Biology subjects

Aubert, A.

Publications and source records attributed to Aubert, A..

7 recordsLinked to original sources

bioRxiv2026

Kruppel-like factors KLF5 & KLF8 emerge as master transcriptional regulators of Alzheimers disease, as revealed on cell fate regulomes in human brain organoids

In addition to the well described beta-amyloid plates accumulation and tau hyper-phosphorylation, Alzheimers disease (AD) is accompanied by major changes in gene expression. Herein, we aimed at revealing master transcription factors (TFs) responsible for gene expression changes during AD progression. For this, we have used human brain organoids (BORGs) harbouring AD-related genetic mutations (APP-Swedish, PSEN1-M146V), which were traced over multiple time-points by bulk and spatially-resolved transcriptomics. By reconstructing gene regulatory networks (GRNs) that recapitulate BORG development, we have identified a subset of 110 AD-specific master TFs, and for 75 of them we retrieved KLF5 and/or KLF8 binding motifs within their promoters. Furthermore, 64 of the AD-specific TFs found in BORGs are significantly over-expressed on AD human patients samples, confirming the relevance of these factors beyond the context of the familial genetic mutations. Finally, we have demonstrated that this AD-specific regulome is at least partially controlled by the aberrant CREB3L2-ATF4 heterodimer previously described as being induced by the beta-amyloid plates deposition. Overall, these findings reconstitute the regulome behind the progression of AD and highlights key TFs as potential druggable targets for the treatment of the disease.

systems biology↗

bioRxiv2025

Variation in aggressiveness plasticity between northern and southern European populations of Hymenoscyphus fraxineus, an invasive fungal pathogen of ash

Hymenoscyphus fraxineus is an invasive fungal pathogen responsible for the ash dieback epidemic, which continues to cause severe mortality of common ash (Fraxinus excelsior L.) across Europe. Following its likely introduction in northeastern Europe, the pathogen rapidly colonized most regions where common ash is present. As it spread southward, H. fraxineus encountered warmer climates and a higher occurrence of Fraxinus ornus L.), a species resistant to the disease, which may have imposed novel selective pressures on H. fraxineus at the epidemic front. Virulence is a key trait that is expected to evolve during epidemics and to exhibit plasticity in response to environmental variation. We investigated whether the plasticity of virulence in response to temperature and ash species has evolved in H. fraxineus. Using leaf inoculations, we characterized individual reaction norms for virulence in a long-established Lithuanian population and a recently established Italian population of H. fraxineus. At moderate temperature, the two H. fraxineus populations showed similar levels of virulence on F. excelsior. Virulence decreased to a similar extent on F. ornus in both pathogen populations, indicating similar plasticity of their virulence in relation to ash species. Interestingly, increasing temperature reduced virulence in the Lithuanian population but did not significantly change the virulence expressed by the Italian population, which remained stable across temperatures. Although these findings warrant further investigation, they suggest that ash populations in southern Europe may be more vulnerable to ash dieback under warm conditions than previously anticipated.

evolutionary biology↗

bioRxiv2025

Maternal n-3 PUFA deficiency alters brain fatty acid and oxylipin profiles across perinatal development in offspring

Long-chain polyunsaturated fatty acids (LC-PUFAs), particularly arachidonic acid (AA, 20:4n-6) and docosahexaenoic acid (DHA, 22:6n-3), are essential for optimal neurodevelopment through their effect on neuronal proliferation, neurite outgrowth and synaptogenesis. Emerging evidence highlights that brain PUFAs are metabolized in oxylipins, the bioactive oxidized PUFA metabolites known to regulate inflammatory processes. Recent data highlighted that both PUFA and oxylipin profiles are modulated in the adult male brain by dietary PUFA content. However, little is known on the impact of maternal dietary n-3 PUFA intake during the perinatal period and the neurodevelopmental profile of brain fatty acids and associated oxylipins in offspring, and whether these effects differ between sexes. To address this question, we first measured fatty acid levels in the placenta and embryonic brain of male and female offspring of mothers fed a sufficient or deficient diet in n-3 PUFAs at embryonic day (E)17.5. Then, fatty acids and oxylipins were measured at different post-natal stages, in the brain at P0 and P7, and in the hippocampus at P14 and P21, in both male and female offspring. Our results show that maternal n-3 PUFA dietary deficiency alters fatty acid profiles as early as E17.5 in both the placenta and the brain. Furthermore, dietary intervention affects both fatty acid and oxylipin profiles throughout postnatal brain development, with notable sex-specific differences. These findings underscore the critical importance of adequate maternal n-3 PUFA intake during the perinatal period for maintaining an optimal PUFA and oxylipin profiles, with potential implications for fetal and postnatal brain development.

