Biology subjects

Bernard, D.

Publications and source records attributed to Bernard, D..

11 recordsLinked to original sources

bioRxiv2026

Design of a Conductive Hydrogel Coating to Improve Catheter-Tissue Coupling in Radiofrequency Ablation

Radiofrequency ablation is a mainstay of cardiac rhythm management despite high recurrence rates. Current radiofrequency ablation catheters are limited by poor contact with trabeculated cardiac tissue that promotes uneven heating with hot spots that cause collateral damage and regions of incomplete ablation that promote recurrence. Herein, we report on a conductive hydrogel coating of radiofrequency ablation catheters to improve tissue contact while promoting efficient energy transfer. A method was developed to graft a polyether urethane diacrylamide hydrogel to the distal tip of the catheter that maintained stable adhesion following drying, sterilization, and rehydration. The coating also remained intact after passage through an introducer sheath and 50 cycles of radiofrequency ablation at clinical power. The hydrogel-coated catheter demonstrated enhanced tissue contact that was dependent on hydrogel modulus. Hydrogel-mediated ablation prevented steam pop incidence and generated homogeneous lesions in an ex vivo ablation model; however, increased hydrogel conductivity is needed to achieve comparable lesion dimensions as the bare metal catheter and prevent coating damage at higher power. Collectively, these results establish a tunable hydrogel coating method that addresses limitations of conventional radiofrequency ablation and offers a promising approach to enhance the safety and efficacy of cardiac ablation therapies.

bioengineering↗

bioRxiv2025

The Pioneer Transcription Factor Oct4 Differentially Co-opts Bcl11a and Bcl11b to Regulate Reprogramming to Pluripotency

Pioneer transcription factors (TFs) orchestrate development, reprogramming, and cancer. Yet, the molecular mechanisms by which they cooperate with endogenous TFs and chromatin to trigger cell fate conversions remain largely unknown. Here, we identified antagonistic functions in reprogramming to pluripotency for the two paralogous somatic zinc finger TFs Bcl11a and Bcl11b. We reveal that Bcl11a and Bcl11b are initially co-expressed in mouse embryonic fibroblasts and then segregate in cellular intermediates respectively prone or refractory to reprogramming, transdifferentiation, and oncogenic transformation. They exert opposite functions - with Bcl11a promoting and Bcl11b hindering - the efficacy of induced pluripotent stem cells generation. During reprogramming, we uncover that Bcl11b safeguards cellular identity by persistently binding to differentiation genes with Runx1 in refractory intermediates. In contrast, in reprogramming intermediates, Bcl11a interacts with Oct4 and is initially displaced from MEF enhancers. Bcl11a then binds transiently and contributes to activate the E3 ubiquitin ligase Pja1 that regulates Smad3, thus promoting mesenchymal-epithelial transition and constraining senescence. Collectively, our work unveils how the differential repurposing of paralogous TFs by Oct4 orchestrates reprogramming to pluripotency.

cell biology↗

bioRxiv2025

Expert-guided multi-objective optimization: an efficient strategy for parameter estimation of biological systems with limited data.

Calibrating biological models is challenging due to high-dimensional parameter spaces and the limited availability of reliable experimental data. In this study, we propose a hybrid calibra- tion framework that integrates expert knowledge into a multi-objective optimization process using NSGA-II algorithm. Our approach combines hard constraints derived from biological measurements with soft constraints encoding qualitative domain expertise, such as expected curve shapes or event timing. This dual-constraint strategy guides the search toward biologi- cally plausible parameter sets while preserving flexibility and interpretability. We demonstrate the effectiveness of our method on a benchmark model of skin wound healing, comparing it to standard and unconstrained optimization strategies. Results show that incorporating expert guidance significantly improves the biological relevance of simulated dynamics and mitigates overfitting, especially in underdetermined or uncertain settings. The framework is flexible, it- erative, and generalizable, offering a principled way to leverage domain knowledge for model calibration in complex biological systems.

systems biology↗

bioRxiv2024

MYC shapes ER-mitochondria calcium transfer by directly targeting ITPR1: implications for MYC-induced safeguard mechanisms and cancer

The MYC and NMYC transcription factors (TFs) play a key role in cell proliferation and are overexpressed in most cancer cells. However, in normal cells their overexpression triggers safeguard mechanisms promoting cell death and cellular senescence, which are bypassed in cancer cells. The mechanisms of action of this TF family are only partially understood. Here, we reveal that in normal cells MYC binds to the Inositol 1,4,5-Trisphosphate Receptor type 1 (ITPR1) gene and upregulates its expression, triggering an ER-mitochondria calcium (Ca2+) transfer, which is involved in MYC-induced cell death and senescence. Supporting a tumor suppressive role of MYC/ITPR1 axis, ITPR1 expression is generally decreased in cancer and reactivation of this pathway induces cancer cell death. Nevertheless, some cancer cells, generally expressing high levels of MYCN and/or MYC, also express high level of ITPR1, which correlates with high expression of BCL2, encoding an inhibitor of ITPR1. Strikingly, in high-risk MYCN-amplified neuroblastoma, ITPR1 expression is controlled by NMYC and its level correlates with worse patient survival. In these cells, blocking the interaction between BCL2 and ITPR1 induces mitochondrial Ca2+ accumulation and cell death, and decreases tumor size. Collectively these data highlight a new function of MYC factors by controlling Ca2+ signaling, which could constitute an unsuspected vulnerability for some cancer cells, including high-risk MYCN-amplified neuroblastoma cells.

