Biology subjects

Aubert, I.

Publications and source records attributed to Aubert, I..

8 recordsLinked to original sources

bioRxiv2026

Aberrant cortical reorganization and astrogliosis underlie memory deficit post-traumatic brain injury: a longitudinal multiscale multimodal study

Integrating high-dimensional neuroimaging data across spatial scales remains a fundamental bottleneck in quantitative neuroscience. Here, we apply emerging analytical techniques including functional connectome gradient mapping and 3D segmentation of whole-brain cellular resolution microscopy data in a mouse model of traumatic brain injury. At the macroscale, longitudinal functional MRI revealed a transition from frontal hyperconnectivity to hippocampal hypoconnectivity and unimodal-transmodal gradient contraction indicating network dedifferentiation. At the cellular scale, deep-learning based segmentation of whole-brain light-sheet fluorescence microscopy volumes quantified regional astrogliosis, neuronal hyperactivity, and single-axon loss undetected by standard diffusion MRI. Multiscale multimodal data integration not only identified quantitative biomarkers predictive of memory performance post-injury but also enabled validation of in vivo modalities against more sensitive ex vivo histology. This study demonstrates a framework for probing complex multi-network cognitive functions and neurological disorders of network dysfunction.

neuroscience↗

bioRxiv2025

Quantitative profiling of whole-brain connectomes at single-axon resolution using deep learning and high-resolution light sheet microscopy

Revealing how individual axons create a brain-wide connectome would be indispensable for understanding brain function and behavior, yet remains technically challenging. We introduce MAPL3, an end-to-end pipeline that integrates self-supervised learning with an innovative deep architecture to capture local and global brain-wide axonal projections. MAPL3 enables subject- and population-level quantitative laminar analysis, generalizes across experiments, and outperforms state-of-the-art methods. We showcase its ability to map the circuitry of the orbitofrontal cortex from single axons to whole-brain projectome.

neuroscience↗

bioRxiv2025

Early micro and nanoscopic responses of microglia to blood-brain barrier modulation by transcranial-focused ultrasound

Modulation of the blood-brain barrier (BBB) using transcranial-focused ultrasound (FUS) has rapidly progressed to clinical trials. In combination with phospholipid microspheres, also known as microbubbles, administered in the bloodstream, ultrasound energy is guided by magnetic resonance imaging (MRI) to target specific brain regions with millimetric precision. At the targeted area, the interaction between FUS and microbubbles increases local BBB permeability for 4 to 6 hours, with an ensuing inflammation that resolves within days to weeks. Microglia, as the resident immune cells of the brain, are triggered by FUS-BBB modulation, although the time course of this response is unclear. Thus, the goal of this study was to characterize the early cellular (i.e., density, distribution, and morphology) and subcellular (i.e., ultrastructure) changes in microglial activities following FUS-BBB modulation. MethodsWe targeted the hippocampi of adult mice with FUS, in the presence of intravenous microbubbles and guided by MRI, and performed analyses 1 hour and 24 hours after FUS-BBB modulation. Microglia were investigated at the population, cellular and subcellular levels, where hippocampal BBB permeability was identified by the entry of endogenous immunoglobulin (Ig)G in the parenchyma. Respective outcome measures included i) the density and distribution of ionized calcium binding adaptor molecule-positive (Iba)1-positive (+) cells; ii) the morphology of the soma and processes of Iba1+ cells; and iii) the quantification of microglial organelles (e.g., phagosomes) and contacts with blood vessels and synapses using chip mapping scanning electron microscopy. ResultsNo significant changes in baseline density and distribution of microglia were found in IgG-positive hippocampal areas at 1 hour and 24 hours after FUS-BBB modulation. By contrast, FUS-BBB modulation was associated with more elongated microglial cell bodies at both time points. The relative distribution of morphologies at 1 hour shifted toward compact shapes with stubby processes, whereas at 24 hours, shapes were bigger, with fewer processes. At the nanoscale, microglia maintained their interactions with blood vessel elements, except vessels most affected by swollen endfeet, which occurred regardless of treatment. In the parenchyma, 24 hours after FUS-BBB modulation, microglia reduced the frequency of contacts with pre-synaptic elements and extracellular space pockets, while showing features of increased metabolic demand and reduced lysosomal activity. ConclusionAt 1 hour and 24 hours after FUS-BBB modulation, traits of microglial surveillance activity were largely maintained, with shifts in the shape of a subset of cells, which adopted a morphology associated with injury shielding. FUS-BBB modulation also appears to temporarily modify the digestive, but not the phagocytic activity, of microglia and to reduce pre-synaptic remodeling early after treatment.

