Biology subjects

Court, F.

Publications and source records attributed to Court, F..

10 recordsLinked to original sources

bioRxiv2026

Genomic imprinting of the metabolic regulator gene Klf14 is regulated by a paternal sub-TAD anchored at Mest and a shared enhancer in mice.

KLF14 acts as a master regulator of gene expression in adipose tissue and variants at the human KLF14 gene show strong and reproducible association with type 2 diabetes and metabolic syndrome. Risk alleles are only pathologic when maternally inherited, consistent with the observation that KLF14/Klf14 is a maternally-expressed imprinted gene in human and mouse. However, how genomic imprinting is regulated at this important locus is currently unknown. In both species, KLF14/Klf14 is located [~]200 kb away from the paternally imprinted gene MEST/Mest, which is regulated by a maternal gametic differentially methylated region (gDMR) at its CpG island (CGI) promoter. Although the Klf14 CGI is kept unmethylated in most tissues, maternally-inherited DNA methylation (DNAme) marks are paradoxically required for Klf14 expression in mouse. Here, we show that Mest and Klf14 reside within the same topologically associating domain (TAD) in both mouse embryonic stem cells (ESCs) and differentiated cells, defined by sites of biallelic CTCF binding at the boundaries. Using allele-specific 4C-seq in F1 hybrid ESCs, we show that CTCF binding specifically to the unmethylated Mest gDMR generates a paternal allele-specific sub-TAD encompassing Klf14. We further show through CRISPR-Cas9-mediated mutagenesis, that deletions of the paternal Mest promoter region in ESCs as well as in vivo in mutant mice, results in both loss of Mest expression and acquisition of biallelic expression at Klf14. By analyzing epigenetic marks and chromatin looping in the Klf14-expressing pituitary cell line AtT-20, we identify a putative enhancer element shared by Mest and Klf14, providing a mechanistic model for the regulation of Klf14 imprinting. This work defines a new role for the Mest maternally methylated gDMR, revealing that it exerts long-range effects via allele-specific modulation of TAD structures and consequently act as an imprinting control region (ICR) in the regulation of Klf14 imprinting. Conservation of this TAD organisation at the human locus suggests that a similar regulatory mechanism operates at KLF14.

developmental biology↗

bioRxiv2026

The elongation of Mest transcript into MestXL sustains, but does not initiate, the maternal allele bias of its convergent gene Copg2 during neurogenesis

Precise gene dosage control is critical for establishing cellular identity and development, especially for imprinted genes, where dosage imbalances are linked to severe pathologies such as neurodevelopmental disorders. The Mest/Copg2 imprinted locus is a paradigm for this fine-tuned regulation. While Mest is constitutively expressed from the paternal allele, Copg2 expression shifts from biallelic to a maternal allele bias specifically during neural differentiation, a transition proposed to involve transcriptional interference mediated by the long Mest isoform, MestXL, which extends into the Copg2 locus. However, the mechanisms underlying this allelic switch, and whether factors beyond MestXL contribute, are elusive. To address this, we employed a stem cell-based brain organoid model, integrating multi-omic analyses, 3D chromatin structure mapping, and functional approaches to dissect the regulatory events governing the induction and maintenance of Copg2 maternal allele bias throughout neural lineage specification. Our findings challenge the prevailing model by demonstrating that the maternal allele bias of Copg2 during neural differentiation is not solely driven by MestXL-mediated transcriptional interference. Instead, our data support a temporal and neural stage-specific two-step mechanism: putative enhancer-driven activation of the maternal allele in neural progenitor cells is followed by MestXL-dependent repression of the paternal allele in neuron-enriched stages. This uncovers an unexpected layer of complexity in the regulation of imprinted gene dosage during brain development, with profound implications for understanding the molecular underpinnings of neurodevelopmental disorders.

