Biology subjects

Dubois, C.

Publications and source records attributed to Dubois, C..

16 recordsLinked to original sources

bioRxiv2026

HKDC1 contributes to aberrant lysosome-mitochondria contact in Niemann-Pick disease type C

Niemann-Pick disease type C (NPC) is a neurovisceral lysosomal storage disorder comprising two clinically indistinguishable but genetically distinct subtypes caused by mutations in NPC1, or NPC2. The specific impact of each deficiency on cellular homeostasis remains poorly defined due to the phenotypic heterogeneity of patient-derived models and a lack of isogenic platforms for comparative study. Here we established isogenic ARPE19 models of NPC1 and NPC2 deficiency that faithfully recapitulate hallmark pathologies, including homogeneous lysosomal expansion and lipid sequestration. Direct comparison of these isogenic lines revealed a fundamental divergence in organelle crosstalk: while both genotypes exhibit comparable lipid accumulation, expanded mitochondria-lysosome contact sites (MLCs) are observed exclusively in NPC1-/- cells. Using StARD3-targeted proximity labelling and quantitative proteomics, we identified the mitochondrial protein HKDC1 as an MLC regulator. We demonstrate that HKDC1 is markedly upregulated in NPC1-/- cells and that its overexpression drives MLC expansion in wild-type cells. Thus our study uncovers a homeostatic role for HKDC1-mediated organelle remodelling and demonstrates the power of isogenic modelling for identifying novel regulators of organelle architecture and potential therapeutic targets.

cell biology↗

bioRxiv2026

Immune checkpoint inhibitors amplify type 2 immune mediated repair bypro-regenerative scaffolds

Extracellular matrix (ECM) scaffolds induce type 2 immunity to promote repair. Here, we show that immune cells recruited to ECM-treated murine muscle injuries and clinical soft tissue defects express immune checkpoints. Specifically, TH2 cells and regulatory T cells (Tregs) increase LAG3 expression, while macrophages express PDL2. TCR analysis and a triple-reporter strain for interleukin (IL)-13 and Treg fate-mapping suggest that Tregs in ECM-treated wounds transition into TH2-like exTregs that express LAG3. Immune checkpoint inhibition (ICI) significantly stimulated type 2 immunity in ECM-treated wounds, including increased TH2 cells, Treg transition to TH2-like exTregs, and pro-regenerative macrophages. Moreover, ICI enhanced muscle repair and reduced fibrosis in ECM-treated wounds. Collectively, these findings show Treg/TH2 plasticity in wound healing and introduce a novel ICI application to enhance immune-mediated regeneration.

bioengineering↗

bioRxiv2025

Optical tweezers combined with FRET tension sensor reveal force-dependent vinculin dynamics

Visualizing and quantifying molecular responses to local forces exerted at cell adhesions is crucial to elucidate how physical forces control cellular behavior. Here, we combine optical tweezers with Forster resonance energy transfer (FRET) microscopy of the vinculin tension sensor, VinTS, to measure the response of vinculin, a key mechanical load-bearing protein, to an applied force. Fibroblasts expressing VinTS formed adhesions on fibronectin-coated, 3m-diameter, polystyrene beads. As the beads were displaced by the cell, we applied an optical trap to counteract this movement and increase the traction force required by the cell to maintain the beads displacement. The median bead displacement after 5 min was [~]200nm in all trapping conditions tested, from zero (no laser) up to 0.26 pN/nm, inducing counteracting forces in the 10-100pN range. To maintain this displacement, vinculin recruitment increased at high stiffness (up to 35% in relative intensity) while vinculin tension increased only moderately in all trapping conditions (1-2% decrease in absolute FRET efficiency). Vinculin recruitment was governed by stiffness rather than the magnitude of the traction force and was correlated with vinculin tension at 0.26 pN/nm but not at lower stiffness. In rare instances, vinculin puncta migrated a few micrometers away from the bead, exceeding the beads movement speed while experiencing an increase in both vinculin intensity and tension. Taken together, the results suggest that combining an optical trap with vinculin tension measurements in living cells uncovers novel vinculin dynamics in the presence of a force. Why it mattersCombining optical tweezers with FRET microscopy we measure vinculin tension in conjunction with its recruitment in response to force at adhesions of living cells. We demonstrate that vinculin recruitment is governed by trap stiffness rather than force and that the cell responds to higher stiffness with an increase in vinculin recruitment but less increase in vinculin tension. At high trap stiffness, a correlation between recruitment and tension is observed but not at low stiffness or with no optical trap. Such dynamic measurements, enabled by the techniques presented here, can help elucidate the mechanisms by which cells sense physical forces and the properties of proteins, such as vinculin, which play a fundamental role in cellular behaviors involving tissue growth and repair.