cancer biology↗

bioRxiv2024

DNA methylation protects cancer cells against non-canonical senescence

Inhibitors of DNA methylation such as 5-aza-deoxycytidine are widely used in experimental and clinical settings. However, their mechanism of action is such that DNA damage inevitably co-occurs with loss of DNA methylation, making it challenging to discern their respective effects. Here we deconvolute the effects of decreased DNA methylation and DNA damage on cancer cells, by using degron alleles of key DNA methylation regulators. We report that cancer cells with decreased DNA methylation --but no DNA damage-- enter cellular senescence, with G1 arrest, SASP expression, and SA-{beta}-gal positivity. This senescence is independent of p53 and Rb, but involves p21, which is cytoplasmic and inhibits apoptosis, and cGAS, playing a STING-independent role in the nucleus. Xenograft experiments show that tumor cells can be made senescent in vivo by decreasing DNA methylation. These findings reveal the intrinsic effects of loss of DNA methylation in cancer cells and have practical implications for future therapeutic approaches.

molecular biology↗

bioRxiv2024

A Comprehensive Framework for Spatio-Temporal Analysis of DNA Damage Foci in Tumor Spheroids.

The evaluation of DNA damage response, particularly DNA damage foci formation, is crucial for understanding tumor biology and assessing the impacts of various drugs. We have developed a sophisticated semi-automated image analysis pipeline which generates quantitative map of the spatiotemporal distribution of DNA damage foci within live tumor spheroids. Our framework seamlessly integrates live imaging of tumor spheroids via Light Sheet Fluorescence Microscopy with a DNA damage foci formation assay using a genetically encoded fluorescently labeled DNA damage sensor. By combining advanced imaging techniques with computational tools, our framework offers a powerful tool for studying DNA damage response mechanisms in complex 3D cellular environments. MOTIVATIONThe motivation of this work is to propose a comprehensive framework that facilitates the study of DNA repair mechanisms within 3D contexts, specifically using tumor spheroid models. By integrating advanced imaging technologies and genetically encoded fluorescent sensors, our goal is to offer researchers a robust methodology for observing and analyzing DNA damage dynamics in realistic tissue-like environments. This framework is designed to enhance accessibility and streamline data processing, thereby empowering the scientific community to investigate DNA repair processes in 3D with greater precision and efficiency.

cell biology↗

bioRxiv2024

Translational control of cell plasticity drives 5-FU tolerance

All routine clinical treatments for colorectal cancer include 5-fluorouracil (5-FU), which cannot counteract recurrence and metastases formation. As the pyrimidine analog 5-FU can impact multiple pathways including both DNA and RNA metabolism, studying its mode of actions could lead to improved therapies. Using a dedicated reporter system for lineage-tracing and deep translatome profiling we demonstrate that 5-FU causes some colorectal cancer cells to tolerate the drug, due to a durable translational reprogramming that sustains cell plasticity. This period of drug tolerance coincides with specific translational activation of genes coding for proteins with major pro-tumoral functions. We unravel a major unexpected translational overexpression of the pro-inflammatory and pro-tumoral IL-8 cytokine, alongside other anti-apoptotic, senescence-associated secretory phenotype and cancer-related senescence phenotype genes. Given the adverse prognostic implications of elevated IL-8 levels across various cancers, our findings suggest IL-8 targeting could counteract 5-FU resistance.

cancer biology↗

bioRxiv2023

Eliminating steam pops and improving lesion safety in atrial ablation with conductive hydrogels

BackgroundAtrial fibrillation (AF) is a significant burden worldwide, and the existing treatments leave much to be desired. There are, however, opportunities to improve the safety and efficacy of the most popular treatment, radiofrequency (RF) cardiac ablation, using conductive hydrogels as an ablation mediator. MethodsLesions were created in ex vivo ventricular tissues using bare metal traditional RF catheters and three different hydrogels with varying conductivities to assess the effect of conductivity on lesion formation. Similar procedures were performed in atrial/esophageal tissue stacks to mimic physiological AF ablation and demonstrate the initial safety profile of conductive hydrogel-mediated ablation. ResultsThe hydrogel mediated lesions were overall shallower and narrower than bare metal, and also exhibited less char and improved lesion homogeneity. The hydrogel also eliminated steam pops. Finally, the hydrogel appeared to be more thermally protective of the esophagus in the atrial/esophageal tissue stack, greatly reducing the lesion formation on the esophagus while still achieving transmural lesions in the atrial tissue. ConclusionsHydrogel-mediated RF ablation holds promise as a novel method to improve ablation outcomes for AF patients. Future work will confirm this in vivo and establish the chemistry required to create a conductive hydrogel coating for RF ablation catheters.

