Biology subjects

Lefevre, L.

Publications and source records attributed to Lefevre, L..

14 recordsLinked to original sources

bioRxiv2026

PSMD14 drives melanoma cell survival and MAPK inhibitor resistance through histone H2A deubiquitination

Melanoma progression and resistance to targeted therapies remain major clinical challenges, driven in part by the remarkable phenotypic plasticity of melanoma cells. Identifying molecular mechanisms that couple tumor survival to adaptative drug responses is therefore essential. Here, we identify PSMD14, a proteasome-associated deubiquitinase, as an essential regulator of melanoma plasticity, growth, survival, and therapeutic resistance with strong prognostic significance in metastatic disease. An unbiased siRNA screen targeting the human deubiquitinase family revealed PSMD14 (proteasome 26S subunit, non-ATPase 14) as a top regulator of melanoma cell proliferation. Integrative analyses of DepMap, TCGA, and patient-derived datasets revealed that PSMD14 is frequently upregulated in melanoma, enriched in metastatic lesions, and significantly associated with poor patient outcome. Functional and pharmacological studies demonstrated that genetic depletion or inhibition of PSMD14 suppresses proliferation, clonogenic and long-term growth, and viability of melanoma cells across BRAF-, NRAS-, and NF1-driven genotypes, while inducing DNA damage and apoptosis. Consistently, PSMD14 inhibition markedly reduced tumor growth in Nras and Braf syngeneic mouse models. Mechanistically, we uncover a non-proteolytic role for PSMD14 as an epigenetic regulator of chromatin state. Proteomic and biochemical analyses identified histone H2A as a direct interactor and substrate of PSMD14. PSMD14 deubiquitinates H2A at lysine 119 independently of the proteasome, antagonizing the Polycomb E3 ligase RING1B. Loss of PSMD14 allows the increment of H2AK119 ubiquitination, transcriptional repression of pro-survival genes, including MCL1 and BCL2, and apoptotic cell death, effects rescued by RING1B depletion. Importantly, we demonstrate that the PSMD14-H2A axis governs melanoma adaptation to MAPK pathway inhibition. PSMD14 expression and H2AK119 ubiquitination dynamically correlate with therapeutic response, drug-tolerant persistence, and acquired resistance. Targeting PSMD14 genetically or pharmacologically enhances the efficacy of BRAF and MEK inhibitors, suppresses the emergence of drug-tolerant persister cells, and prevents tumor relapse in vivo. Together, this findings establish PSMD14 as a chromatin-rewiring enzyme that links proteostasis to epigenetic control of melanoma plasticity and therapy resistance, highlighting PSMD14 as a promising biomarker and therapeutic target in aggressive and drug-resistant melanoma.

cancer biology↗

bioRxiv2025

Oncogenic Stress is a Novel Immunogenic Signal Driven by the Unfolded Protein Response and Detected by Neutrophils

Breast cancer (BC) is the leading cause of cancer-related death in women. However, early detection of BC remains a major clinical challenge and represents a significant obstacle to effective prevention. To improve early clinical management, a deeper understanding of the preneoplastic immune microenvironment of BC is crucial. Among innate immune populations, neutrophils have emerged as important modulators of tumor development, but their role during the initiation of BC remains poorly understood. By integrating depletion experiments with transcriptomic profiling of sorted preneoplatic epithelial cells and neutrophils in spontaneous breast cancer mouse models, we observed that neutrophils contribute to tumor surveillance of preneoplastic stage with the activation of the unfolded protein response (UPR) in the preneoplastic epithelial compartment. To decipher the early anti-tumoral role of neutrophil, we developed an in vitro co-culture model of human mammary epithelial cells undergoing oncogenic stress with activation of the UPR (eHMEC), with human primary neutrophils. eHMEC display an immunoactive secretome as well as immunogenic membrane ligands, and neutrophils are the only immune cell population detecting eHMEC immunogenic signals leading to their recruitment, activation, production of reactive oxygen species and degranulation. Altogether, our work identifies for the first-time neutrophils as the earliest immune cell involved in immunosurveillance of preneoplastic BC epithelial cells, paving the way for potential therapeutic approaches targeting neutrophils to intercept early steps of BC tumorigenesis.