biophysics↗

bioRxiv2025

Isomerized Aβ in the brain can distinguish the status of amyloidosis in the Alzheimer's Disease spectrum

Extracellular amyloid plaques, the pathognomonic hallmark of Alzheimers Disease (AD), are also observed in cognitively unimpaired subjects in the preclinical stages. Progressive accumulation of fibrillar amyloid-{beta} (A{beta}) as plaques and perivascular deposits occur two decades prior to clinical onset, making A{beta} a long-lived peptide. To characterize the amyloid plaques biochemically, both the A{beta}-load as well the post-translational modifications (PTMs) could serve as markers for distinguishing the pre-clinical stage compared to later prodromal and clinical stages of AD. Recently, we described the presence of extensive isomerization of the A{beta} N-terminus in AD post-mortem brains that are significantly increased compared to the age-matched non-AD control brains with A{beta} aggregates in the frontal cortex. In this report, we used targeted mass spectrometry to conduct a quantitative analysis of the most common PTMs associated with A{beta}; pyroglutamation, citrullination, N-terminal truncation (A{beta}4-x), C-terminal truncation (A{beta}42 and A{beta}40), and isomerization of aspartic acid residues (Asp-1 and Asp-7) in postmortem human brain tissue from pathologically negative (no A{beta} plaques) controls, controls with A{beta} plaques, Parkinsons disease (PD) with and without A{beta} accumulation/plaques and symptomatic AD. The AD cases contained statistically significant amounts of Asp-1and Asp-7 isomerized A{beta}1-15 ([~] 90 %) compared to controls (preclinical AD) and PD brains with fibrillar A{beta} aggregates/deposits. We find that ratio of isomerized N-terminus A{beta} (A{beta}1-15) species in the brain detergent soluble pool differentiates older fibrillar A{beta} deposits in symptomatic AD brain compared to A{beta} deposits detected in preclinical AD and PD. Citrullinated A{beta}3pglu-15 was increased only in symptomatic AD, highlighting this A{beta} PTM is a unique feature of parenchymal plaques in advanced AD. Our results have implications for early therapeutic targeting of these modified species as well potential for better biofluid biomarker development for drug efficacy monitoring.

neuroscience↗

bioRxiv2024

HERV-derived epitopes represent new targets for T-cell based immunotherapies in ovarian cancer

