Biology subjects

Borg, J.-P.

Publications and source records attributed to Borg, J.-P..

At least 19 recordsLinked to original sources

bioRxiv2026

A quantitative interactome map reveals affinity tailored hijacking of human cellular functions by resident and pathogenic bacteria

Bacteria employ molecular mimicry to hijack host cellular functions for their own benefit. Despite the wealth of data mapping human-bacteria interactions, a comprehensive view of how these networks are fine-tuned remains elusive. In particular, there have been no large-scale screenings measuring human-bacterial protein-protein binding affinities to explore their role in functional and pathological outcomes. Here, we report the largest quantitative interactome to date between the family of human PDZ domains and C-terminal PDZ-binding motifs (PBMs) in effectors from pathogenic and resident gut bacteria. We show that bacteria tailor effector sequences to bind PDZ domains with similar or higher binding affinities than human PBMs to hijack their associated cellular functions. For a subset of the dataset, we validate PDZ-PBM interactions with the corresponding full-length proteins and show that for pathogenic E. coli effector NleA, its C-terminal PBM is necessary for interactions with proteins involved in intracellular transport and membrane organization, probably impacting the host glycocalyx to favor infection. Finally, we show that motifs overlapping with effector PBMs target interaction modules other than PDZ domains, adding an additional layer of complexity to the host-microbe molecular dialogue.

systems biology↗

bioRxiv2026

The atypical cadherin CELSR2 regulates distinct epithelial-mesenchymal states and oxidative phosphorylation in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is characterized by marked intratumoral heterogeneity, which contributes to metastatic dissemination, therapeutic resistance, and poor clinical outcome. Epithelial-mesenchymal plasticity is a major contributor to this heterogeneity. Identifying the molecular regulators governing epithelial-mesenchymal plasticity is therefore essential to understanding how distinct tumor cell populations arise and fuel TNBC progression. Here, we identify the adhesion G protein-coupled receptor CELSR2 as an independent poor-prognosis marker and regulator of epithelial-mesenchymal plasticity in TNBC. Spatial transcriptomic analyses revealed segregation of CELSR2high tumor cells within the epithelial tumor core and CELSR2low tumor cells at the invasive front. In line with the latter observation, CELSR2 expression decreases during EMT and its loss promotes acquisition of a hybrid epithelial-mesenchymal state. CELSR2high tumor cells display a CREB-associated oxidative phosphorylation (OXPHOS) program and promote cell proliferation and primary tumor growth. Conversely, CELSR2low cells display features of a more migratory phenotype. Collectively, our findings identify CELSR2 as a previously unknown regulator of epithelial-mesenchymal plasticity and reveal that heterogeneous CELSR2 expression shapes spatially and functionally distinct tumor cell populations, thereby contributing to intratumoral heterogeneity in TNBC.

cancer biology↗

bioRxiv2026

Circulating colorectal tumor cells remodel their surfaceome to increase their viability and metastatic potential in the bloodstream

