species we established a core set of 279 highly conserved genes that exhibited intergenerational changes in expression in response to stress in all species tested and provide evidence suggesting that presumed adaptive and deleterious intergenerational effects are molecularly related at the gene expression level. By contrast, we found that these same stresses did not elicit any similarly conserved transgenerational changes in progeny gene expression three generations after stress exposure. We conclude that intergenerational responses to stress play a substantial and evolutionarily conserved role in regulating animal physiology and that the vast majority of the effects of parental stress on progeny gene expression are reversible and not maintained transgenerationally.

genetics↗

bioRxiv2019

Enhancing Myocardial Repair with CardioClusters

BackgroundCellular therapy to treat heart failure is an ongoing focus of intense research and development, but progress has been frustratingly slow due to limitations of current approaches. Engineered augmentation of established cellular effectors overcomes impediments, enhancing reparative activity with improved outcomes relative to conventional techniques. Such next generation implementation includes delivery of combinatorial cell populations exerting synergistic effects. Concurrent isolation and expansion of three distinct cardiac-derived interstitial cell types from human heart tissue, as previously reported by our group, prompted design of a three-dimensional (3D) structure that maximizes cellular interaction, allows for defined cell ratios, controls size, enables injectability, and minimizes cell losses upon delivery. MethodsThree distinct populations of human cardiac interstitial cells including mesenchymal stem cells (MSCs), endothelial progenitor cells (EPCs), and c-Kit+ cardiac interstitial cells (cCICs) when cultured together spontaneously form scaffold-free 3D microenvironments termed CardioClusters. Biological consequences of CardioCluster formation were assessed by multiple assays including single cells RNA-Seq transcriptional profiling. Protective effects of CardioClusters in vitro were measured using cell culture models for oxidative stress and myocardial ischemia in combination with freshly isolated neonatal rat ventricular myocytes. Long-term impact of adoptively transferred CardioClusters upon myocardial structure and function in a xenogenic model of acute infarction using NODscid mice was assessed over a longitudinal time course of 20-weeks. ResultsCardioCluster design enables control over composite cell types, cell ratios, size, and preservation of structural integrity during delivery. Profound changes for biological properties of CardioClusters relative to constituent parental cell populations include enhanced expression of stem cell-relevant factors, adhesion/extracellular-matrix molecules, and cytokines. The CardioCluster 3D microenvironment maximizes cellular interaction while maintaining a more native transcriptome similar to endogenous cardiac cells. CardioCluster delivery improves cell retention following intramyocardial injection with preservation of long-term cardiac function relative to monolayer-cultured cells when tested in an experimental murine infarction model followed for up to 20 weeks post-challenge. CardioCluster-treated hearts show increases in capillary density, preservation of cardiomyocyte size, and reduced scar size indicative of blunting pathologic infarction injury. ConclusionsCardioClusters are a novel next generation development and delivery approach for cellular therapeutics that potentiate beneficial activity and enhance protective effects of human cardiac interstitial cell mixed populations. CardioClusters utilization in this preclinical setting establishes fundamental methodologic and biologic insights, laying the framework for optimization of CardioCluster design to provide greater efficacy in cell-based therapeutic interventions intended to mitigate cardiomyopathic damage.

cell biology↗

bioRxiv2019

Skeletal Muscle mTORC1 Activation Increases Energy Expenditure and Reduces Longevity in Mice

The mechanistic target of rapamycin (mTORC1) is a nutrient responsive protein kinase complex that helps co-ordinate anabolic processes across all tissues. There is evidence that signaling through mTORC1 in skeletal muscle may be a determinant of energy expenditure and aging and therefore components downstream of mTORC1 signaling may be potential targets for treating obesity and age-associated metabolic disease. Here, we generated mice with Ckmm-Cre driven ablation of Tsc1, which confers constitutive activation of mTORC1 in skeletal muscle and performed unbiased transcriptional analyses to identify pathways and candidate genes that may explain how skeletal muscle mTORC1 activity regulates energy balance and aging. Activation of skeletal muscle mTORC1 produced a striking resistance to diet-and age-induced obesity without inducing systemic insulin resistance. We found that increases in energy expenditure following a high fat diet were mTORC1-dependent and that elevated energy expenditure caused by ablation of Tsc1 coincided with the upregulation of skeletal muscle-specific thermogenic mechanisms that involve sarcolipin-driven futile cycling of Ca2+ through SERCA2. Additionally, we report that constitutive activation of mTORC1 in skeletal muscle reduces lifespan. These findings support the hypothesis that activation of mTORC1 and its downstream targets, specifically in skeletal muscle, may play a role in nutrient-dependent thermogenesis and aging.

physiology↗