BackgroundOvarian cancer represents the most lethal gynecological cancer with poor results of checkpoint inhibitors. Human endogenous retroviruses (HERVs) are aberrantly expressed by tumor cells and may represent a source of shared T cell epitopes for cancer immunotherapy regardless of the tumor mutational burden. MethodsA transcriptomic analysis based on RNA-sequencing (RNA-seq) was developed to quantify the expression of HERV-K sequences containing the selected epitopes. The presence of HERV-K/HML-2 Gag antigen was then assessed by immunohistochemistry (IHC) on tumor microarrays from ovarian cancer samples and normal ovarian tissues. A specific immunopeptidomics approach was developed to detect epitopes on HLA molecules. Epitope-specific CD8+ T cells were quantified by multimer staining and in vitro target cell killing was evaluated using xCELLigence technology. In vivo antitumor efficacy of HERV-specific T cells was assessed in an avian embryo model. ResultsEpitope-containing HERV transcripts were significantly higher in ovarian cancers compared to normal tissues. The presence of HERV-K/HML-2 Gag antigen was confirmed by IHC in 20/40 (50%) ovarian cancers while no Gag expression was found in normal ovarian tissue samples. Immunopeptidomics analysis showed the presence of epitopes on HLA molecules on the surface of ovarian tumor cell lines but not on normal primary cells from critical tissues. HERV-specific T cells were detected among tumor infiltrating lymphocytes (TILs) from ovarian cancers, confirming the immunogenicity of these epitopes in patients. In vitro, HERV-specific T cells specifically killed ovarian cancer cells in an HLA class I-restricted manner while sparing normal HLA-A2-positive primary cells derived from critical tissues. Epitope-specific CD8+ T cells exhibited a strong anti-tumoral activity in vivo, inducing a highly significant decrease in tumor volume in comparison with control groups. ConclusionThese results provide the preclinical rationale for developing T-cell based approaches against HERV-K-derived epitopes in ovarian cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/603392v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1c889b8org.highwire.dtl.DTLVardef@c9b0c5org.highwire.dtl.DTLVardef@1748100org.highwire.dtl.DTLVardef@1c129cc_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LISome HERVs are specifically overexpressed in ovarian cancer compared to normal tissues. C_LIO_LIHERV-K/HML-2 Gag antigen is detected by immunohistochemistry in ovarian cancers but not in normal ovarian tissues. Furthermore, HERV-K-derived epitopes are presented on HLA molecules on the surface of ovarian cancer cells but not on normal cells. C_LIO_LIThese epitopes are immunogenic in patients and induce high-avidity CD8+ T cells that specifically kill ovarian cancer cells in vitro and in vivo while sparing normal cells. C_LI

immunology↗

bioRxiv2024

CCR2 silencing in sensory neurons blocks bone cancer progression

The peripheral nervous system contributes to cancer growth, in part by shaping the immunological niche of the tumor. How the nervous system influences bone cancer progression, and whether the underlying neuroimmune pathways can be targeted therapeutically, remain unclear. Here we demonstrate a profound influence of the peripheral nervous system on tumor progression that can be countered by silencing chemokine receptor signaling in sensory neurons. Axotomy of the tumor-innervating femoral nerve inhibits tumor progression in animals bearing bone cancer, whereas intrathecal delivery of the tumor-associated proinflammatory chemokine CCL2 promotes both tumor growth and allodynia. Silencing CCR2 in dorsal root ganglion (DRG) neurons with a newly developed lipid nanoparticle-formulated Dicer-substrate siRNA impedes tumor progression and pathological bone remodeling, and relieves bone cancer-associated pain. Mechanistically, bone cancer drives CCR2-dependent transport of substance P and CGRP along the tumor-innervating femoral nerve, and these neuropeptides expand the tumor-associated macrophage population; silencing CCR2 in DRG neurons normalizes the neuropeptide milieu and ameliorates altered bone remodeling. We thus define a targetable neuroimmune axis that contributes to cancer progression. HighlightsO_LICancer progression activates sensory neurons, driving pain hypersensitivity and neuropeptide release. C_LIO_LIAxotomy of the tumor-innervating femoral nerve impedes tumor progression. C_LIO_LICCL2-CCR2 signaling in DRG neurons promotes pain hypersensitivity and cancer growth. C_LIO_LISilencing CCR2 in the DRG reduces pain hypersensitivity, tumor-associated macrophage numbers and cancer growth. C_LI

neuroscience↗

bioRxiv2024

Targeting a shared neoepitope derived from non-canonical translation of c-MYC oncogene in cancer cells