Circulating tumor cells (CTCs) are the potential seeds of distant metastases; however, little is known about how they survive in the bloodstream. Using a large cohort of colorectal cancer (CRC) patients, we found that the pseudokinase receptor PTK7 is highly expressed in primary tumors and metastatic lesions. Consistent with previous reports, high PTK7 expression is associated with reduced disease-free survival and increased metastatic dissemination. Surprisingly, PTK7 is absent from most CTCs and undergoes a cell-autonomous ONtumor/OFFCTC/ONmetastasis switch that can be recapitulated in a xenografted mouse model, in in vitro systems, and a fluidic platform. PTK7-negative cancer cells exhibit increased expression of YAP1-driven genes, senescence-like features, and enhanced resistance to hemodynamic stress following loss of cell-cell and cell-matrix adhesion. This adaptive phenotype depends on metalloproteases, notably ADAM17, whose cleavage activity remodels the CTCs surfaceome. Functionally, the PTK7 OFFCTC state confers enhanced metastatic potential in vivo, and can be pharmacologically suppressed using metalloprotease inhibitors. Collectively, our findings identify a reversible, cell-autonomous, protease-driven surfaceome remodeling program that enables metastatic adaptation during hematogenous dissemination. Highlights / statement of significanceBy investigating potential markers for circulating colorectal tumor cells with strong metastatic potential, we describe a reversible and cell-autonomous remodeling of the circulating tumor cell surfaceome in patients that confers resistance to anoikis and stress induced by entry into the bloodstream. One Sentence SummaryThe dynamic regulation of PTK7 serves as a surrogate marker for tumor cell plasticity, aggressiveness, survival in the bloodstream, and efficiency in forming metastases. Trial registrationCTC colon Cohort: registered on https://ClinicalTrials.gov identifier NCT03256084; date of registration 2017-07-17 B-Org cohort: registered on https://ClinicalTrials.gov NCT05384184; date of registration 2019-06-06 Ethics statement for animal experimentsStudies on animals were conducted in accordance with the current ethical standards of the European Community (Directive 2010/63/EU), the Ethics Committee for Animal Experimentation (CEEA#14) and the French Ministry of Higher Education and Research, which approved and authorized the entire procedure described in this paper (project number APAFIS #35294).

cancer biology↗

bioRxiv2025

TTLL6-mediated Polyglutamylation of PurA Maintains Colonic Crypt Integrity

The tubulin tyrosine ligase-like (TTLL) family comprises enzymes catalyzing posttranslational modifications of tubulin, including glutamylation and glycylation. We previously described a critical role for the monoglycylase TTLL3 in colon. Here, we identified TTLL6 as the predominant polyglutamylase in the colon, specifically expressed in epithelial cells of distal and transverse segments. TTLL6 expression decreases during CRC progression, correlating with poor patient prognosis. Deletion of Ttll6 in mice resulted in elongated colonic crypts, expansion of stem and transit-amplifying compartments, and increased numbers of differentiated epithelial cells. Moreover, Ttll6-deficient mice showed an elevated susceptibility to chemically induced colon carcinogenesis. Notably, we identified the nucleic acid-binding protein PurA as a novel TTLL6 substrate with both proteins mutually required for nuclear localization. Consistently, both nuclear polyglutamylation and PurA were present in the bottom compartment of control colons, but reduced in Ttll6-deficient colons. These findings reveal a TTLL6-PurA axis being critical in maintaining colonic homeostasis.

cell biology↗

bioRxiv2025

Deciphering the dynamic proteome of multiciliated cells

Multiciliated cells (MCCs) are essential for generating directional fluid flow across specialized epithelia in various vertebrate organs. MCC differentiation involves a unique, tightly regulated program characterized by massive centriole amplification, independently of DNA replication. Although much is known about the transcriptional control of MCC development, insights into proteome dynamics have been limited due to the lack of suitable models. In this study, we report the generation of a stable inducible MCC line, derived from Xenopus laevis A6 kidney epithelial cells. Upon induction of the MCC master regulator Multicilin (MCI), most A6-MCI cells synchronously differentiate into mature MCCs in 48 hours. Using this novel resource, custom antibodies and super-resolution imaging, we characterized Xenopus deuterosomes, the platforms that allow massive centriole synthesis in vertebrate MCCs. We performed a detailed proteomic profiling throughout MCC differentiation, and uncovered previously uncharacterized regulators. Notably, we highlight a critical role for CDK7 in MCC differentiation in both Xenopus and human systems. Our work provides a valuable resource for mechanistic studies of MCC biology and opens avenues to identify novel therapeutic targets for motile ciliopathies.

