Biology subjects

Zeef, L.

Publications and source records attributed to Zeef, L..

8 recordsLinked to original sources

bioRxiv2026

In situ programming of intratumoural stem cell-like memory CD8+ T cells enables durable antitumour immunity in immunosuppressive tumours

Tumours with an immunosuppressive microenvironment often respond poorly to radiotherapy (RT) and immune checkpoint inhibitors, and durable clinical responses remain rare. These failures are not solely explained by insufficient immune activation, but instead reflect an inability of current therapies to establish CD8 T-cell infiltration and states required for long-term tumour control. Although stem cell-like memory CD8 T cells (Tscm) are critical for durable antitumour immunity, they are typically rare within solid tumours, and strategies to selectively augment the expansion of intratumoural Tscm within immunosuppressive tumours are lacking. Here, we show that intratumoural immune modulation via pattern recognition receptor (PRR) activation, using a double-stranded RNA-based agonist (BO-112), promotes Tscm expansion and, in combination with radiation, enhances antitumour immunity in poorly immunogenic lung and bladder cancer models. PRR activation enabled selective in situ expansion of intratumoural Tscm, rather than global CD8 T-cell activation. Therapeutic efficacy required pre-existing intratumoural CD8 T cells and was associated with qualitative reprogramming of the immune landscape, including depletion of exhausted CD8 T cells and regulatory T cells. Transcriptomic analyses showed that PRR activation preferentially enriched programmes associated with Tscm formation and self-renewal, whereas durable effector differentiation emerged only following combined RT-PRR agonist treatment, consistent with antigen-driven execution of the expanded progenitor pool. A Tscm-associated gene signature derived from these preclinical datasets correlated with improved survival across independent human lung and bladder cancer cohorts. Together, our data identify intratumoural Tscm as a therapeutically targetable immune-control axis and establish in situ programming of Tscm as a route to durable antitumour immunity.

cancer biology↗

bioRxiv2025

Regional Vulnerability of Cardiac Chambers to Radiotherapy: A Multi-Omics Perspective

The heart is highly vulnerable to radiotherapy (RT)-induced injury, leading to molecular and structural remodeling collectively termed radiation-induced cardiac toxicity (RICT). Although several biological pathways have been implicated, the regional, cardiac-specific molecular responses to radiation exposure remain incompletely understood. Here, a multi-omics approach was adopted to longitudinally characterise the unique responses to radiation of the heart base (including ventricular base and right atrium), or the heart apex. Ventricular base irradiation induced a cardiomyopathy phenotype, with pronounced molecular perturbations in metabolism and electrical conduction, while changes related to tissue structure were predominant following apex-directed RT. In the right atrium, irradiation drives fibrotic tissue remodelling, leading to an increased propensity for atrial fibrillation, underpinned by changes in sarcomere organisation. This study represents a comprehensive characterisation of differential spatiotemporal radiation effects in the heart and highlights biological and functional pathways that are potentially clinically actionable for cardiac radioprotection and monitoring.

cell biology↗

bioRxiv2025

Unveiling the genetic basis of the low pH response in the acidophilic yeast Maudiozyma bulderi as a potential host for biorefinery

Non-conventional yeasts represent a great genetic and phenotypic diversity with potential for industrial strain development in the bio-production of green chemicals. In recent years, mass genome sequencing of non-conventional yeasts has opened avenues to improved understanding of transcriptional networks and phenotypic plasticity and gene function, including the discovery of novel genes. Here, we investigated the expressional and morphological changes at low-pH in three strains of the acidophilic yeast Maudiozyma bulderi (previously Kazachstania bulderi and Saccharomyces bulderi): CBS 8638, CBS 8639 and NRRL Y-27205. The comparison of the transcriptome of cells growing in a bioreactor at pH=5.5 vs pH= 2.5, primarily showed dysregulation of genes involved in cell wall integrity, with NRRL Y-27205 the least acidophilic strain, showing the largest transcriptional response when compared to the other two strains. We identified four uncharacterised genes, unique to M. bulderi, and predicted function as transporters, upregulated at low pH. Microscopy studies showed that M. bulderi cell wall is not damaged in acidic environment, and the membrane lipid composition remains stable at low pH, unlike S. cerevisiae. Overall, our data on transcriptional variability in M. bulderi highlights genes and cellular pathways involved in the acidophilic adaptation of this species and can aid further strain development.

genomics↗

bioRxiv2024

Impact of inter-species hybridisation on antifungal drug response in the Saccharomyces genus.

