Biology subjects

Leroy, A.

Publications and source records attributed to Leroy, A..

10 recordsLinked to original sources

bioRxiv2026

Morphodynamic domains enable integration of live morphometrics and spatial transcriptomics

Tissue development emerges from the coordinated behaviors of thousands of cells, orchestrated by gene regulatory networks. Recent methodological advances now enable high-resolution live imaging of cell- and tissue-scale dynamics and the construction of spatially resolved gene expression atlases. However, quantitatively linking these modalities remains a central challenge, limiting our ability to understand how gene regulatory networks drive cell- and tissue-scale behaviors. Here, using the Drosophila thorax epithelium as a model system, we introduce an analytical and computational framework based on tissue morphodynamic domains: regions defined by coherent cell and tissue dynamics extracted from live imaging morphometrics. Integrating morphodynamic domains with spatial transcriptomics enables the inference of gene regulatory networks associated with distinct spatial cell- and tissue-level behaviors. Statistical cross-scale analyses further allow the interrogation and validation of gene function, confirming or revealing regulators of specific morphogenetic dynamics. In particular, our framework uncovers a role for the Toll-like receptor Tollo in modulating tissue flow, contraction, and apoptosis. Together, our work establishes a framework that integrates spatial transcriptomics with quantitative, multiscale live morphometrics, providing a generalizable strategy to probe and understand developmental processes.

developmental biology↗

bioRxiv2026

Analysis of the principles governing the dimensionality reduction performed by Lobula Plate Tangential Cells

Lobula Plate Tangential Cells (LPTCs) are critical for visual navigation in flies, enabling efficient processing of optical flow. Unlike upstream neurons in the visual pathway, such as those in the Lobula, Medulla, and T4/T5 layers, which retain a retinotopic organisation, LPTCs perform the first major dimensionality reduction of visual signals. This reduction simplifies the vast amount of visual information into key motion signals essential for navigation. In this paper, we investigate the principles governing this dimensionality reduction and explore with a data-based approach the efficiency of LPTCs in compressing optical flow information while preserving critical motion cues for navigation and their role in transmitting information to descending neurons. More specifically, our contribution is as follows: (i) we demonstrate, using Principal Component Analysis (PCA) as a reference, that global optical flow patterns, as also found in LPTC response maps, are efficient to describe and encode the variation in the optical flow experienced during visual navigation tasks; (ii) we show that LPTCs present a strong alignment with Principal Components of the experienced optical flow, supporting the hypothesis that the LPTCs maximize the flow of signal energy from the T4/T5 cells to the descending neurons; and (iii) we show that whilst LPTCs encode optical flow information in a lossy fashion, it can be reconstructed. Using optical flow priors, such as the complementarity of LPTCs in contralateral hemispheres and continuity of the flow in navigation tasks, we performed a reconstruction of the original flow from LPTCs response. Our analysis reveals the dual potential of LPTCs: selectively relaying signals for navigation that are fine-tuned in relation to the flys own dynamics; and broadly compressing the optical flow information that is sensed by the flys visual system.

animal behavior and cognition↗

bioRxiv2025

Endothelial NMDA receptor involvement in retinal neurovascular damage following prenatal alcohol exposure in mouse model