Cancer cells rely on alternative modes of translation for protein synthesis, promoting internal ribosome entry site (IRES)-dependent translation of mRNA encoding pro-oncogenic factors. Furthermore, ribosomes translate mRNA with lower fidelity in tumor cells. We proposed that these translational modifications in cancer produce shared tumor-specific epitopes derived from IRES-containing oncogenes. To identify such neoepitopes, we developed an in silico-based method that we applied to c-MYC. We showed that the non-canonical translation of c-MYC mRNA in cancer cells, involving a (+1) ribosomal frameshift, generates a shared neoepitope which induces high-avidity T cells able to kill tumor cells in vitro and in vivo while sparing normal cells. Our data provide preclinical rationale for developing immunotherapies targeting this c-MYC-derived neoepitope and validate a new type of shared translation-associated neoantigens.

immunology↗

bioRxiv2024

Caspase cleavage of Influenza A virus M2 disrupts M2-LC3 interaction and regulates virion production

Influenza A virus (IAV) Matrix 2 (M2) protein is an ion channel, required for efficient viral entry and egress. M2 interacts with the small ubiquitin-like LC3 protein through a cytoplasmic C-terminal LC3 interacting region (LIR). Here, we report that M2 is cleaved by caspases, abolishing the M2-LC3 interaction. A crystal structure of the M2 LIR in complex with LC3 indicates the caspase cleavage tetrapeptide motif (82SAVD85) is an unstructured linear motif that does not overlap with the LIR. Furthermore, an IAV mutant expressing a permanently truncated M2, mimicking caspase cleavage, is impaired in M2 plasma membrane transport and produces a significantly attenuated virus. Our results reveal a dynamic regulation of the M2-LC3 interaction by caspases. This highlights the role of host proteases in regulating IAV exit, relating virion production with host cell state.

microbiology↗

bioRxiv2024

Consequences of platelet-educated cancer cells on the expression of inflammatory and metastatic glycoproteins.

Cancer-associated thrombosis, a major cause of mortality in cancer patients, exhibits a 4 to 7 times higher incidence compared to the general population. Platelet activation by tumor cells contributes to this pro-thrombotic state. Cancer cell-educated platelets have also been described to be implicated in promoting metastasis. Intriguingly, our team, among others, unveils a reverse process, wherein platelets educate cancer cells by transferring lipids, RNAs, and proteins. Here, focusing on colorectal and pancreatic cancers, our study investigates genes and proteins mediating platelet education of cancer cells. We demonstrated, for the first time, that platelets can educate cancer cells by inducing changes in the transcription of genes related to glycosylation, inflammation, and metastasis in cancer cells themselves. These results indicate a direct impact of platelets on cancer cell phenotype. This novel insight suggests potential therapeutic avenues for cancer treatment, disrupting platelet-mediated alterations and influencing the course of cancer progression.

cancer biology↗

bioRxiv2024

ADP-dependent platelet activation is required for thrombus formation during a long-distance flight

The association between venous thromboembolism (VTE) and air travel is well documented. Prolonged exposure to reduced atmospheric pressure and low oxygen levels during flights triggers coagulation disorders, representing the primary risk factor for Deep Vein Thrombosis (DVT), surpassing immobility. In our study, we investigated how long-distance flight conditions affect VTE development in mice exposed to 6h of hypobaric hypoxia or normobaric normoxia after inferior vena cava (IVC) ligation. We observed a pro-thrombotic profile under flight-simulated conditions, characterized by larger thrombi with higher neutrophil and fibrin densities. However, no difference was observed in neutrophil extracellular traps (NETs) or fibrin-positive neutrophils in thrombi between groups, indicating that neutrophils/NETs may not be involved in DVT development during flight. Considering the elevated ADP levels observed at high altitudes, we further assessed thrombus formation in wild-type and P2RY12-deficient mice. Remarkably, thrombus formation was no longer affected by aircraft conditions in P2RY12-deficient or wild type mice treated with clopidogrel. We conclude that ADP-induced platelet activation is involved in the development of DVT during flight, suggesting that the use of P2RY12 inhibitors may be of interest to prevent DVT in susceptible patients.

pathology↗

bioRxiv2023

Targeting BTN2A1 enhances Vγ9Vδ2 T cell effector functions and triggers tumor cells pyroptosis