cell biology↗

bioRxiv2024

Testing and overcoming the limitations of Modular Response Analysis

Modular Response Analysis (MRA) is an effective method to infer biological networks from perturbation data. However, it has several limitations, such as strong sensitivity to noise, need of performing independent perturbations that hit a single node at a time, and linear approximation of dependencies within the network. Previously, we addressed MRA sensitivity to noise by revisiting MRA as a multilinear regression problem. Here, we provide new contributions to complement this theory. First, we overcame the need of perturbations to be independent, thereby augmenting MRA applicability. Second, using analysis of variance (ANOVA) and lack of fit tests, we assessed MRA compatibility with the data and identified the primary source of errors. If nonlinearity prevails, we propose a polynomial extension to the model. Third, we demonstrated how to effectively use the prior knowledge of the network studied. Finally, we added these innovations to our R software package MRARegress to provide a complete, extended theory around MRA and to facilitate its access by the community.

bioinformatics↗

bioRxiv2023

Downregulation of stromal syntenin sustains AML development

The crosstalk between cancer and stromal cells plays a critical role in tumor progression. Syntenin is a small scaffold protein involved in the regulation of intercellular communication that is emerging as a target for cancer therapy. Here, we show that certain aggressive forms of acute myeloid leukemia (AML) reduce the expression of syntenin in bone marrow stromal cells (BMSC), stromal syntenin deficiency, in turn, generating a pro-tumoral microenvironment. From serial transplantations in mice and co-culture experiments, we conclude that syntenin-deficient BMSC stimulate AML aggressiveness by promoting AML cell survival and protein synthesis. This pro-tumoral activity is supported by increased expression of endoglin, a classical marker of BMSC, which in trans stimulates AML translational activity. In short, our study reveals a vicious signaling loop potentially at the heart of AML-stroma crosstalk and unsuspected tumor-suppressive effects of syntenin that need to be considered during systemic targeting of syntenin in cancer therapy.

cancer biology↗

bioRxiv2021

Discovery of small molecule inhibitors of the PTK7/β-catenin interaction targeting the Wnt signaling pathway in colorectal cancer

Second cause of death due to cancer worldwide, colorectal cancer (CRC) is a major public health issue. The discovery of new therapeutic targets is thus essential. The pseudokinase PTK7 intervenes in the regulation of the Wnt/{beta}-catenin pathway signaling, in part, through a kinase-domain dependent interaction with the {beta}-catenin protein. PTK7 is overexpressed in CRC; an event associated with metastatic development and reduced survival of non-metastatic patient. In addition, numerous alterations have been identified in CRC inducing constitutive activation of Wnt/{beta}-catenin pathway signaling through {beta}-catenin accumulation. Thus, we thought that targeting PTK7/{beta}-catenin interaction could be of interest for future drug development. In this study, we have developed a NanoBRET screening assay recapitulating the interaction between PTK7 and {beta}-catenin to identify compounds able to disrupt this protein-protein interaction. A high-throughput screening allowed us to identify small molecule inhibitors targeting the Wnt pathway signaling and inducing anti-proliferative effect in vitro in CRC cells harboring {beta}-catenin or APC mutations downstream of PTK7. Thus, inhibition of the PTK7/{beta}-catenin interaction could represent, in the future, a new therapeutic strategy to inhibit cell growth dependent on Wnt signaling pathway. Moreover, despite a lack of enzymatic activity of its tyrosine kinase domain, targeting the PTK7 kinase domain-dependent functions appears to be of interest for further therapeutic development.

pharmacology and toxicology↗

bioRxiv2021

The serine/threonine kinase MINK1 directly regulates the function of promigratory proteins