neuroscience↗

bioRxiv2025

The Modulation of the Blood-Brain Barrier by Focused Ultrasound Stimulates Oligodendrogenesis

ObjectiveThe current study aims to fill a gap in knowledge on the effects of focused ultrasound (FUS)-mediated blood-brain-barrier (BBB) modulation on the proliferation and development of oligodendrocyte progenitor cells (OPCs). Researchers established that FUS combined with intravenous microbubbles can modulate the BBB in a controlled, reversible, localized, and non-invasive manner to facilitate the delivery of intravenous therapeutics to the brain. Over a decade ago, we discovered that, even without intravenous therapeutics, FUS-BBB modulation stimulates elements of brain repair, including hippocampal neurogenesis. MethodsIn adult mice, FUS-BBB modulation was targeted unilaterally to the hippocampus and proliferation of OPCs was quantified at 1, 4, 7, and 10 days post-FUS. Mature oligodendrocytes were quantified at 30 days post-FUS. OPC proliferation was assessed at 7 days post-FUS, and mature oligodendrocytes at 30 days. ResultsThe proliferation of hippocampal OPCs was increased by 6.8-fold and 2.3-fold between 1 and 4 days post-sonication, respectively, resulting in a 5.3-fold increase in mature oligodendrocytes one month later. To test the robustness of oligodendrogenesis following FUS-BBB modulation, the striatum was targeted as a second brain region with an independent experimental design. In line with hippocampal results, striatal FUS-BBB modulation promoted the generation of OPCs by 3.9-fold during the first week, leading to a 5.2-fold increase in oligodendrogenesis 30 days post-treatment. InterpretationWe conclude that FUS-BBB modulation in the hippocampus and striatum promotes oligodendrogenesis by stimulating the proliferation of OPCs and being permissive to their maturation. HighlightsO_LIBeyond the potential for the delivery of therapeutics to the brain, the modulation of the BBB by FUS can stimulate regenerative effects, including oligodendrogenesis. C_LIO_LIFUS-BBB modulation induced a significant proliferation of OPCs which resulted in increases in oligodendrogenesis of 5.3-fold in the hippocampus and 6.7-fold in the striatum C_LI

neuroscience↗

bioRxiv2024

Glycolytic flux controls retinal progenitor cell differentiation via regulating Wnt signaling

Metabolic pathways are remodeled in response to energy and other homeostatic demands and are dynamically regulated during embryonic development, suggesting a role in guiding cellular differentiation. Here, we show that glycolytic flux is required and sufficient to bias multipotent retinal progenitor cells (RPCs) to acquire a rod photoreceptor fate in the murine retina. In RPC-specific Phosphatase and tensin homolog conditional knock-out (Pten-cKO) and RPC-specific conditional gain-of-function of dominant active PFKB3 (cytoPFKB3) mice, glycolytic gene expression and activity are elevated, correlating with precocious rod photoreceptor differentiation and outer segment maturation. Conversely, glycolytic inhibition in retinal explants suppresses RPC proliferation and photoreceptor differentiation, achieved either with 2-deoxy-d-glucose, a competitive inhibitor of glucose metabolism, by lowering media pH, which disables PKM2, a rate-limiting enzyme, or by inhibiting lactate/H+ symporters, which lowers intracellular pH. Mechanistically, we show that Wnt signaling, the top-upregulated pathway in Pten-cKO retinas, is a glycolysis-dependent pathway. Pharmacological and genetic perturbation of Wnt signaling by knocking-out Ctnnb1, encoding {beta}-catenin, phenocopies glycolytic inhibition, suppressing RPC proliferation, photoreceptor differentiation and outer segment maturation. Thus, developmental rewiring of glycolytic flux modulates Wnt signaling to drive rod photoreceptor differentiation and maturation, an instructive role that may be exploited therapeutically for cell replacement strategies. IMPACT STATEMENTTransgenic and pharmacological approaches reveal developmental elevations in glycolytic flux have an instructive role in promoting rod photoreceptor differentiation and maturation via activation of Wnt signaling.

