Biology subjects

Leboeuf, M.

Publications and source records attributed to Leboeuf, M..

10 recordsLinked to original sources

bioRxiv2025

A linear regression model predicts human brain ageing and reveals differential neuronal biological ageing relevant for Parkinson's disease susceptibility

Biological brain ageing is a major risk factor for neurodegenerative diseases, which are characterized by selective degeneration of particular neuron types. We analyzed the impact of ageing on the transcriptome of neurons in the ventral tegmental area (VTA), substantia nigra pars compacta (SNc) and locus coeruleus (LC), that show differential vulnerabilities to Parkinsons disease. Neurons were isolated from human post mortem brain tissues originating from 48 individuals ranging from 17 to 102 years of age and subjected to Smart-seq2 RNA sequencing. We identified 2,764 genes that were correlated with chronological ageing. This gene expression data was used to develop a feature selection-based Time Traversal algorithm, utilizing functionally grouped gene sets, GO terms, with high predictive accuracy of biological brain ageing. We identified 59 GO terms that can predict biological age using a linear regression model, where leave-one-out cross validation demonstrated a strong correlation between chronological age and predicted biological age (Pearson correlation coefficient = 0.946; adjusted R{superscript 2} = 0.771). The algorithm was validated on five independent datasets with high predictive performance, demonstrating shared ageing features across the human brain. Nonetheless, our analysis also highlights brain region and neuron type specificity in particular ageing features. Resilient neurons showed a weaker association with age-related transcriptional changes, indicating that they age slower than their vulnerable counterparts, thus revealing targets that may be used to slow down ageing and prevent disease development.

neuroscience↗

bioRxiv2025

Reevaluating the Role of Beta2-Microglobulin: New Insights on Selective Vulnerability in ALS Pathology

Amyotrophic lateral sclerosis (ALS) is characterized by the selective loss of motor neurons (MNs). Why these neurons show particular vulnerability in ALS is still debated, and also why certain MNs remain resilient. We investigated the importance of the human leukocyte antigen (HLA) and particularly beta2-microglobulin ({beta}2m) in MN susceptibility to ALS as these molecules have been implicated both in prolonging and shortening disease. RNA-sequencing demonstrated that disease-resistant oculomotor neurons (OMNs) and Onufs MNs had similar {beta}2m and HLA mRNA levels to vulnerable spinal MNs in control tissues. Thus, baseline differences in these transcripts do not explain the differential vulnerabilities of these neurons to disease. Nonetheless, the HLA protein level showed an inverse correlation with spinal MN size, where large MNs, which are lost early in ALS, had low HLA levels. HLA protein levels were also reduced in end-stage ALS patient spinal MNs, while remaining unchanged in OMNs with disease. Spinal MNs uniquely exhibited a significant upregulation of {beta}2m and HLA-C transcripts with disease, likely as a protective compensatory response. Thus, {beta}2m and HLA may relate to vulnerability to ALS. Cross-breeding of {beta}2m knockout mice with SOD1G93A ALS mice resulted in modest transient worsening of functional motor performance, but did not affect life span. There was partial preservation of innervation of particular muscles in SOD1G93A mice lacking {beta}2m, which was insufficient to improve motor behavior. These findings indicate that {beta}2m and HLAs are dynamically regulated in ALS, and may influence MN vulnerability, but they are not major disease modifiers in ALS.

neuroscience↗

bioRxiv2025

The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity

Polycomb group proteins maintain gene expression patterns established during early development, with Polycomb Repressive Complex 2 (PRC2) methyltransferase a key regulator of cell differentiation, identity and plasticity. Consequently, extensive somatic mutations in PRC2, including gain- or loss- of function (GOF or LOF), are observed in human cancers. The regulation of chromatin structure by PRC2 is critically dependent on its EZH2 (Enhancer of Zeste Homolog 2) subunit, which catalyzes the methylation of histone H3 lysine 27 (H3K27). Recent structural studies of PRC2 revealed extensive conformational changes in the non-catalytic EZH2 N-terminal SANT-Binding Domain (SBD) during PRC2 activation, though the functional significance remains unclear. Here, we investigate how the SBD regulates PRC2 function. The domain is highly conserved in metazoans, dispensable for PRC2 assembly and chromatin localization, yet required for genome-wide histone H3K27 methylation. Further, we show that an intact SBD is necessary for the proliferation of EZH2- addicted lymphomas, and its deletion in the presence of EZH2 GOF mutations inhibits cancer cell growth. These observations provide new insights to the regulation of PRC2 activity in normal development and malignancy.

genetics↗

bioRxiv2024

Posterior specification of multi-lineage axial assembloids from human pluripotent stem cells.

