Biology subjects

Dubois, S.

Publications and source records attributed to Dubois, S..

11 recordsLinked to original sources

bioRxiv2026

Motor experience leads to structural changes in the adult male mouse inferior olive

The activity of the inferior olive (IO), conveyed to the cerebellar cortex via climbing fibers and manifesting as the complex spikes (CSs) in Purkinje neurons, is at the core of major theories of cerebellar function and motor learning. While the computational meaning of the CSs remains under intense debate, it is well accepted that changes in their occurrence and timing play a critical role in guiding cerebellar plasticity. However, it has not been examined whether the plastic processes leading to these changes in cerebellar CS activity are expressed in the IO, or whether they are entirely caused by changes in brain structures upstream of the climbing fibers, including the cerebellar nuclei. Here, we examine whether prolonged, kinematically challenging motor experience can lead to detectable changes in the IO network structure that could underlie shifts in cerebellar CS activity. As the IO neurons communicate exclusively via electrical synapses (gap junctions) residing on dendritic structures, we hypothesized that if long-term increases in electrical coupling related to the insertion of new gap junctions occur in response to novel motor experiences, morphological changes in the dendrites would also be expected. To investigate this, we quantitatively characterized the geometry of the IO neuropil revealed by immunohistochemical staining in adult male mice. We found that the neuropil structure varies across olivary subnuclei in naive animals, possibly underlying known differences in cerebellar complex spike co-activation patterns. Geometrical measures related to structural complexity also revealed that exposing the animals to a challenging high-speed treadmill running task requiring full-body coordination led to localized changes suggestive of increased network connectivity. In addition, the density of immunofluorescence puncta labeling Cx36 increased in the same regions, supporting the notion that exposure to contexts where novel motor skills need to be acquired may lead to changes in the clustering strength among IO neurons and thereby restructuring of the olivo-cerebellar micromodules. To our knowledge, this is the first report of experience-related plasticity within the IO, calling for renewed attention to the role of the IO in olivocerebellar function.

neuroscience↗

bioRxiv2026

Machine Learning-Guided Engineering of High-Affinity Cross-Reactive Antibodies with Minimal Mutations

Antibodies raised against human targets often fail to recognize their animal orthologs, limiting preclinical evaluation in relevant models. We developed a Deep Mutational Scanning (DMS)-coupled deep learning strategy to engineer potent cross-reactive antibodies with minimal sequence divergence. Starting from C4, a fully human anti-PD-L1 antibody with weak recognition of murine PD-L1, DMS identified substitutions that improved binding to both human and mouse antigens. Conventional recombination of beneficial mutations generated highly cross-reactive antibodies but required 13 to 15 substitutions. To reduce this mutational burden, a deep learning model trained on DMS-derived sequence-binding data was used to identify minimal mutation combinations predicted to retain high affinity. This approach yielded variants carrying only 4 to 5 substitutions, with in vitro and cellular binding properties comparable to highly mutated antibodies. Epitope mapping, structural modeling and in vivo assessment further confirmed that these engineered antibodies retained PD-1/PD-L1 blockade and demonstrated therapeutic activity in a mouse tumor model.

molecular biology↗

bioRxiv2026

Simulating population pangenomes under coalescent demographic models with MSpangenome

MotivationPangenome variation graphs (PVGs) are increasingly used to represent genomic diversity, yet there is currently no general framework for generating population pangenomes directly from explicit evolutionary histories. Existing simulators typically focus on individual classes of variation and do not integrate these variations within a genealogy-aware framework driven by explicit demographic histories. As a result, evaluating pangenome methods in realistic population-genetic settings remains challenging, and benchmark datasets with known evolutionary ground truth are scarce. ResultsWe present MSpangenome, a genealogy-aware framework that bridges coalescent population genetic simulations and pangenome graph analyses. The pipeline combines ancestry simulation with msprime and a de novo graph construction algorithm to generate PVGs directly from simulated genealogies. By explicitly modeling recombination, demographic history and incomplete lineage sorting, MSpangenome produces structurally complex pangenomes in which nested and overlapping structural variants emerge naturally from the underlying genealogies, while their evolutionary history and graph topology remain known by construction. This provides a general framework for generating realistic population pangenomes and establishing ground-truth datasets for methodological evaluation. We demonstrate its utility by generating population-scale pangenomes and using them as controlled references to benchmark the widely used graph construction tools, PGGB and Minigraph-Cactus. Our analyses reveal contrasting performance regimes across levels of sequence diversity, sample sizes and classes of structural variation, highlighting the value of simulation-based benchmarking for identifying reconstruction errors that are hard to detect using empirical datasets alone. Availability and implementationMSpangenome is implemented in Python, fully containerized, freely available at https://forge.inrae.fr/pangepop/MSpangepop and mirrored at https://github.com/inrae/MSpangepop.