Prenatal alcohol exposure (PAE) induces neurodevelopmental damage leading to fetal alcohol spectrum disorders (FASD) by altering both brain and ocular development. Recent data showed that PAE impairs brain cortical and retinal vasculature leading to defective positioning of interneurons. In the retina, PAE disturbs vascular development and the association of calretinin neurons with vessels. The NMDA receptor (NMDAR) is a major target of alcohol in the brain, and both ligand binding to NMDARs and the expression of NMDAR subunits are altered in FASD. Given that NMDAR is also expressed in endothelial cells and that glutamate stimulation of endothelial NMDAR (eNMDAR) regulates cortical interneuron positioning along blood vessels, we hypothesize that eNMDAR is critical for retinal vascular development and mediates PAE-induced defects. Using an in vivo model of FASD and transgenic mice lacking, specifically in endothelial cells, the GluN1 subunit of the NMDAR, this study aimed to characterize the neurovascular phenotype of the developing retina. The results show that eNMDAR knockout delays the formation of the superficial vascular plexus and prevents the alterations in vascular organization and neuronal density induced by PAE, particularly cells positioned closer to the retinal vasculature, namely ganglion, amacrine, and horizontal cells. Moreover, eNMDAR deletion led to an increased number of calretinin-positive interneurons in contact with perforating vessels and prevents the decrease induced by PAE. Together, these findings demonstrate that eNMDARs are essential for normal retinal neurovascular development and mediate, at least in part, the detrimental effects of ethanol exposure in FASD. Significance statementUsing a murine model of Fetal Alcohol Spectrum Disorder (FASD) and transgenic mice lacking the GluN1 subunit of the NMDA receptor specifically in endothelial cells (eNMDAR), this study demonstrates that eNMDAR plays a critical role in mediating prenatal alcohol exposure (PAE)-induced neurovascular abnormalities in the retina. Loss of eNMDAR alters the progression of the superficial vascular plexus and prevents the vascular impairments typically observed following PAE. In addition, eNMDAR deletion protects against PAE-induced neuronal damage, particularly affecting retinal ganglion cells, calbindin-positive, and calretinin-positive interneurons. Notably, this study identifies, for the first time, a role for endothelial NMDAR in regulating neurovascular interactions between retinal vessels and calretinin-positive neurons, highlighting this receptor as a key molecular mediator of ethanol-induced retinal damage.

neuroscience↗

bioRxiv2025

Characterization of the African Swine Fever Virus transcriptome and the associated innate immune response reveals key features of virulence

African Swine Fever Virus (ASFV) represents a looming threat to animal health, food safety and to the livestock industry. Virulent strains of ASFV cause a severe and often fatal illness, while attenuated strains are usually associated with mild symptoms. Naturally-occurring attenuated strains are typically deleted of more than 20 genes located at the viral genomes extremities. Whether other key differences between virulent and attenuated ASFV strains may contribute to the virulence phenotype remains however largely unexplored. In this work, we sought to determine how the dynamics of viral gene expression may shape the hosts innate immune response to ASFV infection and contribute to ASFV virulence. We conducted a medium-throughput transcriptomic study to characterize the viral transcriptome of a panel of virulent and attenuated strains (171 viral genes), as well as the host response of ASFV-infected macrophages (92 host genes). Confocal imaging allowed further characterization of cellular response to infection, by assessing the dynamics of IFN and NF-{kappa}B pathway activation in ASFV-infected cells. Our results indicate that the two types of viral pathotypes exhibit global differences in the dynamics of genome replication and viral transcription. Virulent ASFV strains displayed a burst of viral transcription early on, while attenuated strains tended to replicate to higher levels at late time points. The host response was much more pronounced in cells infected with attenuated strains compared to virulent ones, with higher expression levels of interferon-stimulated genes, some innate immunity sensors, and the inducible chaperone HSP70.2. Unexpectedly, genotype I and genotype II virulent strains exhibited some notable differences in their kinetics of viral genome replication and in the host response they provoked, with higher levels of pro-inflammatory cytokines being induced by genotype II strains. Confocal imaging analysis of ASFV-infected primary macrophages revealed that attenuated strains, but not virulent ones, caused the translocation of both p65 and STAT2 to the nucleus. Strikingly, we identified a group of 26 viral genes that were either expressed at higher levels or at an earlier stage of infection by virulent strains. Several of these genes, such as R298L, H233R, DP71L and MGF505-7R encode for proteins that inhibited the type I Interferon response in a reporter cell line system. This work sheds new light on the mechanistical drivers of ASFV virulence and will in the long run help to better understand the protection offered by ASFV Live-Attenuated Vaccine candidates. Author summaryAfrican Swine Fever (ASF), a severe infectious disease affecting domestic pigs and wild boars, presents a global threat to the livestock industry. It is caused by African Swine Fever Virus (ASFV), a large DNA virus encoding between 150 and 200 genes. While virulent ASFV strains cause a fatal illness in infected animals, attenuated strains induce only minor symptoms and some can confer subsequent protection against a pathogenic infection. While Live-Attenuated Vaccines for ASFV are under development and represent a promising tool in the fight against ASF, the mechanisms of ASFV virulence (and conversely, attenuation) are not fully understood. In particular, it is unclear whether key differences may exist between attenuated and virulent ASFV strains, beyond the extensive genomic deletions harbored by the former. In this work, we explored for the first time how the dynamics of viral gene expression may influence the innate immune response to different ASFV strains. We found that attenuated ASFV strains trigger a stronger host response compared to virulent ASFV strains, with higher expression levels of innate immune genes and a stronger activation of key signaling hubs. Finally, we identified a group of 26 ASFV genes that may drive this phenomenon and represent novel virulence factors.