Elongation of the posterior body axis is driven by multi-potent neuromesodermal progenitors (NMPs), which both self-renew and simultaneously generate neural tube, neural crest, and presomitc mesoderm lineages at successive anterior posterior (A-P) levels. The ensuing diversification of these three NMP lineages is remarkably extensive, and also essential for an immense range of clinically important adult posterior body tissues. Here, we describe a human pluripotent stem cell protocol that successfully specifies authentic NMPs using a cocktail of seven factors (7F). 7F-NMPs express requisite markers, exhibit co-linear HOX activation, and can be purposely specified into each of the three NMP daughter lineages, demonstrating genuine multi-potency. 3D assembly of neural tube, neural crest, and presomitic mesoderm spheroids followed by long-term floating culture derives mature, multi-compartment Posterior Axial Assembloids, or PAXAs. PAXAs constitute a complex heterogeneous tissue containing spinal motor neurons and interneurons, central and peripheral glia, connective tissues, muscle satellite cells and contractile muscle fibres. Together, 7F-NMP and PAXA protocols establish a versatile in vitro platform to model mechanisms of human posterior body axis development, and for the study of a wide range of human diseases.

cell biology↗

bioRxiv2024

Transcriptional modulation unique to vulnerable motor neurons predict ALS across species and SOD gene mutations

Amyotrophic lateral sclerosis (ALS) is characterized by the progressive loss of motor neurons that innervate skeletal muscles. However, certain motor neuron groups including ocular motor neurons, are relatively resilient. To reveal key drivers of resilience versus vulnerability in ALS, we investigate the transcriptional dynamics of four distinct motor neuron populations in SOD1G93A ALS mice using LCM-seq and single molecule fluorescent in situ hybridization. We find that resilient ocular motor neurons regulate few genes in response to disease. Instead, they exhibit high baseline gene expression of neuroprotective factors including En1, Pvalb, Cd63 and Gal, some of which vulnerable motor neurons upregulate during disease. Vulnerable motor neuron groups upregulate both detrimental and regenerative responses to ALS and share pathway activation, indicating that breakdown occurs through similar mechanisms across vulnerable neurons, albeit with distinct timing. Meta-analysis across four rodent mutant SOD1 motor neuron transcriptome datasets identify a shared vulnerability code of 39 genes including e.g Atf4, Nupr1, Ddit3 and Penk, involved in apoptosis, as well as a proregenerative and anti-apoptotic signature consisting of Atf3, Vgf, Ina, Sprr1a, Fgf21, Gap43, Adcyap1, and Mt1. Machine learning using genes upregulated in SOD1G93A spinal motor neuron predicts disease in human stem cell-derived SOD1E100G motor neurons, and shows that dysregulation of VGF, INA, PENK and NTS are strong disease-predictors across species and SOD1 mutations. Our study reveals motor neuron population-specific gene expression and temporal disease-induced regulation that together provide a basis to explain ALS selective vulnerability and resilience and that can be used to predict disease.

neuroscience↗

bioRxiv2022

Microbiota-dependent histone butyrylation in the mammalian intestine

Posttranslational modifications (PTMs) on histone proteins are a key source of regulation on chromatin through impacting genome organization and important cellular processes, including gene expression. These PTMs often arise from small metabolites and are thus impacted by cellular metabolism and environmental cues. One such class of metabolically regulated PTMs are histone acylations, which include histone acetylation, along with butyrylation, crotonylation, and propionylation. We asked whether histone acylations of intestinal epithelial cells (IECs) are regulated through the availability of short chain fatty acids (SCFAs), which are generated by the commensal microbiota in the intestinal lumen. We identified IECs from the cecum and distal mouse intestine as sites of high levels of histone acylations, including histone butyrylation and propionylation. We identified specific sites of butyrylation and propionylation on lysine 9 and 27 on histone H3. We demonstrate that these acylations are regulated by the microbiota, whereas histone butyrylation is additionally regulated by the metabolite tributyrin. Furthermore, we identify tributyrin-regulated gene programs that correlate with histone butyrylation and demonstrate that histone butyrylation (H3K27bu) is associated with active gene regulatory elements and levels of gene expression. Together, our observations demonstrate a physiological setting in which previously uncharacterized histone acylations are dynamically regulated and associated with gene expression.

molecular biology↗

bioRxiv2022

ENGRAILED-1 transcription factor exerts a paracrine neurotrophic activity on adult spinal cord α-motoneurons.