immunology↗

bioRxiv2023

Organizing the coactivity structure of the hippocampus from robust to flexible memory

New memories are integrated into prior knowledge of the world. But what if consecutive memories exert opposing demands on the host brain network? We report that acquiring a robust (food-context) memory constrains the hippocampus within a population activity space of highly correlated spike trains that prevents subsequent computation of a flexible (object-location) memory. This densely correlated firing structure developed over repeated mnemonic experience, gradually coupling neurons of the superficial CA1 pyramidale sublayer to whole population activity. Applying hippocampal theta-driven closed-loop optogenetic suppression to mitigate this neuronal recruitment during (food-context) memory formation relaxed the topological constraint on hippocampal coactivity and restored subsequent flexible (object-location) memory. These findings uncover an organizational principle for the peer-to-peer coactivity structure of the hippocampal cell population to successfully meet memory demands.

neuroscience↗

bioRxiv2023

Leishmania infantum-exploited Nrf2 transcription factor as a virulence process to escape macrophage-driven ferroptosis-like leishmanicidal process

Macrophages are the main effector cells during Leishmania infection. They contribute to the detection and elimination of Leishmania spp. and may also promote parasite resilience. Here, we report that the activation of the transcription factor Nrf2 in macrophages plays a pivotal role in the progression of Leishmania infantum infection by controlling inflammation and redox balance of macrophages. We also highlight the involvement of NOX2/ROS axis in the early Nrf2 activation and subsequently of PGE2/EP2r signalling in the sustainment of Nrf2 activation upon L. infantum infection. Moreover, we establish macrophage-driven ferroptosis-like process as a cell death program of L. infantum and the protective effect of Nrf2 in macrophages against L. infantum death. Altogether, these results identify Nrf2 as a critical factor for the susceptibility of Leishmania infantum infection, highlighting Nrf2 as a promising pharmacological target for the development of new therapeutic approaches for the treatment of visceral leishmaniasis.

microbiology↗

bioRxiv2023

Phenotypic and spatial heterogeneity of brain myeloid cells after stroke is associated with cell ontogeny, tissue damage, and brain connectivity

Acute stroke causes substantial mortality and morbidity and provokes extensive changes to myeloid immune cell populations in the brain that may be targets for limiting brain damage and enhancing brain repair. The most effective immunomodulatory approaches will require precise manipulation of discrete myeloid cell phenotypes in time and space to avoid harmful effects of indiscriminate neuroimmune perturbation. We sought to define how stroke alters the composition and phenotypes of mononuclear myeloid cells with particular attention to how cell ontogeny and spatial organisation combine to expand myeloid cell diversity across the brain after stroke. Multiple reactive microglial states and dual monocyte-derived populations contributed to an extensive repertoire of myeloid cells in post-stroke brain. We identified important overlap and distinctions among different cell types and states that involved ontogeny- and spatial-related properties. Notably, brain connectivity with infarcted tissue underpinned the pattern of local and remote altered cell accumulation and reactivity. Our discoveries suggest a global but anatomically-governed brain myeloid cell response to stroke that comprises diverse phenotypes arising through intrinsic cell ontogeny factors interacting with exposure to spatially-organised brain damage and neuroaxonal cues.

neuroscience↗

bioRxiv2022

Cystatin F (Cst7) drives sex-dependent changes in microglia in an amyloid-driven model of Alzheimer's Disease

