Biology subjects

Dubois, T.

Publications and source records attributed to Dubois, T..

10 recordsLinked to original sources

bioRxiv2026

A green fluorescent protein for live imaging in hyperthermophiles

Hyperthermophiles, organisms that thrive at temperatures above 60 {degrees}C, have played important roles in biotechnology and promise to reveal new biology. However, how these cells live remains poorly understood in part due to the lack of bright, thermostable fluorescent proteins that can be used to study protein localisation and dynamics at high temperatures. To overcome this challenge, here we describe the development of "Matcha", a green fluorescent protein that we have engineered from Thermal Green Protein by directed evolution in the thermophilic archaeon Sulfolobus acidocaldarius. The screen identified 7 mutations that when combined led to an [~]50-fold increase in the brightness of Matcha in vivo at physiological temperatures. Since this is sufficient for live cell imaging, we were then able to use Matcha-fusion proteins to study the division ring dynamics in Sulfolobus. Remarkably, this analysis reveals that, while ESCRT-III rings are disassembled as cells complete division, CdvA forms a stable polymeric ring that persists, and is asymmetrically inherited by one of the two daughter cells following cytokinesis. This study highlights the power of Matcha as a tool to shed light on our understanding of the cell biology of hyperthermophiles.

cell biology↗

bioRxiv2025

CD133 shapes extracellular vesicle cargo and angiogenic function in basal-like triple-negative breast cancer

Extracellular vesicles (EVs) are central mediators of tumor-stroma communication, yet the mechanisms governing their biogenesis and functional cargo remain poorly understood. Here, we identify CD133 (Prominin-1), selectively expressed in basal-like triple-negative breast cancer (BL-TNBC) cells, as a key regulator of EV production and cargo composition. CD133 localizes to plasma membrane protrusions and lipid rafts, maintaining membrane architecture, promoting EV release, and shaping selective protein loading, including the pro-angiogenic factor CD105. Functionally, CD133 EVs potently induce endothelial tubulogenesis in a CD105-dependent manner, independently of EV uptake or endothelial proliferation. In vivo, these EVs preferentially accumulate in the lung and liver, highlighting organ-specific communication. Mechanistically, CD133 maintains lipid raft integrity, facilitating CD105 selective incorporation into vesicles, thereby establishing a spatially coordinated CD133-CD105 axis. Together, our findings define a subtype-specific EV population whose identity and angiogenic activity are dictated by membrane organization. By linking protrusion architecture to vesicle-mediated signaling, this study highlights CD133-enriched EVs as potential biomarkers and therapeutic targets in aggressive BL-TNBC.

cell biology↗

bioRxiv2025

Inhibition of PTCH1 drug efflux activity enhances chemotherapy efficacy against triple negative breast cancer

Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subgroup characterized by a high risk of resistance to chemotherapies and high relapse potential. High levels of mRNA from the Hedgehog receptor PTCH1 are associated with poor prognosis in TNBC. PTCH1 is overexpressed in many aggressive cancers. We previously reported that PTCH1 is a multidrug transporter that triggers resistance to chemotherapy of adrenocortical carcinoma and melanoma cells, and that inhibiting PTCH1 drug efflux strongly enhanced chemotherapy efficacy on these cell lines both in vitro and in vivo. In the present study, we found that PTCH1 inhibition also significantly inhibited doxorubicin efflux in three TNBC cell lines leading to a strong increase of the cytotoxic effect of doxorubicin and docetaxel, and an inhibition of cell migration. Altogether, our data highlight the therapeutic potential of targeting PTCH1 drug efflux activity using drug association strategies for the treatment of TNBC patients.

cancer biology↗

bioRxiv2025

Wnt signaling promotes inflammation and EMT-associated gene expression in mesenchymal TNBC