developmental biology↗

bioRxiv2024

Focused ultrasound increases gene delivery to deep brain structure following the administration of a recombinant adeno-associated virus in the cerebrospinal fluid

Gene delivery via adeno-associated viral vectors can provide lasting clinical benefits following a one-time treatment. Delivery throughout the brain is needed for the treatment of neurological disorders with widespread pathology, including Alzheimer and Parkinson diseases, and amyotrophic lateral sclerosis. Most gene vectors have poor diffusion in the brain tissue. Furthermore, it is only at high intravenous doses that gene vectors can overcome the blood-brain barrier. In contrast, relatively lower doses of gene vectors injected in the cerebrospinal fluid enable significant transduction of superficial brain regions. The remaining challenge and unmet need of gene therapy is to deliver gene vectors to deep brain structures using a minimally invasive strategy. Here, we demonstrate that non-invasive focused ultrasound blood-brain barrier modulation can increase the delivery of recombinant adeno-associated virus by 5-fold to deep brain structures following injection in the cisterna magna. Delivery of adeno-associated viral vectors to the central nervous system, via administration in the cerebrospinal fluid, is being evaluated in several clinical trials for treating beta-galactosidase-1 deficiency, Batten disease, Alzheimer disease, Parkinson disease, amyotrophic lateral sclerosis, and spinal muscular atrophy. Our findings suggest that the efficacy of gene therapies delivered in the cerebrospinal fluid can be enhanced by targeting brain areas of interest with focused ultrasound. Significance statementAdministration of viral vectors in the cerebrospinal fluid through the cisterna magna is being evaluated in patients with neurological disorders. Focused ultrasound combined with intravenous microbubbles safely increases the permeability of the blood-brain barrier in humans and enables delivery of intravenous adeno-associated virus in non-human primates. Here, we demonstrate that combining these two clinically relevant gene delivery methods, intracisterna magna administration and focused ultrasound with microbubbles, can facilitate gene delivery to superficial and deep brain structures. Our findings have the potential to increase the efficacy of gene therapies, particularly for disorders with brain regions that have remained difficult to reach.

neuroscience↗

bioRxiv2021

Plagl1 is part of the mammalian retinal injury response and a critical regulator of Muller glial cell quiescence

Retinal damage triggers reactive gliosis in Muller glia across vertebrate species, but only in regenerative animals, such as teleost fish, do Muller glia initiate repair; proliferating and undergoing neurogenesis to replace lost cells. By mining scRNA-seq and bulk RNA-seq datasets, we found that Plagl1, a maternally imprinted gene, is dynamically regulated in reactive Muller glia post-insult, with transcript levels transiently increasing before stably declining. To study Plagl1 retinal function, we examined Plagl1+/-pat null mutants postnatally, revealing defects in retinal architecture, visual signal processing and a reactive gliotic phenotype. Plagl1+/-pat Muller glia proliferate ectopically and give rise to inner retinal neurons and photoreceptors. Transcriptomic and ATAC-seq profiles revealed similarities between Plagl1+/-pat retinas and neurodegenerative and injury models, including an upregulation of pro-gliogenic and pro-proliferative pathways, such as Notch, not observed in wild-type retinas Plagl1 is thus an essential component of the transcriptional regulatory networks that retain mammalian Muller glia in quiescence.

neuroscience↗

bioRxiv2020

MORPHIOUS: A Machine Learning Workflow to Naively Detect the Activation of Microglia and Astrocytes.

In cases of brain injury, degeneration and repair, defining microglia and astrocytic activation using cellular markers alone remains a challenging task. We developed MORPHIOUS, an unsupervised machine learning workflow that utilizes a one-class support vector machine to segment clusters of activated glia by only referencing examples of non-activated glia. Here, glial activation was triggered using focused ultrasound to permeabilize the hippocampal blood-brain barrier. Analyzing the hippocampal sections seven days later, MORPHIOUS identified two classes of microglia which showed characteristic activation features, including increases in ionized calcium-binding adapter molecule 1 expression, soma size, and de-ramification. MORPHIOUS was further used to identify clusters of activated astrocytes, which showed increased expression of glial fibrillary acidic protein and branching. Thus, by only referencing untreated glia morphologies, MORPHIOUS can identify diverse and novel manifestations of glial activation. This provides significant improvements for characterizing glial activation in cases of injury, neurodegeneration, and regeneration.

neuroscience↗