Antifungal drug resistance across fungal and yeast pathogens presents one of the major concerns for global public health. Understanding the interactions between genetic background and environment is important for the development of new, effective treatments of infections. Allelic variation within populations of Ascomycota as well as hybridisation impacts the phenotype in response to stressful conditions, including to antifungal drugs. We exploited recent advances in multigenerational breeding of Saccharomyces interspecies hybrids to study the impact of hybridisation on antifungal resistance and identify quantitative trait loci (QTL) responsible for the phenotypes observed. A library of Saccharomyces cerevisiae x S. kudriavzevii hybrid offspring was screened in the presence of sub-lethal concentrations of six antifungal drugs and revealed a broad phenotypic diversity across the progeny. QTL analysis was carried out comparing alleles between the pools of high and low fitness offspring, identifying hybrid-specific genetic regions involved in resistance to fluconazole, micafungin and flucytosine. We found both drug specific and pleiotropic regions, and through gene ontology and SIFT analysis we identify potential causal genes, such as BCK2 and DNF1 that were validated via reciprocal hemizygosity analysis. We highlight 41 regions that contain genes not previously associated with resistance phenotypes in the literature. The results of this screening will help identify new pathways contributing to drug resistance, and lead to greater understanding of how allelic variation, hybridisation and evolution affect antifungal drug resistance in yeast and fungi.

genetics↗

bioRxiv2023

PAK1-dependant mechanotransduction enables myofibroblast nuclear adaptation and chromatin organisation during fibrosis

Myofibroblasts are responsible for scarring and organ stiffness during fibrosis. The scar propagates mechanical signals inducing a radical transformation in myofibroblast cell state linked to an increasingly pro-fibrotic phenotype. Here, we have discovered mechanical stress from progressive scarring induces nuclear softening and de-repression of heterochromatin. The parallel loss of H3K9Me3 enables a permissive state for distinct chromatin accessibility and profibrotic gene regulation. By integrating chromatin accessibility profiles (ATAC sequencing) we provide insight into the transcription network and open chromatin landscape underlying the switch in profibrotic myofibroblast states, emphasizing mechanoadaptive pathways linked to PAK1 as key drivers. Through genetic manipulation in liver and lung fibrosis, uncoupling PAK1-dependant signaling impaired the mechanoadaptive response in vitro and dramatically improved fibrosis in vivo. Moreover, we provide human validation for mechanisms underpinning PAK1 mediated mechanotransduction in liver and lung fibrosis. Collectively, these observations provide new insight into the nuclear mechanics driving the profibrotic chromatin landscape in fibrosis, highlighting actomyosin-dependent mechanisms linked to chromatin organisation as urgently needed therapeutic targets in fibrosis.

cell biology↗

bioRxiv2023

Novel in-silico predicted matrikines are differential mediators of in vitro and in vivo cellular metabolism

The exogenous application of small peptides can beneficially affect clinical skin appearance (wrinkles) and architecture (collagen and elastic fibre deposition and epidermal thickness). However, the discovery of new bioactive peptides has not been underpinned by any guiding hypothesis. As endogenous extracellular matrix (ECM)-derived peptides produced during tissue remodelling can act as molecular signals influencing cell metabolism, we hypothesised that protease cleavage site prediction could identify putative novel matrikines with beneficial activities. Here, we present an in silico to in vivo discovery pipeline, which enables the prediction and characterisation of peptide matrikines which differentially influence cellular metabolism in vitro. We use this pipeline to further characterise a combination of two novel ECM peptide mimics (GPKG and LSVD) which act in vitro to enhance the transcription of ECM organisation and cell proliferation genes and in vivo to promote epithelial and dermal remodelling. This pipeline approach can both identify new matrikines and provide insights into the mechanisms underpinning tissue homeostasis and repair.

cell biology↗

bioRxiv2020

Zebrafish IL-4-like cytokines and IL-10 suppress inflammation but only IL-10 is essential for gill homeostasis.

Healthy fish stocks are central to global food security. Key to fish health is robust immunity at mucosal surfaces, and especially at the gills. However, a balance must be struck between tolerating commensal microorganisms and reacting appropriately toward pathogens. In mammals, IL-4 and IL-13 in concert with IL-10 are essential for balancing immune response to pathogens and suppressing inflammation. Whether their fish counterparts perform similar roles is an open question. Here, we have generated IL-4/13A and IL-4/13B mutant zebrafish and, together with existing IL-10 mutants, characterized the consequences of loss-of-function of these cytokines. We demonstrate that these cytokines are required to suppress inflammation. Further, IL-4/13A and IL-4/13B are required for the maintenance of a Th2-like phenotype in the gills. As in mammals, IL-10 appears to have a more striking anti-inflammatory function than IL-4-like cytokines. Thus, both IL-10 and IL-4/13 paralogues in zebrafish exhibit aspects of conserved function with their mammalian counterparts.

immunology↗

bioRxiv2019

SOX9 is required for kidney fibrosis and regulates NAV3 to control renal myofibroblast function in mice and humans

Renal fibrosis is a common endpoint for many chronic kidney diseases. Extracellular matrix (ECM) from myofibroblasts causes progressive scarring and organ failure. The mechanisms underlying fibrogenesis and how it is sustained are incompletely understood. Here, we show that the transcription factor, Sex determining region Y-box 9 (SOX9), is required for kidney fibrosis. From genome-wide analysis we identify Neuron navigator 3 (NAV3) downstream of SOX9. NAV3 was upregulated in kidney disease in patients and following renal injury in mice colocalised with SOX9. By establishing an in vitro model of renal pericyte transition to myofibroblast we demonstrated that NAV3 is required for multiple aspects of fibrogenesis including actin polymerization linked to cell migration and sustaining SOX9 and active YAP1 levels. In summary, our work discovers novel SOX9-NAV3-YAP1/SOX9 circuitry as a new mechanism to explain the progression of kidney fibrosis and points to NAV3 as a novel target for pharmacological intervention.

cell biology↗