Aberrant activation of the Wnt signaling pathway in triple-negative breast cancer (TNBC) is linked to treatment resistance and recurrence, yet its role in tumoral heterogeneity remains unclear. We developed Wnt reporter cell lines from two mesenchymal TNBC models (MDA-MB-231 and MDA-MB-436) using a Tcf/Lef-eGFP vector and observed intra- and inter-tumoral variation in Wnt activity. Paired Wnt-positive and Wnt-negative TNBC cell lines were established and profiled by RNA-Seq. Integrative analyses revealed that Wnt-positive cells consistently upregulate genes involved in epithelial-to- mesenchymal transition, inflammation (e.g., IL6/JAK/STAT3, TNF via NF-{kappa}B), and extracellular matrix remodeling. A 55-gene Wnt signature common to both nutrient conditions captured these features. Wnt-related gene sets were also enriched in the Mesenchymal-like Immune-Altered subtype of 699 primary TNBC tumors. These findings highlight the role of basal Wnt activity in driving pro-tumorigenic transcriptional programs in TNBC and provide new insight into its contribution to subtype-specific disease features.

bioinformatics↗

bioRxiv2025

CARM1-mediated methylation controls interactions of ALIX with key partners important for cytokinesis

CARM1 is an arginine methyltransferase with a well-established role in regulating gene expression, but its cytoplasmic functions remain largely uncharacterized. Here, we identified ALIX, a protein acting with the ESCRT-III machinery in numerous membrane remodeling events, as a main cytoplasmic partner and a relevant substrate of CARM1. We demonstrate that CARM1 methylates arginine residues within the proline-rich motif of ALIX. At the molecular level, ALIX methylation impairs SH3-dependent association with CD2AP, CIN85, and endophilin-A2 that are required for cytokinesis. Using a mutant of ALIX that is unable to bind these proteins, we further show that these interactions are essential for ALIX functions during cytokinesis. Altogether, this work highlights the significance of arginine methylation as a regulatory post-translational modification important for the final step of cell division, by modulating interactions between proline-rich domains and their SH3-containing partners.

cell biology↗

bioRxiv2022

Genetic glyco-profiling and rewiring of insulated flagellin glycosylation pathways

Glycosylation of surface structures diversifies cells chemically and physically. Sialic acids commonly serve as glycosyl donors, particularly pseudaminic (Pse) or legionaminic acid (Leg) that prominently decorate eubacterial and archaeal surface layers or appendages. We investigated a new class of FlmG protein glycosyltransferases that modify flagellin, the structural subunit of the flagellar filament. Functional insulation of orthologous Pse and Leg biosynthesis pathways accounted for the flagellin glycosylation specificity and motility conferred by the cognate FlmG in the -proteobacteria Caulobacter crescentus and Brevundimonas subvibrioides, respectively. Exploiting these functions, we conducted genetic glyco-profiling to classify Pse or Leg biosynthesis pathways and we used heterologous reconstitution experiments to unearth a signature determinant of Leg biosynthesis in eubacteria and archaea. These findings and our chimeric FlmG analyses reveal two modular determinants that govern flagellin glycosyltransferase specificity: a glycosyltransferase domain that accepts either Leg or Pse and that uses specialized flagellin-binding domain to identify the substrate.

microbiology↗

bioRxiv2021

PRMT1 regulates EGFR and Wnt signaling pathways and is a promising target for combinatorial treatment of breast cancer