V{gamma}9V{delta}2 T cells are potent but elusive cytotoxic effectors. Means to stimulate their function could lead to powerful new cancer immunotherapies. BTN2A1, a surface protein has recently been shown to bind the V{gamma}9 chain of the {gamma}{delta} TCR but its precise role in modulating V{gamma}9V{delta}2 T cells functions remains unknown. Here we show that 107G3B5, a monoclonal anti-BTN2A1 agonist antibody, significantly enhances V{gamma}9V{delta}2 T cell functions against hematological or solid cell lines and against primary cells from adult acute lymphoblastic leukemia patients. New computer vision strategies applied to holotomographic microscopy videos show that 107G3B5 enhances the interaction between V{gamma}9V{delta}2 T cells and target cells in a quantitative and qualitative manner. In addition, we provide evidence that V{gamma}9V{delta}2 T cells activated by 107G3B5 induce caspase 3/7 activation in tumor cells, thereby triggering their death by pyroptosis. We thus demonstrate that targeting BTN2A1 with 107G3B5 enhances the V{gamma}9V{delta}2 T cell antitumor response by triggering the pyroptosis-induced immunogenic cell death.

cancer biology↗

bioRxiv2022

A single mild juvenile TBI in mice leads to regional brain tissue abnormalities at 12 months of age that correlate with cognitive impairment at the middle age in male mice

Traumatic brain injury (TBI) has the highest incidence amongst the pediatric population and its mild severity represents the most frequent cases. Moderate and severe injuries as well as repetitive mild TBI result in lasting morbidity. However, whether a single mild TBI sustained during childhood can produce long-lasting modifications within the brain is still debated. We aimed to assess the consequences of a single juvenile mild TBI (jmTBI) at 12 months post-injury in a mouse model. Non-invasive diffusion tensor imaging (DTI) revealed significant microstructural alterations in the hippocampus and the in the substantia innominata/nucleus basalis (SI/NB), structures known to be involved in spatial learning and memory. DTI changes paralled neuronal loss, increased astrocytic AQP4 and microglial activation in the hippocampus. In contrast, decreased astrocytic AQP4 expression and microglia activation were observed in SI/NB. Spatial learning and memory were impaired and correlated with alterations in DTI-derived derived fractional ansiotropy (FA) and axial diffusivity (AD). This study found that a single juvenile mild TBI leads to significant region-specific DTI microstructural alterations, distant from the site of impact, that correlated with cognitive discriminative novel object testing and spatial memory impairments at 12 months after a single concussive injury. Our findings suggest that exposure to jmTBI leads to a chronic abnormality, which confirms the need for continued monitoring of symptoms and the development of long-term treatment strategies to intervene in children with concussions.

neuroscience↗

bioRxiv2022

Precise temporal control of neuroblast migration through combined regulation and feedback of a Wnt receptor

Many developmental processes depend on precise temporal control of gene expression. We have previously established a theoretical framework for regulatory strategies that can govern such high temporal precision, but experimental validation of these predictions was still lacking. Here, we use the time-dependent expression of a Wnt receptor that controls neuroblast migration in C. elegans as a tractable system to study a robust, cell-intrinsic timing mechanism in vivo. Single molecule mRNA quantification showed that the expression of the receptor increases non-linearly, a dynamic that is predicted to enhance timing precision over an unregulated, linear increase in timekeeper abundance. We show that this upregulation depends on transcriptional activation, providing in vivo evidence for a model in which the timing of receptor expression is regulated through an accumulating activator that triggers expression when a specific threshold is reached. This timing mechanism acts across a cell division that occurs in the neuroblast lineage, and is influenced by the asymmetry of the division. Finally, we show that positive feedback of receptor expression through the canonical Wnt pathway enhances temporal precision. We conclude that robust cell-intrinsic timing can be achieved by combining regulation and feedback of the timekeeper gene.

developmental biology↗

bioRxiv2021

Maternal age affects equine Day 8 embryo gene expression both in trophoblast and inner cell mass