neuroscience↗

bioRxiv2023

PSEN1-M146V and PSEN1-A246E mutations associated with Alzheimers disease impair proper microglia differentiation

Genetic variants associated with the late onset of Alzheimers disease (AD), were correlated with genes known to be expressed in microglia, suggesting for an AD-genetic component directly influencing microglia behavior. Instead, the role of the familial AD (fAD) genetic mutations was systematically studied from the angle of the Amyloid-Beta pathway; leaving their participation in microglia homeostasis unexplored. Here we demonstrate that two previously described fAD-related PSEN1 mutations directly impair proper microglia differentiation. While human induced pluripotent stem cells harboring the PSEN1-M146V mutation did not give rise to hematopoietic precursor (HPC) intermediate during microglia differentiation, a PSEN1-A246E mutant line managed to produce HPCs, but died within the first days of microglia differentiation. Detailed transcriptomics/epigenomics and functional assays revealed the setup of a pro-apoptotic program in the PSEN1-A246E mutant, which was circumvented when HPCs were grafted in brain organoids (BORGs). Microglia obtained in BORGs presented preferentially pro-inflammatory signatures, further supported by their correlation with recent data providing a detailed stratification of the various microglia populations within AD-patient samples. Overall, this study contributes to reconsider the influence of the previously identified familial mutations in the homeostasis of this immune component of the central nervous system.

neuroscience↗

bioRxiv2023

A 3-dimensional molecular cartography of human cerebral organoids revealed by double-barcoded spatial transcriptomics

Spatially-resolved transcriptomics is revolutionizing our understanding of complex tissues, but their current use for the exploration of a few sections is not representative of their 3-dimensional architecture. In this work we present a low-cost strategy for manufacturing molecularly double-barcoded DNA arrays, enabling large-scale spatially-resolved transcriptomics studies. We applied this technique to spatially resolve gene expression in several human brain organoids, including the reconstruction of a 3-dimensional view from multiple consecutive sections, revealing gene expression divergencies throughout the tissue.

systems biology↗

bioRxiv2020

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Enhancer-promoter dynamics are crucial for the spatiotemporal control of gene expression, but it remains unclear whether these dynamics are controlled by chromatin regulators, such as the nucleosome remodelling and deacetylase (NuRD) complex. The NuRD complex binds to all active enhancers to modulate transcription and here we use Hi-C experiments to show that it blurs TAD boundaries and increases the proximity of intermediate-range (~1 Mb) genomic sequences and enhancer-promoter interactions. To understand whether NuRD alters the dynamics of 3D genome structure, we developed an approach to segment and extract key biophysical parameters from 3D single-molecule trajectories of the NuRD complex determined using live-cell imaging. Unexpectedly, this revealed that the intact NuRD complex decompacts chromatin structure and makes NuRD-bound enhancers move faster, increasing the overall volume of the nucleus that these key regulatory regions explore. Interestingly, we also uncovered a rare fast-diffusing state of NuRD bound enhancers that exhibits directed motion. The NuRD complex reduces the amount of time that enhancers remain in this fast-diffusing state, which we propose might otherwise re-organise enhancer-promoter proximity. Thus, we uncover an intimate connection between a chromatin remodeller and the spatial dynamics of the local regions of the genome to which it binds.

cell biology↗

bioRxiv2019

Essential omega-3 fatty acids tune microglial phagocytosis of synaptic elements in the developing brain

Omega-3 fatty acids (n-3 polyunsaturated fatty acids; n-3 PUFAs) are essential for the functional maturation of the brain. Westernization of dietary habits in both developed and developing countries is accompanied by a progressive reduction in dietary intake of n-3 PUFAs. Low maternal intake of n-3 PUFAs has been linked to neurodevelopmental diseases in epidemiological studies, but the mechanisms by which a n-3 PUFA dietary imbalance affects CNS development are poorly understood. Active microglial engulfment of synaptic elements is an important process for normal brain development and altered synapse refinement is a hallmark of several neurodevelopmental disorders. Here, we identify a molecular mechanism for detrimental effects of low maternal n-3 PUFA intake on hippocampal development. Our results show that maternal dietary n-3 PUFA deficiency increases microglial phagocytosis of synaptic elements in the developing hippocampus, through the activation of 12/15- lipoxygenase (LOX)/12-HETE signaling, which alters neuronal morphology and affects cognition in the postnatal offspring. While women of child bearing age are at higher risk of dietary n-3 PUFA deficiency, these findings provide new insights into the mechanisms linking maternal nutrition to neurodevelopmental disorders.\n\nOne Sentence SummaryLow maternal omega-3 fatty acids intake impairs microglia-mediated synaptic refinement via 12-HETE pathway in the developing brain.

neuroscience↗