Identifying new therapeutic strategies for triple-negative breast cancer (TNBC) patients is a priority as these patients are highly prone to relapse after chemotherapy. Here, we found that protein arginine methyltransferase 1 (PRMT1) is highly expressed in all breast cancer subtypes. Its depletion decreases cell survival by inducing DNA damage and apoptosis in various breast cancer cell lines. Transcriptomic analysis and chromatin immunoprecipitation revealed that PRMT1 regulates the epidermal growth factor receptor (EGFR) and the Wnt signaling pathways, reported to be activated in TNBC. The enzymatic activity of PRMT1 is also required to stimulate the canonical Wnt pathway. Recently developed type I PRMT inhibitors decrease breast cancer cell proliferation and show anti-tumor activity in a TNBC xenograft model. These inhibitors display synergistic interactions with some chemotherapies used to treat TNBC patients, as well as the EGFR inhibitor, erlotinib. Therefore, targeting PRMT1 in combination with drugs used in the clinic may improve current treatments for TNBC patients. SignificanceThis study highlights the requirement of PRMT1 for breast cancer cell survival and demonstrates the potential of targeting type I PRMTs in combination with chemotherapies in triple-negative breast cancer.

cancer biology↗

bioRxiv2020

Bumblebees develop more efficient traplines than honey bees

Central place foraging pollinators, such as bees, tend to learn multi-destination routes (traplines) to efficiently visit known feeding locations and return to their nest. To what extent these routing behaviours are shared across species is unknown. Here we ran laboratory experiments to compare trapline formation and efficiency by foragers of two social bee species that differ in their collective foraging strategies: the solo foraging bumblebee Bombus terrestris and the mass foraging honey bee Apis mellifera. In a simple routing task with four artificial flowers, both bumblebees and honey bees developed a stable route, although honey bees were slower and less efficient to do so. In a more complex routing task with six flowers, only bumblebees developed a stable route. Honey bees took a longer time to discover all flowers and never integrated them in a single route. Simulations of a model of trapline formation show that these inter-specific differences can be replicated by adjusting the strength of a single learning parameter. Comparing bumblebees and honey bees in the same experimental conditions thus revealed key differences in their spatial foraging strategies, potentially driven by social constraints.

animal behavior and cognition↗

bioRxiv2020

A model of resource partitioning between foraging bees

Central place foraging pollinators tend to develop multi-destination routes (traplines) to visit patchily distributed plant resources. While the formation of traplines by individual pollinators has been studied in details, how populations of foragers exploit resources in a common area is an open question, difficult to address experimentally. We explored conditions for the emergence of resource partitioning among traplining bees using agent-based models built from experimental data of bumblebees foraging on artificial flowers. In the models, bees learn to develop routes as a consequence of feedback loops that change their probabilities of moving between flowers. While a positive reinforcement of movements leading to rewarding flowers is sufficient for the emergence of resource partitioning when flowers are evenly distributed, addition of negative reinforcement of movements leading to unrewarding flowers is necessary when flowers are patchily distributed. In environments with more complex spatial structure, the negative experiences of individual bees on flowers favour spatial segregation and efficient collective foraging.

animal behavior and cognition↗

bioRxiv2018

Identification of microRNA clusters cooperatively acting on Epithelial to Mesenchymal Transition in Triple Negative Breast Cancer

MicroRNAs play important roles in many biological processes. Their aberrant expression can have oncogenic or tumor suppressor function directly participating to carcinogenesis, malignant transformation, invasiveness and metastasis. Indeed, miRNA profiles can distinguish not only between normal and cancerous tissue but they can also successfully classify different subtypes of a particular cancer. Here, we focus on a particular class of transcripts encoding polycistronic miRNA genes that yields multiple miRNA components. We describe clustered MiRNA Master Regulator Analysis (ClustMMRA), a fully redesigned release of the MMRA computational pipeline (MiRNA Master Regulator Analysis), developed to search for clustered miRNAs potentially driving cancer molecular subtyping. Genomically clustered miRNAs are frequently co-expressed to target different components of pro-tumorigenic signalling pathways. By applying ClustMMRA to breast cancer patient data, we identified key miRNA clusters driving the phenotype of different tumor subgroups. The pipeline was applied to two independent breast cancer datasets, providing statistically concordant results between the two analysis. We validated in cell lines the miR-199/miR-214 as a novel cluster of miRNAs promoting the triple negative subtype phenotype through its control of proliferation and EMT.

systems biology↗