bioinformatics↗

bioRxiv2026

A Drosophila eye modifier screen identifies TBC1D25 as a modulator of RAB21 phenotypes

Membrane trafficking is essential to maintain cellular homeostasis, enabling cells and organelles to exchange molecular components via vesicle transport. Therefore, it is tightly regulated, including by RAB GTPases. Among these, RAB21, which is primarily associated with early endosomes, plays a central role in coordinating endocytosis, sorting, and degradation. Like other RABs, it cycles between GTP- and GDP-bound forms. Although three specific guanine exchange factors (GEFs) for RAB21 have been identified, surprisingly, no GTPase-activating proteins (GAPs) have been found to directly modulate RAB21. Here, we describe a genetic modifier screen in Drosophila that identified Tre/Bub2/Cdc16 (TBC) domain family member 25 (TBC1D25) as a potential negative regulator of RAB21. We confirmed the RAB21-TBC1D25 interaction using co-immunoprecipitation and proximity ligation assays and further demonstrated that their association depends on the catalytic activity of TBC1D25. Genetic interaction studies revealed a functional link between TBC1D25 and RAB21 in autophagy and cargo sorting. Collectively, our results indicate that TBC1D25 negatively regulates RAB21, potentially by serving as a RAB21-specific GAP.

cell biology↗

bioRxiv2025

Integration of sensory and cortical information in the brainstem during mastication in mice

Mastication is a vital function that relies on precise synchronization among multiple brainstem regions, known as being part of a central pattern generator (CPG). Movements can be triggered either by stimulating a sensory-motor region called the cortical masticatory area (CMA), well-documented in various species but not yet formally identified in mice, or by stimulating the oro-facial sensory primary afferents which fibers form the trigeminal tract (Vtr). However, its unclear whether these different inputs activate distinct components of the CPG or converge on the same. This study aims at mapping brainstem areas activated by cortical and sensory inputs using immunohistochemistry against the cellular activity marker, c-Fos and Ca2+-imaging, respectively. Optogenetic stimulation of the cortical masticatory area (CMA) in awake, head-fixed mice reliably induced rhythmic jaw movements (RJMs) and increased c-Fos expression in multiple brainstem regions, with strongest activation in the peritrigeminal area (PeriV) and parvocellular reticular formation (PCRt) ventral to the trigeminal motor nucleus (NVmt). In contrast, in vitro electrical stimulation of trigeminal sensory afferents (Vtr) predominantly activated neurons and astrocytes in the main sensory nucleus (NVsnpr), the dorsal area of PeriV, adjacent to it, and PCRt. The areas containing the highest numbers of activated cells differed clearly according to the type of inputs and overlapped only in the PCRt, ventral and slightly medial to the trigeminal motor nucleus and the most dorso-medial part of PeriV. These findings demonstrate that cortical and sensory inputs take part in distinct components of the brainstem masticatory circuitry, with PCRt emerging as a point of convergence and provide new insights into the components of the CPG of mastication.