molecular biology↗

bioRxiv2026

The RNA and protein landscapes of mouse brain organoids

Organoids are powerful models of brain development and function. Mouse brain organoids reproduce the main steps of neurodevelopment in vivo and differentiate more rapidly than human organoids, making them scalable for screening applications. However, mouse brain organoids remain poorly defined. Here, we showed that the transcriptome of mouse brain organoids developed for three weeks is close to that of a neonatal mouse brain. Strikingly, organoids reproduced the majority of alternative splicing and polyadenylation site events that define a neural identity in vivo. Proteomics revealed that most changes in mRNA expression were translated into proteins. Mouse brain organoids differentiated for only three weeks already harboured a complex network of synaptic proteins, including the ionotropic and metabotropic receptors for the neurotransmitters glutamate and GABA. To conclude, our study provides compelling evidence that mouse brain organoids are a rapidly maturing and relevant model of mammalian brain development and function in a neonatal-like environment.

neuroscience↗

bioRxiv2024

The Neuroactive Potential of the Elderly Human Gut Microbiome is Associated with Mental Health Status

Ageing is usually associated with physiological decline, increased mental health issues, and cognitive deterioration, alongside specific changes in the gut microbiome. However, the relationship between the neuroactive potential of the gut microbiome and mental health and cognition among the elderly remains less explored. This study examines a cohort of 153 older Chilean adults with cognitive complaints, assessing anthropometric data, mental health via five distinct tests, and gut microbiome composition through 16SV4 sequencing. Our findings reveal associations between anthropometric factors and depression scores in mental tests of participants with their gut microbiome composition. Notably, depression was associated with changes in the abundance of Lachnospiraceae Eubacterium xylanophilum group and Fusobacteriaceae Fusobacterium. Additionally, bacterial pathways involved in metabolising neuroactive compounds such as tryptophan, short-chain fatty acids, p-cresol, glutamate, and nitric oxide were associated with participant age, sex, and cognitive performance. Moreover, participants sex was associated with the neuroactive potential of specific bacteria, suggesting a role of the gut microbiome in sex-related mental health differences in the elderly. Together, to the best of our knowledge, this study demonstrates for the first time the association between the neuroactive potential of the human gut microbiome and mental health status in older individuals with cognitive complaints.

animal behavior and cognition↗

bioRxiv2024

Impact of cardiometabolic factors and blood beta-amyloid on the volume of white matter hyperintensities in dementia-free subjects with cognitive complaints

IntroductionWhite matter hyperintensities (WMH) in Alzheimers disease (AD) have traditionally been associated with cerebrovascular diseases. Amyloid {beta} (A{beta}) deposition reportedly contributes to WMHs; however, this relationship remains unclear in dementia-free subjects with cognitive complaints (CC). Here, we explored the relationship between WMHs and cardiometabolic and A{beta} blood biomarkers in a community-based cohort of Latin American CC participants. MethodsWe recruited 112 individuals with CC (69 - 92 YO, 90 females) with available plasma A{beta} biomarkers and cardiometabolic markers (systolic - diastolic blood pressure and glycaemia). WMHs were quantified using a lesion segmentation tool based on SPM12 and segmented using the John Hopkins University (JHU) Atlas and ALVIN segmentation for periventricular and subcortical white matter. Linear multiple regression models were fitted to assess total WMH lesions and the segmented tract, using demographics, cardiometabolic, and A{beta} blood biomarker measures as independent variables. ResultsAfter multiple comparison corrections, diastolic blood pressure was associated with WMHs, specifically in the right anterior thalamic radiation, left cingulum, minor forceps, and subcortical ALVIN segmentation. Glycaemia was associated with WMH volume in forceps major, forceps minor, and right fronto-occipital fasciculi. Conversely, A{beta} blood biomarkers and systolic blood pressure showed no association with WMH overall or in specific tracts. ConclusionOur findings suggest that, in dementia-free CC individuals, WMH volume was more related to cardiometabolic factors, whereas A{beta} blood biomarkers might be of less relevance. Dementia prevention strategies in individuals might be a useful focus for managing high peripheral vessel resistance and endothelial damage due to hypertension and hyperglycaemia.