BackgroundBreeding a mare until she is not fertile or even until her death is common in equine industry but the fertility decreases as the mare age increases. Embryo loss due to reduced embryo quality is partly accountable for this observation. Here, the effect of mares age on blastocysts gene expression was explored. Day 8 post-ovulation embryos were collected from multiparous young (YM, 6-year-old, N = 5) and older (OM, > 10-year-old, N = 6) non-nursing Saddlebred mares, inseminated with the semen of one stallion. Pure or inner cell mass (ICM) enriched trophoblast, obtained by embryo bisection, were RNA sequenced. Deconvolution algorithm was used to discriminate gene expression in the ICM from that in the trophoblast. Differential expression was analyzed with embryo sex and diameter as cofactors. Functional annotation and classification of differentially expressed genes and gene set enrichment analysis were also performed. ResultsMaternal aging did not affect embryo recovery rate, embryo diameter nor total RNA quantity. In both compartments, the expression of genes involved in mitochondria and protein metabolism were disturbed by maternal age, although more genes were affected in the ICM. Mitosis, signaling and adhesion pathways and embryo development were decreased in the ICM of embryos from old mares. In trophoblast, ion movement pathways were affected. ConclusionsThis is the first study showing that maternal age affects gene expression in the equine blastocyst, demonstrating significant effects as early as 10 years of age. These perturbations may affect further embryo development and contribute to decreased fertility due to aging.

physiology↗

bioRxiv2020

Sensitivity to perturbations of a cell migration under temporal regulation

Few studies have measured the robustness to perturbations of the final position of a long-range migrating cell. In the nematode Caenorhabditis elegans, the QR neuroblast migrates anteriorly in the young larva, while undergoing three rounds of division. The daughters of QR.pa stop their migration at an anterior body position and acquire a neuronal fate. Previous studies showed that the migration stops upon expression of the Wnt receptor MIG-1, which surprisingly is not induced by positional cues but by a timing mechanism (Mentink et al. 2014). Given this temporal regulation, we wondered 1) how precise QR.pax positioning is when confronted with various challenges, such as stochastic noise, environment or body size variation and 2) whether QR.pax position varies among C. elegans wild isolates. We find that the variance of QR.pax final position is similar to that of other long-range migrating neurons. Its mean position undergoes a slight posterior shift at higher temperature, while its variance is greatly increased following sustained starvation at hatching. We manipulated body size using mutants and tetraploid animals. As expected from the temporal mechanism, smaller mutants display anteriorly shifted QR.pax cells, while longer mutants and tetraploids display posteriorly shifted QR.pax cells. Using a mathematical model, we show however that body size variation is partially compensated. We find that cell speed is indeed altered in body size mutants. Finally, we could detect highly significant variation among C. elegans wild isolates. Overall, this study reveals that the final cell position of QR.pax shows some degree of sensitivity to external perturbations and natural genetic variation.

developmental biology↗

bioRxiv2019

A broad mutational target explains an evolutionary trend

An evolutionary trend, the rapid evolution of a trait in a group of organisms, can in some cases be explained by the mutational variance, the propensity of a phenotype to change under spontaneous mutation. However, the causes of high mutational variance are still elusive. For some morphological traits, fast evolution was shown to depend on the high mutation rate of one or few underlying loci with short tandem repeats. Here, we investigate the case of the fastest evolving cell fate among vulva precursor cells in Caenorhabditis nematodes, that of the cell called P3.p. For this, we combine mutation accumulation lines, whole-genome sequencing, genetic linkage analysis of the phenotype in recombinant lines, and candidate testing through mutant and CRISPR genome editing to identify causal mutations and the corresponding loci underlying the high mutational variance of P3.p. We identify and validate molecular lesions responsible for changes in this cells phenotype during a mutation accumulation experiment. We find that these loci do not present any characteristics of a high mutation rate, are scattered across the genome and belong to distinct biological pathways. Our data instead indicate that a broad mutational target size is the cause of the high mutational variance and of the corresponding evolutionary trend.

evolutionary biology↗