neuroscience↗

bioRxiv2025

Investigating the topological motifs of inversions in pangenome graphs

BackgroundPangenome graphs are increasingly used in genetic diversity anal-yses because they reduce reference bias in read mapping and enhance variant discovery and genotyping from SNPs to Structural Variants. In pangenome graphs, variants appear as bubbles, which can be detected by dedicated bubble calling tools. Although these tools report essential information on the variant bubbles, such as their position and allele walks in the graph, they do not annotate the type of the detected variants. While simple SNPs, insertions, and deletions are easily distinguishable by allele size, large balanced variants like inversions are harder to differentiate among the large number of unannotated bubbles and remain underexplored in pangenome graph benchmarks and analyses. ResultsIn this work we focused on inversions, which have been drawing renewed attention in evolutionary genomics studies in the past years, and aimed to assess how this type of variant is handled by state of the art pangenome graph pipelines. We identified two distinct topological motifs for inversion bubbles: one path-explicit and one alignment-rescued, and developed a tool to annotate them from bubble-caller outputs. We constructed pangenome graphs with both simulated data and real data using four state of the art pipelines, and assessed the impact of inversion size, genome divergence and variant density on inversion representation and accuracy. ConclusionsOur results reveal substantial differences between pipelines in simulated graphs, with some inversions either misrepresented or lost. In addition, recovery rates are strikingly low in real human datasets, highlighting major challenges in analyzing inversions through pangenomic approaches.

bioinformatics↗

bioRxiv2024

Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs

MotivationPangenome variation graphs are an increasingly used tool to perform genome analysis, aiming to replace a linear reference in a wide variety of genomic analyses. The construction of a variation graph from a collection of chromosome-size genome sequences is a difficult task that is generally addressed using a number of heuristics. The question that arises is to what extent the construction method influences the resulting graph, and the characterization of variability. ResultsWe aim to characterize the differences between variation graphs derived from the same set of genomes with a metric which expresses and pinpoint differences. We designed a pairwise variation graph comparison algorithm, which establishes an edit distance between variation graphs, threading the genomes through both graphs. We applied our method to pangenome graphs built from yeast and human chromosome collections, and demonstrate that our method effectively characterizes discordances between pangenome graph construction methods and scales to real datasets. Availabilitypancat compare is published as free Rust software under the AGPL3.0 open source license. Source code and documentation are available at https://github.com/dubssieg/rs-pancat-compare. Contactsiegfried.dubois@inria.fr Supplementary informationSupplementary data are available online at https://doi.org/10.5281/zenodo.10932490. Code to replicate figures and analysis is available online at https://github.com/dubssieg/pancat_paper.

bioinformatics↗

bioRxiv2024

From local seafloor imagery to global patterns in benthic habitat states: contribution of citizen science to habitat classification across latitudes

AimThe aim of this study was to define reef benthic habitat states and explore their spatial and temporal variability at a global scale using an innovative clustering pipeline. LocationThe study uses data on the transects surveyed on shallow (< 20m) reef ecosystems across the globe. Time period: Transects sampled between 2008 and 2021. Major taxa studied: Macroalgae, sessile invertebrates, hydrozoans, seagrass, corals. MethodsPercentage cover was estimated for 24 functional groups of sessile biota and substratum from annotated underwater photoquadrats taken along 6,554 transects by scuba divers contributing to the Reef Life Survey dataset. A clustering pipeline combining a non-linear dimension-reduction technique (UMAP), with a density-based clustering approach (HDBSCAN), was used to identify benthic habitat states. Spatial and temporal variation in habitat distribution was then explored across ecoregions. ResultsThe UMAP-HDBSCAN pipeline identified 17 distinct clusters representing different benthic habitats and gradients of ecological state. Certain habitat states displayed clear biogeographic patterns, predominantly occurring in temperate regions or tropical waters. Notably, some reefs dominated by turf algae were ubiquitous across latitudinal zones. Transition zones between temperate and tropical waters emerged as spatial hotspots of habitat state diversity. Temporal analyses revealed changes in the proportion of certain states over time, notably an increase in turf algae occurrence. Main ConclusionsThe UMAP-HDBSCAN clustering pipeline effectively characterised fine-scale benthic habitat states at a global scale, confirming known broader biogeographic patterns, including the importance of temperate-tropical transition zones as hotspots of habitat state diversity. This fine-scale, yet broadly-scalable habitat classification could be applied as a standardised template for tracking benthic habitat change across space and time at a global scale. The UMAP-HDBSCAN pipeline has proven to be a powerful and versatile approach for analysing complex biological datasets and can be applied in various ecological domains.