neuroscience↗

bioRxiv2023

Applying the area fraction fractionator (AFF) probe for total volume estimations of somatic, dendritic and axonal domains of the nigrostriatal dopaminergic system in a murine model

Using the nigrostriatal dopaminergic system as a case example, we describe a protocol based on Cavalieris principle to estimate the total volume of its somatic, nuclear, dendritic and axonal domains in the adult mouse. This protocol requires serial section analysis, a confocal laser scanning microscope (CLSM), and a stereological software combining the serial section manager (SSM) tool and the area fraction fractionator (AFF) probe. The protocol consists of the following steps: 1) systematic random sampling (SRS) of sites across sections for relevant regions of interest (ROI), which in this study included the substantia nigra pars compacta (SNc) and pars reticulata (SNr), the nigrostriatal tract, and the caudate-putamen complex (CP), 2) high resolution image acquisition of all SRS sites within and across sections, 3) loading of images on the previously defined SRS sites, 4) marking of all cellular structures of interest (cSOI) in the images, including perikarya and cell nuclei, dendrites, axonal segments and varicosities, using Cavalieris point-counting grids, and 5) estimation of cSOI total volume using the estimated area of each cSOI in every brain section, and the distance between sections. The added volume for all cSOI comprising the nigrostriatal dopaminergic system, in this murine model is around 0.37 mm3, with approximately 5% corresponding to perikarya and cell nuclei, 10% to neuropil/dendrites in substantia nigra, and 85% to axonal segments and varicosities within the CP. The use of a simple quantitative approach to assess the global state of a system may allow quantification of compartment-specific changes that may accompany neurodegenerative processes.

neuroscience↗

bioRxiv2023

Biallelic non-productive enhancer-promoter interaction precedes imprinted expression of Kcnk9 during mouse neural commitment

How constitutive allelic methylation at imprinting control regions (ICRs) interacts with other levels of regulation to drive timely parental allele-specific expression along large imprinted domains remains partially understood. To gain insight into the regulation of the Peg13-Kcnk9 domain, an imprinted domain with important brain functions, during neural commitment, we performed an integrative analysis of the epigenetic, transcriptomic and cis-spatial organisation in an allele-specific manner in a mouse stem cell-based model of corticogenesis that recapitulates the control of imprinted gene expression during neurodevelopment. We evidence that despite an allelic higher-order chromatin structure associated with the paternally CTCF-bound Peg13 ICR, the enhancer-Kcnk9 promoter contacts can occur on both alleles, although they are only productive on the maternal allele. This observation challenges the canonical model in which CTCF binding isolates the enhancer and its target gene on either side, and suggests a more nuanced role for allelic CTCF binding at some ICRs.

molecular biology↗

bioRxiv2021

Aβ oligomers trigger necroptosis-mediated neurodegeneration via microglia activation in Alzheimer's disease.

Alzheimers disease (AD) is a major adult-onset neurodegenerative condition with no available treatment. Compelling reports point amyloid-{beta} (A{beta}) as the main etiologic agent that triggers AD. Although there is extensive evidence of detrimental crosstalk between A{beta} and microglia that contributes to neuroinflammation in AD, the exact mechanism leading to neuron death remains unknown. Using postmortem human AD brain tissue, we show that A{beta} pathology is associated with the necroptosis effector pMLKL. Moreover, we found that the burden of A{beta}o correlates with the expression of key markers of necroptosis activation. Additionally, inhibition of necroptosis by pharmacological or genetic means, reduce neurodegeneration and memory impairment triggered by A{beta}o in mice. Since microglial activation is emerging as a central driver for AD pathogenesis, we then tested the contribution of microglia to the mechanism of A{beta}o-mediated necroptosis activation in neurons. Using an in vitro model, we show that conditioned medium from A{beta}o-stimulated microglia elicited necroptosis in neurons through activation of TNF- signaling, triggering extensive neurodegeneration. Notably, necroptosis inhibition provided significant neuronal protection. Together, these findings suggest that A{beta}o-mediated microglia stimulation in AD contributes to necroptosis activation in neurons and neurodegeneration. As necroptosis is a druggable degenerative mechanism, our findings might have important therapeutic implications to prevent the progression of AD.