Upregulation of the developmental Wnt/planar cell polarity pathway is observed in many cancers and is associated with cancer development at early and late stages. We recently showed that PRICKLE1 and VANGL2, two core Wnt/PCP components, are overexpressed in triple negative breast cancer and associated with poor prognosis. PRICKLE1 is a cytoplasmic protein phosphorylated by the poorly described serine/threonine kinase MINK1 which triggers its localization at the plasma membrane, a key step for its function. Knockdown experiments have demonstrated that MINK1 and PRICKLE1 contribute to TNBC cell motility and spreading in vitro and in vivo. However, the identity of MINK1 substrates and the role of MINK1 enzymatic activity in this process have not yet been addressed issues. We carried out a phosphoproteomic strategy and identified novel MINK1 substrates including LL5{beta}. LL5{beta} is a membrane scaffold molecule that anchors microtubules at the cell cortex through its association with the plus-end MT proteins CLASPs to trigger focal adhesion disassembly. LL5{beta} is a prominent member of the MINK1-PRICKLE1 protein complex and is directly phosphorylated by MINK1 that promotes its interaction with CLASP. Using a kinase inhibitor, we demonstrate that the enzymatic activity of MINK1 is involved in the protein complex assembly and localization, and cell migration. Analysis of gene expression data show that the concomitant up-regulation of PRICKLE1 and LL5{beta} mRNA levels encoding MINK1 substrates is associated with a poor metastasis-free survival for TNBC patients. Altogether, our results suggest that MINK1 may represent a potential target in TNBC.

cell biology↗

bioRxiv2021

Interactome and structural basis for targeting the human T-cell leukemia virus Tax oncoprotein

Human T-cell leukemia virus type-1 (HTLV-1) is the causative agent of adult T-cell leukemia (ATL). Although ATL is a well-characterized T-cell neoplasm, linked to intermittent expression of the viral Tax-1 protein, there is currently no strategy to target Tax-1 functions using small molecules. Here, we report a comprehensive interaction map between Tax-1 and human PDZ domain-containing proteins (hPDZome). We show that Tax-1 interacts with more than one-third of hPDZome components, including proteins involved in cell cycle, cell-cell junctions, cytoskeleton organization, and membrane complex assembly. Using nuclear magnetic resonance (NMR) spectroscopy, we have determined the structural basis of the interaction between the C-terminal PDZ binding motif (PBM) of Tax-1, and the PDZ domains of syntenin-1, an evolutionary conserved hub that controls exosome trafficking. Finally, we have used confocal imaging, molecular modelling, NMR and mammalian cell-based assays to demonstrate that the Tax-1/syntenin-1 interaction is amenable to small-molecule inhibition. Altogether, our study highlights the biological significance of Tax-PDZ interactome and its interplay with exosome formation. It shows a direct link between extracellular vesicles and HTLV-1 transmission, providing a novel framework for the design of targeted therapies for HTLV-1-induced diseases.

biochemistry↗

bioRxiv2021

The unique Brucella effectors NyxA and NyxB target SENP3 to modulate the subcellular localisation of nucleolar proteins

The cell nucleus is a primary target for intracellular bacterial pathogens to counteract immune responses and hijack host signalling pathways to cause disease. The mechanisms controlling nuclear protein localisation in the context of stress responses induced upon bacterial infection are still poorly understood. Here we show that the Brucella abortus effectors NyxA and NyxB interfere with the host sentrin specific protease 3 (SENP3), which is essential for intracellular replication. Translocated Nyx effectors directly interact with SENP3 via a defined acidic patch identified from the crystal structure of NyxB, preventing its nucleolar localisation at the late stages of the infection. By sequestering SENP3, the Nyx effectors induce the cytoplasmic accumulation of the nucleolar AAA-ATPase NVL, the large subunit ribosomal protein L5 (RPL5) and the ribophagy receptor NUFIP1 in Nyx-enriched structures in the vicinity of replicating bacteria. This shuttling of ribosomal biogenesis-associated nucleolar proteins is negatively regulated by SENP3 and dependent on the autophagy-initiation protein Beclin1, indicative of a ribophagy-derived process induced during Brucella infection. Our results highlight a new nucleomodulatory function by two unique Brucella effectors, and reveal that SENP3 is a critical regulator of the subcellular localisation of multiple nucleolar proteins during Brucella infection, promoting intracellular replication.