ecology↗

bioRxiv2024

Birnaviral Hijacking of Endosomal Membranes

Birnaviruses are a group of double-stranded RNA (dsRNA) viruses infecting birds, fish and insects. Early endosomes (EE) constitute the platform for viral replication. Here, we study the mechanism of birnaviral targeting of EE membranes. Using the Infectious Bursal Disease Virus (IBDV) as a model, we validate that the viral protein 3 (VP3) binds to phosphatidylinositol-3-phosphate (PI3P) present in EE membranes. We identify the domain of VP3 involved in PI3P-binding, named P2 and localized in the core of VP3, and establish the critical role of the arginine at position 200 (R200), conserved among all known birnaviruses. Mutating R200 abolishes viral replication. Moreover, we propose a two-stage modular mechanism for VP3 association with EE. Firstly, the carboxy-terminal region of VP3 adsorbs on the membrane, and then the VP3 core reinforces the membrane engagement by specifically binding PI3P through its P2 domain, additionally promoting PI3P accumulation. Significance StatementBirnaviruses are a family of viruses unique among the group of dsRNA viruses. Here, we show that VP3 seizes the endosomes by anchoring to the PI3P lipids in the luminal side of the EE membrane, in order to organize the viral replication factory. We propose a two-stage modular mechanism for VP3 association with PI3P-enriched EE. The significance of this work resides in the biochemical and biophysical insights on the mechanism of association of VP3 with EE and its role in the viral life cycle, which represents a substantial contribution toward understanding the replication strategy of these "non-canonical" viruses.

microbiology↗

bioRxiv2021

Deep Mutational Engineering of broadly-neutralizing and picomolar affinity nanobodies to accommodate SARS-CoV-1 & 2 antigenic polymorphism

We report in this study the molecular engineering of nanobodies that bind with picomolar affinity to both SARS-CoV-1 and SARS-CoV-2 Receptor Binding Domains (RBD) and are highly neutralizing. We applied Deep Mutational Engineering to VHH72, a nanobody initially specific for SARS-CoV-1 RBD with little cross-reactivity to SARS-CoV-2 antigen. We first identified all the individual VHH substitutions that increase binding to SARS-CoV-2 RBD and then screened highly focused combinatorial libraries to isolate engineered nanobodies with improved properties. The corresponding VHH-Fc molecules show high affinities for SARS-CoV-2 antigens from various emerging variants and SARS-CoV-1, block the interaction between ACE2 and RBD and neutralize the virus with high efficiency. Its rare specificity across sarbecovirus relies on its peculiar epitope outside the immunodominant regions. The engineered nanobodies share a common motif of three amino acids, which contribute to the broad specificity of recognition. These nanobodies appears as promising therapeutic candidates to fight SARS-CoV-2 infection.

biochemistry↗

bioRxiv2020

Robust differentiation of human enteroendocrine cells from intestinal stem cells

Enteroendocrine (EE) cells are the most abundant hormone-producing cells in humans and are critical regulators of energy homeostasis and gastrointestinal function. Challenges in converting human intestinal stem cells (ISCs) into functional EE cells, ex vivo, have limited progress in elucidating their role in disease pathogenesis and in harnessing their therapeutic potential. To address this, we employed small molecule targeting of the endocannabinoid receptor signaling pathway, JNK and FOXO1, known to mediate endodermal development and/or hormone production, together with directed differentiation of human ISCs from the duodenum and rectum. We observed marked induction of EE cell differentiation and gut-derived expression and secretion of SST, 5HT, GIP, CCK, GLP-1 and PYY upon treatment with various combinations of three small molecules: rimonabant, SP600125 and AS1842856. Robust differentiation strategies capable of driving human EE cell differentiation is a critical step towards understanding these essential cells and the development of cell-based therapeutics.

developmental biology↗