microbiology↗

bioRxiv2025

Graph Neural Networks for Likelihood-Free Inference in Diversification Models

A common approach to infer the processes that gave rise to past speciation and extinction rates across taxa, space and time is to formulate hypotheses in the form of probabilistic diversification models and estimate their parameters from extant phylogenies using Maximum Likelihood or Bayesian inference. A drawback of this approach is that likelihoods can easily become computationally intractable, limiting our ability to extend current diversification models with new hypothesized mechanisms. Neural networks have been proposed as a likelihood-free alternative for parameter inference of stochastic models, but so far there is little experience in using this method for diversification models, and the quality of the results is likely to depend on finding the right network architecture and data representation. As phylogenies are essentially graphs, graph neural networks (GNNs) appear to be the most natural architecture but previous results on their performance are conflicting, with some studies reporting poor accuracy of GNNs in practice. Here, we show that this underperformance was likely caused by optimization issues and inappropriate pooling operations that flatten the information along the phylogeny and make it harder to extract relevant information about the diversification parameters. When equipped with PhyloPool, a new time-informed pooling procedure, GNNs show similar or better performance compared to all other architectures and data representations (including Maximum Likelihood Estimation) that we tested for two common diversification models, the Constant Rate Birth-Death and the Binary State Speciation and Extinction. We conclude that GNNs could serve as a generic tool for estimating diversification parameters of complex diversification models with intractable likelihoods.

evolutionary biology↗

bioRxiv2025

Drosophila Toll-2 controls homeotic domain formation and timing of folding

Tissue compartmentalization is a fundamental feature of animal development, crucial for determining cell fate, growth, and organ morphogenesis. Hox genes play essential and conserved roles in specifying homeotic compartments along the antero-posterior axis of the body. Despite extensive characterization of homeotic gene regulation, the mechanisms underlying the formation, maintenance, and reshaping of homeotic compartments during development remain incompletely understood. Here, we investigate the role of the Toll-2 receptor in the formation and folding of the Deformed (Dfd) homeotic compartment, which produces the neck of adult Drosophila. We show that Toll-2 is essential for properly forming the bilateral Dfd compartment through the fusion of the two eye-antennal imaginal discs. Additionally, we find that Toll-2 regulates the timing of neck morphogenesis by promoting cell apoptosis and cell-cell rearrangements preceding neck folding. Last, we establish that Toll-2 independently and sequentially governs both homeotic compartment formation and the timing of its morphogenesis via PI3K and Src signaling, respectively. Altogether, our findings provide novel insights into the spatiotemporal regulation of homeotic compartment development.

developmental biology↗

bioRxiv2024

Second generation of LNP based mRNA vaccine leads to a T-cell-inflamed tumor microenvironment favorable for improving PD-1/PD-L1 blocking therapy and long-term immunity in a cold tumor model

The delivery of mRNA-based cancer vaccines has demonstrated significant promise in triggering antitumor immune responses. With the aim of using them in combination with other immunotherapies already used in the clinical appropriately, the modifications of the intratumoral immune microenvironment needs to be deeply characterized. We have shown that the second generation of lipid nanoparticles (LNPs), nanostructured lipid carriers (so-called Lipidots(R)), are able to vector protein antigens and nucleic acids. Here, we test Lipidots(R) for the delivery of mRNA encoding OVA antigen and eliciting a specific antitumor immune response. We demonstrate in vitro that our LNPs deliver mRNA into dendritic cells (DCs), when complexed with mRNA, activate DCs through the TLR4/8 and ROS signaling pathways and induce specific CD4+ and CD8+ T cell activation. Our vaccinal strategy exhibits significant antitumor efficacy both in the context of tumor prevention and as a therapeutic vaccine in B16OVA and E.G7-OVA cold tumors. The LNP-Ova mRNA vaccine induces a profound intratumoral remodeling of the innate and adaptive immunity associated with an increase in the gene expression of chemokines (Cxcl10, Cxcl11, Cxcl9) involved in CD8+ T cell attraction. Additionally, the vaccine induces the establishment of an escape mechanism mediated by PD-1/PDL-1 axis, making it an adjuvant therapy for optimized responses to the blocking of this signaling pathway. Finally, the combination of vaccine and anti-PD-1 therapy achieves a much higher rate of complete responses and memory immune responses compared to monotherapies. Our work demonstrates the capability of Lipidots(R) as an effective platform for the development of preventive and therapeutic vaccines against cancer based on mRNA delivery and that combination with other immunotherapies such as immune checkpoint blockers could counter tumor resistance and promote long-term antitumor immunity.