Microglial endolysosomal (dys)function is strongly implicated in neurodegeneration. Transcriptomic studies show that a microglial state characterised by a set of genes involved in endolysosomal function is induced in both mouse Alzheimers Disease (AD) models and in human AD brain and that the onset of this state is emphasized in females. Cst7 (encoding protein Cystatin F) is among the most highly upregulated genes in these microglia. However, despite such striking and robust upregulation, the sex-specific function of Cst7 in neurodegenerative disease is not understood. Here, we crossed Cst7-/- mice with the AppNL-G-F mouse to test the role of Cst7 in a model of amyloid-driven AD. Surprisingly, we found that Cst7 plays a sexually dimorphic role regulating microglia in this model. In females, Cst7-deficient microglia had greater endolysosomal gene expression, lysosomal burden, and amyloid beta (A{beta}) burden in vivo and were more phagocytic in vitro. However, in males, Cst7-deficient microglia were less inflammatory and had a reduction in lysosomal burden but had no change in A{beta} burden. This study has important implications for AD research, confirming the functional role of a gene which is commonly upregulated in disease models, but also raising crucial questions on sexual dimorphism in neurodegenerative disease and the interplay between endolysosomal and inflammatory pathways in AD pathology.

neuroscience↗

bioRxiv2021

Stem cell-derived macrophages as a new platform for studying host-pathogen interactions in livestock

Infectious diseases of farmed and wild animals pose a recurrent threat to food security and human health. The macrophage, a key component of the innate immune system, is the first line of defence against many infectious agents and plays a major role in shaping the adaptive immune response. However, this phagocyte is a target and host for many pathogens. Understanding the molecular basis of interactions between macrophages and pathogens is therefore crucial for the development of effective strategies to combat important infectious diseases. We explored how pluripotent stem cells (PSCs) can provide a limitless in vitro supply of genetically and experimentally tractable macrophages from livestock. Porcine and bovine PSC-derived macrophages (PSCdMs) exhibited molecular and functional characteristics of ex vivo primary macrophages. Pig PSCdMs were productively infected by Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and African Swine Fever Virus (ASFV), two of the most economically important and devastating viruses in pig farming. Moreover, Pig PSCdMs were readily amenable to genetic modification by CRISPR/Cas9 gene editing applied in parental stem cells, or directly by lentiviral vector transduction. PSCs and differentiated derivatives therefore provide a useful and ethical experimental platform to investigate the genetic and molecular basis of host-pathogen interactions in livestock.

immunology↗

bioRxiv2021

Defining the pig microglial transcriptome reveals their core signature, regional heterogeneity, and similarity with humans

Microglia play key roles in brain homeostasis as well as responses to neurodegeneration and neuroinflammatory processes caused by physical disease and psychosocial stress. The pig is a physiologically-relevant model species for studying human neurological disorders, many of which are associated with microglial dysfunction. Furthermore, pigs are an important agricultural species, and there is a need to understand how microglial function affects their welfare. As a basis for improved understanding to enhance biomedical and agricultural research, we sought to characterise pig microglial identity at genome-wide scale and conduct inter-species comparisons. We isolated pig hippocampal tissue and microglia from frontal cortex, hippocampus and cerebellum, as well as alveolar macrophages from the lungs and conducted RNA-sequencing (RNAseq). By comparing the transcriptomic profiles between microglia, macrophages, and hippocampal tissue, we derived a set of 365 highly-enriched genes defining the porcine core microglial signature. We found brain regional heterogeneity based on 215 genes showing significant (adjusted p<0.01) regional variations and that cerebellar microglia were most distinct. We compared normalized gene expression for microglia from human, mice and pigs using microglia signature gene lists derived from each species and demonstrated that a core microglial marker gene signature is conserved across species, but that species-specific expression subsets also exist. Importantly, pig and human microglia shared greater similarity than pig and murine microglia. Our data provide a valuable resource defining the pig microglial transcriptome signature that highlights pigs as a useful large animal species bridging between rodents and humans in which to study the role of microglia during homeostasis and disease. Main Points- Defined a pig microglial transcriptome signature comprising 365 genes. - Demonstrated regional variance in the pig microglial transcriptome across the brain. - Revealed greater similarity between pig and human microglia than mouse.