cell biology↗

bioRxiv2020

Insulin-like growth factor 2 (IGF2) protects against Huntington's disease through the extracellular disposal of protein aggregates

Impaired neuronal proteostasis is a salient feature of many neurodegenerative diseases, highlighting alterations in the function of the endoplasmic reticulum (ER). We previously reported that targeting the transcription factor XBP1, a key mediator of the ER stress response, delays disease progression and reduces protein aggregation in various models of neurodegeneration. To identify disease-modifier genes that may explain the neuroprotective effects of XBP1 deficiency, we performed gene expression profiling of brain cortex and striatum of these animals and uncovered insulin-like growth factor 2 (Igf2) as the major upregulated gene. Here we studied the impact of IGF2 signaling on protein aggregation in models of Huntingtons disease (HD) as proof-of-concept. Cell culture studies revealed that IGF2 treatment decreases the load of intracellular aggregates of mutant huntingtin and a polyglutamine peptide. These results were validated using induced pluripotent stem cells (iPSC)-derived medium spiny neurons from HD patients. The reduction in the levels of mutant huntingtin was associated with a decrease in the half-life of the intracellular protein. The decrease in the levels of abnormal protein aggregation triggered by IGF2 were independent of the activity of autophagy and the proteasome pathways, the two main routes for mutant huntingtin clearance. Conversely, IGF2 signaling enhanced the secretion of soluble mutant huntingtin species through exosomes and microvesicles involving changes in actin dynamics. Administration of IGF2 into the brain of HD mice using gene therapy led to a significant decrease in the levels of mutant huntingtin in three different animal models. Moreover, analysis of human post-mortem brain tissue, and blood samples from HD patients showed a reduction of IGF2 level. This study identifies IGF2 as a relevant factor deregulated in HD, operating as a disease modifier that buffers the accumulation of abnormal protein aggregates. One sentence summaryIGF2 reduces the load of intracellular protein aggregates through the extracellular disposal of the mutant protein.

neuroscience↗

bioRxiv2019

Most of the deregulated CpG-island-controlled genes in glioma do not show DNA methylation defects

BackgroundAberrant DNA methylation is a cancer cell feature that is commonly associated with transcriptional alterations. However, the primary role of this defect in the genome-wide cancer-associated gene deregulation is not clear. Here, we evaluated the relative contribution of DNA methylation-dependent and -independent mechanisms to transcriptional alterations at CpG-island/promoter-associated genes in samples of adult glioma, a widespread type of brain tumor. ResultsExtensive molecular analyses of glioma samples with wild type IDH (IDHwt) and mutated IDH (IDHmut) found DNA hypermethylation only in a minority of genes showing loss or gain of expression. Specifically, in IDHwt samples, more than 75% of aberrantly repressed genes did not display DNA methylation defects at their CpG-island promoter. Conversely, altered H3K27me3 was the predominant molecular defect at deregulated genes. Moreover, the presence of a bivalent chromatin signature at CpG-island promoters in stem cells might not only predispose to hypermethylation, as widely documented, but more generally to all types of transcriptional alterations in transformed cells. In addition, the gene expression strength in healthy brain cells influences the choice between DNA methylation- and H3K27me3-associated silencing in glioma. Our findings support a model whereby the altered control of H3K27me3 dynamics, more specifically defects in the interplay between polycomb protein complexes and the brain-specific transcriptional machinery, is the main cause of transcriptional alteration in glioma cells. ConclusionsOur study provides a comprehensive and updated description of the epigenetic deregulations in glioma that could be useful for the design of drugs to target cancer-related epigenetic defects.

molecular biology↗