immunology↗

bioRxiv2022

Systematic characterization of Drosophila RhoGEF/GAP localizations uncovers regulators of mechanosensing and junction formation during epithelial cell division.

Cell proliferation is central to epithelial tissue development, repair and homeostasis. During cell division, small RhoGTPases control both actomyosin dynamics and cell-cell junction remodelling to faithfully segregate the duplicated genome while maintaining tissue polarity and integrity. To decipher the mechanisms of RhoGTPases spatiotemporal regulation during epithelial cell division, we generated a transgenic fluorescently tagged library for Drosophila Rho Guanine exchange factors (GEF) and GTPase activating proteins (GAP), and systematically characterized their endogenous distributions by time- lapse microscopy. Thereby, we unveiled candidate regulators of the interplay between actomyosin and junctional dynamics during epithelial cell division. Building on these findings, we uncovered that during cytokinesis, Cysts and RhoGEF4 play sequential roles in mechanosensing and de novo junction formation, respectively. We foresee that the RhoGEF/GAP library will be a key resource to understand the broad range of biological processes regulated by RhoGTPases.

developmental biology↗

bioRxiv2021

Endowing Universal CAR T-cell with Immune-Evasive Properties using TALEN-Gene Editing.

Universal CAR T-cell therapies are poised to revolutionize cancer treatment and to improve patient outcomes. However, realizing these advantages in an allogeneic setting requires universal CAR T-cells that can kill target tumor cells, avoid depletion by the host immune system, and proliferate without attacking host tissues. Here, we describe the development of a novel immune-evasive CAR T-cells scaffold that evades NK cell and alloresponsive T-cell attacks and imparts efficient antitumor activity in vitro and in vivo. This scaffold could enable the broad use of universal CAR T-cells in allogeneic settings and holds great promise for future powerful clinical applications.

immunology↗

bioRxiv2020

Intrusive Experiences In Post-Traumatic Stress Disorder: Treatment Response Induces Changes In The Effective Connectivity Of The Anterior Insula

BackgroundOne of the core features of posttraumatic stress disorder (PTSD) is reexperiencing the trauma. The anterior insula (AI) was proposed to play a crucial role in these intrusive experiences. However, the dynamic function of the AI in reexperiencing trauma, as well as its putative modulation by effective therapy, still need to be specified. MethodsThirty PTSD patients were enrolled and exposed to traumatic memory reactivation therapy. Resting-state fMRI scans were acquired before and after treatment. To explore AI directed influences over the rest of the brain, we referred to a mixed-model using pre/post Granger causality analysis seeded on the AI as a within-subject factor and treatment response as a between-subject factor. To further identify correlates of reexperiencing trauma, we investigated how intrusive severity affected: (i) causality maps and (ii) the spatial stability of other intrinsic brain networks. ResultsWe observed dynamic changes in AI effective connectivity in PTSD patients. Many within- and between-network causal paths were found to be less influenced by the AI after effective therapy. Insular influences were found positively correlated with flashback severity, while reexperiencing was linked with a stronger default mode network (DMN) and more unstable central executive network (CEN) connectivity. ConclusionWe showed that directed changes in AI signaling to the DMN and CEN at rest may underlie the degree of intrusive symptoms in PTSD. A positive response to treatment further induced changes in network-to-network anticorrelated patterns. Such findings may guide targeted neuromodulation strategies in PTSD patients not suitably improved by conventional treatment.

neuroscience↗