microbiology↗

bioRxiv2021

A syntenin-deficient microenvironment educates AML for aggressiveness

In acute myeloid leukemia (AML), the stromal microenvironment plays a prominent role in promoting tumor cell survival and progression. Although widely explored, the crosstalk between leukemic and stromal cells remains poorly understood. Syntenin, a multi-domain PDZ protein, controls both the trafficking and signaling of key molecules involved in intercellular communication. Therefore, we aimed to clarify the role of environmental syntenin in the progression of AML. By in vivo approaches in syngeneic mice, we demonstrate that a syntenin-deficient environment reprograms AML blasts to survive independently of the stroma. Up-regulation of EEF1A2 in the blasts controls this gain of cell survival. Furthermore, using ex vivo co-culture systems, we show that syntenin-deficient bone marrow stromal cells (BMSC) enhance the survival of different types of AML cells, including patient samples, and suffice to educate syngeneic AML, recapitulating micro-environmental effects observed in vivo. We establish that syntenin-deficiency causes an increase of eIF5A and autophagy-related factors in BMSC, and provide evidence that the inhibition of autophagy prevents syntenin-deficient BMSC to stimulate AML survival. Altogether, these findings indicate that host-syntenin in the BM microenvironment acts as a repressor of AML aggressiveness. Key points- A syntenin-deficient host reprograms AML blasts, enhancing total protein synthesis and cell survival pathways - Autophagy in the syntenin-deficient microenvironment is responsible for the gain of AML cell survival

cancer biology↗

bioRxiv2020

PLD2-phosphatidic acid recruit ESCRT-I to late endosomes for exosome biogenesis.

It is important to understand the biogenesis of exosomes, extracellular vesicles of endosomal origin controlling cell-to-cell communication. We previously reported that Phospholipase D2 (PLD2) supports late endosome (LE) budding and the biogenesis of syntenin-dependent exosomes. Here, we reveal that PLD2 has a broader generic effect on exosome production. Combining gain- and loss-of-function experiments, proteomics, microscopy and lipid-binding studies with reconstituted liposomes mimicking LE, we show that: (i) PLD2 activity controls the recruitment of MVB12B to LE and the exosomal secretion of ESCRT-I; (ii) loss-of-MVB12B phenocopies loss-of-PLD2, similarly affecting LE budding, the number of exosomes released and exosome loading with cargo; (iii) MVB12B MABP domain directly interacts with phosphatidic acid, the product of PLD2. We therefore propose that PLD2 and phosphatidic acid support ESCRT-I recruitment to LE for the formation of exosomes. This work highlights a major unsuspected piece of the molecular framework supporting LE and exosome biogenesis.

cell biology↗

bioRxiv2020

A novel Golgi-associated Vangl2 translational variant required for PCP regulation in vertebrates

First described in Drosophila melanogaster, planar cell polarity (PCP) is a developmental process essential for embryogenesis and development of polarized structures in Metazoans. This signaling pathway involves a set of evolutionarily conserved genes encoding transmembrane (Vangl, Frizzled, Celsr) and cytoplasmic (Prickle, Dishevelled) molecules. Vangl2 is of major importance in embryonic development as illustrated by its pivotal role during neural tube closure in human, mouse, Xenopus and zebrafish embryos. The regulated and poorly understood traffic of Vangl2 to the plasma membrane is a key event for its function in development. Here we report on the molecular and functional characterization of a novel 569-amino acid N-terminally extended Vangl2 isoform, Vangl2-Long, that arises from an alternative non-AUG translation initiation site, lying 144 base pair upstream of the conventional start codon. While missing in Vangl1 paralogs and in all invertebrates, including Drosophila melanogaster, this N-terminal extension is conserved in all vertebrate Vangl2 sequences and confers a subcellular localization in the Golgi apparatus, probably as a result of an extended retention time in this organelle. Vangl2-Long belongs to a multimeric complex with Vangl1 and Vangl2 and we show that its down-regulation leads to severe PCP-related phenotypes in Xenopus embryos, including shorter body axis and neural tube closure defects. Altogether, our study unveils a novel level of complexity in Vangl2 expression, trafficking and function.

cell biology↗

bioRxiv2020

The human PDZome 2.0: characterization of a new resource to test for PDZ interactions by Yeast Two-Hybrid