bioinformatics↗

bioRxiv2021

Blockade of pro-fibrotic response mediated by the miR-143/-145 cluster prevents targeted therapy-induced phenotypic plasticity and resistance in melanoma

Lineage dedifferentiation towards a mesenchymal-like state is a common mechanism of adaptive response and resistance to targeted therapy in melanoma. Yet, the transcriptional network driving this phenotypic plasticity remains elusive. Remarkably, this cellular state displays myofibroblast and fibrotic features and escapes MAPK inhibitors (MAPKi) through extracellular matrix (ECM) remodeling activities. Here we show that the anti-fibrotic drug Nintedanib/BIBF1120 is active to normalize the fibrous ECM network, enhance the efficacy of MAPK-targeted therapy and delay tumor relapse in a pre-clinical model of melanoma. We also uncovered the molecular networks that regulate the acquisition of this resistant phenotype and its reversion by Nintedanib, pointing the miR-143/-145 pro-fibrotic cluster as a driver of the therapy-resistant mesenchymal-like phenotype. Upregulation of the miR-143/-145 cluster under BRAFi/MAPKi therapy was observed in melanoma cells in vitro and in vivo and was associated with an invasive/undifferentiated profile of resistant cells. The 2 mature miRNAs generated from this cluster, miR-143-3p and miR-145-5p collaborated to mediate phenotypic transition towards a drug resistant undifferentiated mesenchymal-like state by targeting Fascin actin-bundling protein 1 (FSCN1), modulating the dynamic crosstalk between the actin cytoskeleton and the ECM through the regulation of focal adhesion dynamics as well as contributing to a fine-tuning of mechanotransduction pathways. Our study brings insights into a novel miRNA-mediated regulatory network that contributes to non-genetic adaptive drug resistance and provides proof-of-principle that preventing MAPKi-induced pro-fibrotic stromal response is a viable therapeutic opportunity for patients on targeted therapy.

cancer biology↗

bioRxiv2021

Phospholipid peroxidation fuels ExoU phospholipase-dependent cell necrosis and supports Pseudomonas aeruginosa-driven pathology

Regulated cell necrosis supports immune and anti-infectious strategies of the body; however, dysregulation of these processes drives pathological organ damage. Pseudomonas aeruginosa expresses a phospholipase, ExoU that triggers pathological host cell necrosis through a poorly characterized pathway. Here, we investigated the molecular and cellular mechanisms of ExoU-mediated necrosis. We show that cellular peroxidised phospholipids enhance ExoU phospholipase activity, which drives necrosis of immune and non-immune cells. Conversely, both the endogenous lipid peroxidation regulator GPX4 and the pharmacological inhibition of lipid peroxidation delay ExoU-dependent cell necrosis and improve bacterial elimination in vitro and in vivo. Our findings also pertain to the ExoU-related phospholipase from the bacterial pathogen Burkholderia thailandensis, suggesting that exploitation of peroxidised phospholipids might be a conserved virulence mechanism among various microbial phospholipases. Overall, our results identify an original lipid peroxidation-based virulence mechanism as a strong contributor of microbial phospholipase-driven pathology.