Several homeoprotein transcription factors transfer between cells and regulate gene expression, protein translation, and chromatin organization in recipient cells. ENGRAILED-1 is one such homeoprotein expressed in spinal V1 interneurons synapsing on -motoneurons. Neutralizing extracellular ENGRAILED-1 by expressing a secreted single-chain antibody blocks its capture by spinal motoneurons resulting in -motoneurons loss and limb weakness. A similar but stronger phenotype is observed in the Engrailed-1 heterozygote mouse, confirming that ENGRAILED-1 exerts a paracrine neurotrophic activity on spinal cord -motoneurons. Intrathecal injection of ENGRAILED-1 leads to its specific internalization by spinal motoneurons and has long-lasting protective effects against neurodegeneration and weakness. Midbrain dopaminergic neurons express Engrailed-1 and, similarly to spinal cord -motoneurons, degenerate in the heterozygote. By identifying genes expressed in spinal cord motoneurons also showing modified expression in mouse Engrailed-1 heterozygote midbrain neurons, we identified p62/SQTSM1 as an age marker in spinal cord motoneurons with increased expression during aging, in the Engrailed-1 heterozygote and upon extracellular ENGRAILED-1 neutralization. We conclude that ENGRAILED-1 is a regulator of motoneuron ageing with non-cell autonomous neurotrophic activity.

neuroscience↗

bioRxiv2021

Stable Isotope Tracing In Vivo Reveals A Metabolic Bridge Linking The Microbiota To Host Histone Acetylation

The gut microbiota influences host epigenetics by fermenting dietary fiber into butyrate. Although butyrate could promote histone acetylation by inhibiting histone deacetylases, it may also undergo oxidation to acetyl-CoA, a necessary cofactor for histone acetyltransferases. Here, we find that epithelial cells from germ-free mice harbor a loss of histone H4 acetylation across the genome except at promoter regions. Using stable isotope tracing in vivo with 13C-labeled fiber, we demonstrate that the microbiota supplies carbon for histone acetylation. Subsequent metabolomic profiling revealed hundreds of labeled molecules and supported a microbial contribution to host fatty acid metabolism, which declined in response to colitis and correlated with reduced expression of genes involved in fatty acid oxidation. These results illuminate the flow of carbon from the diet to the host via the microbiota, disruptions to which may affect energy homeostasis in the distal gut and contribute to the development of colitis.

biochemistry↗

bioRxiv2019

The homeoprotein ENGRAILED-1 promotes motoneuron survival and sustains motor functions

Motoneuron degeneration leads to skeletal muscle denervation and impaired motor functions, yet the signals involved remain poorly understood. We find that extracellular ENGRAILED-1, a homeoprotein expressed in spinal cord V1 interneurons that synapse on -motoneurons, has non-cell autonomous activity. Mice heterozygote for Engrailed-1 develop muscle weakness, abnormal spinal reflex and partial neuromuscular junction denervation. A single intrathecal injection of ENGRAILED-1 restores innervation, limb strength, extensor reflex and prevents lumbar -motoneuron death for several months. The autophagy gene p62, which was found to network with Engrailed-1 and amyotrophic lateral sclerosis genes, is misregulated in Engrailed-1 heterozygote mice -motoneurons and is rescued following ENGRAILED-1 injection. These results identify ENGRAILED-1 as an -motoneuron trophic factor with long-lasting protective activity.

neuroscience↗

bioRxiv2019

Homeoprotein neuroprotection of embryonic neuronal cells.

Most homeoprotein transcription factors have a highly conserved internalization domain used in intercellular transfer. Internalization of homeoproteins ENGRAILED1 or ENGRAILED2 promotes the survival of adult dopaminergic cells, whereas that of OTX2 protects adult retinal ganglion cells. Here we characterize the in vitro neuroprotective activity of several homeoproteins in response to H2O2. Protection is observed with ENGRAILED1, ENGRAILED2, OTX2, GBX2 and LHX9 on midbrain and striatal embryonic neurons whereas cell-permeable c-MYC shows no protective effects. Therefore, five homeoproteins belonging to 3 different classes (ANTENNAPEDIA, PAIRED and LIM) share the ability to protect embryonic neurons from midbrain and striatum. Because midbrain and striatal neurons do not express the same repertoire of the 4 proteins, a lack of neuronal specificity together with a general protective activity can be proposed. In contrast, hEN1 and GBX2 exerted no protection on non-neuronal cells including mouse embryo fibroblasts, macrophages or HeLa cells. For the 4 proteins, protection against cell-death correlated with a reduction in the number of H2O2-induced DNA break foci in midbrain and striatal neurons. In conclusion, within the limit of the number of cell types and homeoproteins tested, homeoprotein protection against oxidative stress-induced DNA breaks and death is specific to neurons but shows no homeoprotein or neuronal type specificity.\n\nSIGNIFICANCE STATEMENTHomeoproteins are DNA binding proteins regulating gene expression throughout life. Many of them transfer between cells and are thus internalized by live cells. This has allowed for their use as therapeutic proteins in animal models of Parkinson disease and glaucoma. Part of their therapeutic activity is through a protection against neuronal death. Here we show that internalized homeoproteins from three different classes protect embryonic ventral midbrain and striatal neurons from oxidative stress, both at the level of DNA damage and survival. The interest of this finding is that it lends weight to the possibility that many homeoproteins play a role in neuroprotection through shared mechanisms involving, in particular, DNA protection against stress-induced breaks.

neuroscience↗