PSD95-disc large-zonula occludens (PDZ) domains are globular modules of 80-90 amino acids that co-evolved with multicellularity. They commonly bind to carboxy-terminal sequences of a plethora of membrane-associated proteins and influence their trafficking and signaling. We previously built a PDZ resource (PDZome) allowing to unveil human PDZ interactions by Yeast two-hybrid. Yet, this resource is partial according to the current knowledge on the human PDZ proteome. Here we built the PDZome 2.0 library for Yeast two-hybrid, based in a PDZ library manually curated from online resources. The PDZome2.0 contains 305 individual clones (266 PDZ domains in isolation and 39 tandems), for which all boundaries have been designed based on available PDZ structures. Using as bait the E6 oncoprotein from HPV16, a known promiscuous PDZ interactor, we show that PDZome 2.0 outperforms the previous resource.

molecular biology↗

bioRxiv2020

Modeling heterogeneity of Triple-Negative Breast Cancer highlights potency of WEE1 and BCL-XL targeting

Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer subtype characterized by a remarkable molecular heterogeneity. Currently, there are no effective druggable targets and advanced preclinical models of the human disease. Here, we generated a unique mouse model (MMTV-R26Met mice) of mammary tumors driven by a subtle increase in the expression of the wild-type MET receptor. MMTV-R26Met mice develop spontaneous, exclusive TNBC tumors, recapitulating primary resistance to treatment of patients. Proteomic profiling of MMTV-R26Met tumors and machine learning approach showed that the model faithfully recapitulates inter-tumoral heterogeneity of human TNBC. Further signaling network analysis highlighted potential druggable targets, of which co-targeting of WEE1 and BCL-XL synergistically killed TNBC cells and efficiently induced tumor regression. Mechanistically, BCL-XL inhibition exacerbates the dependency of TNBC cells on WEE1 function, leading to Histone H3 and phosphoS33RPA32 upregulation, RRM2 downregulation, cell cycle perturbation, mitotic catastrophe and apoptosis. Our study introduces a unique, powerful mouse model for studying TNBC formation and evolution, its heterogeneity, and for identifying efficient therapeutic targets.

cancer biology↗

bioRxiv2019

CRB2 controls primary ciliogenesis in association with PAR6α, HOOK2 and RAB8A

Ciliogenesis is an essential process in animal development and physiology and when affected, the origin of severe pathologies called ciliopathies. CRB2 has been recently implicated when mutated in several pathologies such as retina degeneration and a ciliopathy-like syndrome. Here, we have investigated the role of CRB2 in primary ciliogenesis and showed that CRB2 depletion blocks the formation of the ciliary vesicle after activation of the mother centriole, indicating a defect in either transport or anchoring of the ciliary vesicle. CRB2 is accumulated in intracellular vesicles in the vicinity of the centrosome and we showed here that CRB2 forms a complex made of HOOK2 and PAR6, two proteins important for primary ciliogenesis or centrosome integrity. In addition, CRB2 interacts with RAB8A which over-expression rescued CRB2 knockdown. All together, these findings indicate that CRB2 regulates a membrane transport step essential for the formation of the ciliary vesicle.

cell biology↗

bioRxiv2019

Brucella effector hijacks endoplasmic reticulum quality control machinery to prevent premature egress

Perturbation of endoplasmic reticulum (ER) functions can have critical consequences for cellular homeostasis. An elaborate surveillance system known as ER quality control (ERQC) ensures that only correctly assembled proteins reach their destination. Persistence of misfolded or improperly matured proteins upregulates the unfolded protein response (UPR) to cope with stress, activates ER associated degradation (ERAD) for delivery to proteasomes for degradation. We have identified a Brucella abortus type IV secretion system effector called BspL that targets Herp, a key component of ERQC and is able to augment ERAD. Modulation of ERQC by BspL results in tight control of the kinetics of autophagic Brucella-containing vacuole formation, preventing premature bacterial egress from infected cells. This study highlights how bacterial pathogens may hijack ERAD components for fine regulation of their intracellular trafficking.

microbiology↗