bioengineering↗

bioRxiv2023

ISiCell: involving biologists in the design process of agent-based models in cell biology

Agent-based models are commonly used in biology to study tissue-scale phenomena by reproducing the individual behavior of the cells. They offer the possibility to study cellular biology at the individual cell scale to explore the basic behavior of cells which are responsible of the emergence of more complex phenomena at the tissue scale. Additionally, they can produce a predictive tool that will help taking decisions for biologic experiments based on in silico simulations. However these models require a good intercomprehension between the biologists and the modelers and thus it may take weeks or months to end up providing a usable prototype. To address this limitation, we propose a new methodology to facilitate the dialog between biologists and modelers and improve biologists involvement in the design of the model. For this purpose, UML diagrams, in particular, state-transition and activity diagrams, are used. They allow a better comprehension of the model for the biologists and offer a general frame for structuring models. Visualization of simulations is also used to have qualitative feedbacks from the biologist on the model. They are instrumental to validate or refine the prototype before exploring it. Alongside this methodology, we propose a web platform that enables to build state-transition and activity diagrams to describe a model and translate them into code. The generated code is then compiled on-the-fly and simulations are ready to visualize and explore. The platform also disposes of tools to directly visualize and manually explore the model. These tools allow for qualitative validation of the model and additional interaction with the biologists. Finally in this article, we show the capacity of our platform to reproduce models from the literature and to build new models starting from workshops with biologists. Its range of application is wide and includes immunology, oncology or cell biology. Author summaryWe developed a methodology based on diagrams to facilitate the dialog between computer scientists and biologists when building in silico models. The main idea is to limit misunderstandings and improve the involvement of the biologists in the prototyping process. For this purpose, we use visual methods to simplify the modeling phase. Alongside this methodology, we propose a web platform, called ISiCell, which enables to visually code thanks to diagrams that will be translated into code. The platform allows for compiling the generated code on the fly and to visualize and explore the model directly with the platform. The strong advantage of the platform is that one day workshop biologist/modeler allows to build new models. Additionally, we were able to reproduce models from the literature within the modeling platform showing the versatility of the tool. Our long-term objective is to use our methodology and platform in new contexts to develop new models. We intend the make the platform more user friendly in order to expand the community of users. Involving biologists in the conception of in silico models might improve their acceptability in the community.

systems biology↗

bioRxiv2021

Cholesterol biosynthetic pathway induces cellular senescence through ERRa

Cellular senescence is a cell program induced by various stresses that leads to a stable proliferation arrest and to a senescence-associated secretory phenotype. Accumulation of senescent cells during age-related diseases participates in these pathologies and regulates healthy lifespan. Recent evidences point out a global dysregulated intracellular metabolism associated to senescence phenotype. Nonetheless, the functional contribution of metabolic homeostasis in regulating senescence is barely understood. In this work, we describe how the mevalonate pathway, an anabolic pathway leading to the endogenous biosynthesis of poly-isoprenoids, such as cholesterol, acts as a positive regulator of cellular senescence in normal human cells. Mechanistically, this mevalonate-induced senescence is partly mediated by the downstream cholesterol biosynthetic pathway. This pathway promotes transcriptional activity of ERR leading to dysfunctional mitochondria, ROS production, DNA damage and a p53-dependent senescence. Supporting the relevance of these observations, increase of senescence in liver due to a high-fat diet regimen is abrogated in ERR knockout mouse. Overall, this work unravels the role of cholesterol biosynthesis in the induction of an ERR-dependent mitochondrial program leading to cellular senescence and related pathological alterations.

cell biology↗

bioRxiv2019

ORP5 REGULATES TRANSPORT OF LIPIDS AND CALCIUM TO MITOCHONDRIA AT ENDOPLASMIC RETICULUM-MITOCHONDRIA MEMBRANE CONTACT SITES

Mitochondria are dynamic organelles essential for cell survival whose structural and functional integrity rely on selective and regulated transport of lipids from/to the endoplasmic reticulum (ER) and across the mitochondrial intermembrane space. As they are not connected by vesicular transport, the exchange of lipids between ER and mitochondria occurs at sites of close organelle apposition called membrane contact sites. However, the mechanisms and proteins involved in these processes are only beginning to emerge. Here, we show that the main physiological localization of the lipid transfer proteins ORP5 and ORP8 is at mitochondria-associated ER membranes (MAMs) subdomains, physically linked to the MIB/MICOS complexes that bridge the two mitochondrial membranes. We also show that ORP5/8 mediate non-vesicular transport of phosphatidylserine (PS) lipids from the ER to mitochondria by cooperating with the MIB/MICOS complexes. Overall our study reveals a novel physical and functional link between ER-mitochondria contacts involved in lipid transfer and intra-mitochondrial membranes contacts maintained by the MIB/MICOS complexes.

cell biology↗