immunology↗

bioRxiv2020

The deep and slow breathing characterizing rest favors brain respiratory-drive

A respiration-locked activity in the olfactory brain, mainly originating in the mechano-sensitivity of olfactory sensory neurons to air pressure, propagates from the olfactory bulb to the rest of the brain. Interestingly, changes in nasal airflow rate result in reorganization of olfactory bulb response. Therefore, if the respiratory drive of the brain originates in nasal airflow movements, then it should vary with respiration dynamics that occur spontaneously during natural conditions. We took advantage of the spontaneous variations of respiration dynamics during the different waking and sleep states to explore respiratory drive in various brain regions. We analyzed their local field potential activity relative to respiratory signal. We showed that respiration regime was state-specific, and that quiet waking was the only vigilance state during which all the recorded structures can be respiration-driven whatever the respiration frequency. We used a CO2-enriched air to change the respiratory regime associated to each state and, using a respiratory cycle-by-cycle analysis, we evidenced that the large and strong brain entrainment during quiet waking was the consequence of its associated respiration regime consisting in an optimal trade-off between deepness and duration of inspiration. These results show for the first time that changes in respiration regime alter the cortical dynamics and that the respiratory regime associated with rest is optimal for respiration to drive the brain.

neuroscience↗

bioRxiv2018

Mesenchymal stromal cells release CXCL1/2/8 and induce chemoresistance and macrophage polarization

Factors released by surrounding cells such as cancer-associated mesenchymal stromal cells (CA-MSCs) are involved in tumor progression and chemoresistance. We determine the mechanisms by which a naive MSC could become a CA-MSC and characterize CA-MSCs. Ovarian tumor cells (OTC) trigger the transformation of MSCs to CA-MSCs expressing different pro-tumoral, genes and secreting high amounts of CXCR1/2 ligands (CXCL1, CXCL2 and IL-8) implicated in the chemoresistance of cancer cells. CXCR1/2 ligands can also inhibit the immune response against OTC. Indeed, through their released factors, CA-MSCs can trigger the differentiation of monocytes to pro-tumoral M2 phenotype macrophages known to promote the tumor progression. When CXCR1/2 receptors are inhibited, these CA-MSC-activated macrophages lose their M2 functions and acquire an anti-tumoral phenotype. Both ex vivo and in vivo a CXCR1/2 inhibitor can sensitize OTC to carboplatin even in the presence of a pro-tumoral microenvironment. This inhibitor can circumvent the pro-tumoral effects of CA-MSCs. As high concentrations of CXCR1/2 ligands in blood from patients can be associated with chemoresistance, CXCR1/2 inhibition could be a potential therapeutic strategy to revert chemoresistance.

cancer biology↗

bioRxiv2018

Maternal tamoxifen treatment expands the macrophage population of early mouse embryos.

Several different transgenic tamoxifen-inducible cre reporter lines have been used to analyse the contribution of embryonic precursors to the development of the mononuclear phagocyte system in mice. Here we show that tamoxifen treatment of the mother at 8.5dpc with doses commonly-used in lineage trace studies produces a 4-5-fold expansion of the embryonic leukocyte populations by 10.5dpc, detected in whole mounts of embryos using a Csf1r reporter gene or separately by expression of Csf1r, Itgam (CD11b), Adgre1 (F4/80) or Ptprc (CD45) mRNA. These findings indicate that tamoxifen cannot be considered a neutral agonist in macrophage lineage trace studies.\n\nSummary sentenceTreatment of pregnant mice with tamoxifen in early gestation produces a large expansion of the embryonic macrophage population.

immunology↗

bioRxiv2017

A High Resolution Atlas Of Gene Expression In The Domestic Sheep (Ovis aries)

Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of guilt by association was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.\n\nAuthor SummarySheep are ruminant mammals kept as livestock for the production of meat, milk and wool in agricultural industries across the globe. Genetic and genomic information can be used to improve production traits such as disease resiliance. The sheep genome is however missing important information relating to gene function and many genes, which may be important for productivity, have no informative gene name. This can be remedied using RNA-Sequencing to generate a global expression profile of all protein-coding genes, across multiple organ systems and developmental stages. Clustering genes based on their expression profile across tissues and cells allows us to assign function to those genes. If for example a gene with no informative gene name is expressed in macrophages and is found within a cluster of known macrophage related genes it is likely to be involved in macrophage function and play a role in innate immunity. This information improves the quality of the reference genome and provides insight into biological processes underlying the complex traits that influence the productivity of sheep and other livestock species.

genomics↗