Biology subjects

Urbach, A.

Publications and source records attributed to Urbach, A..

12 recordsLinked to original sources

bioRxiv2025

DNMT1 Coordinates PV Interneuron-Glia Coupling to Maintain Cortical Network Stability and Regulate Behavior

Parvalbumin (PV) interneurons are central to cortical network stability and psychiatric vulnerability. Here, we identify DNA methyltransferase 1 (DNMT1) as a key epigenetic regulator linking PV interneuron function to glial and extracellular matrix remodeling. Conditional PV-specific Dnmt1 deletion combined with single-cell RNA-seq, in vivo electrophysiology, histology, and behavioral analyses revealed that loss of DNMT1 increases PV spiking activity but reduces inhibitory efficacy, leading to network desynchronization and depression- and anxiety-like behavior in mice. These physiological alterations were accompanied by broad, non-cell-autonomous transcriptional changes in astrocytes and oligodendroglial populations, prominently affecting pathways involved in perineuronal-net (PNN) organization and neuron-glia communication. Cell-cell interaction analyses revealed disrupted NRXN-NLGN, TNR-integrin, and semaphoring signaling, consistent with weakened perisomatic adhesion and PNN integrity. Together, our findings demonstrate that DNMT1 maintains inhibitory circuit stability through cell-autonomous regulation of PV interneuron function, which secondarily shapes glial transcriptional states and extracellular scaffolds to preserve cortical network synchronization and emotional behavior.

neuroscience↗

bioRxiv2024

Dnmt1-deficiency in PV interneurons alters cortical circuit function and leads to depression-like behavior

Neuropsychiatric disorders, including major depressive disorder (MDD), are highly prevalent in modern society, arising from a complex interplay of genetic and environmental factors. Alterations in the function of cortical inhibitory GABAergic interneurons, along with dysregulations of epigenetic signatures and key regulators such as DNA methyltransferase 1 (DNMT1), have been implicated in these conditions. Through its role in catalyzing DNA methylation, DNMT1 modulates the synaptic activity of parvalbumin-expressing (PV) interneurons, which are essential for cortical inhibition. However, the functional consequences of DNMT1 activity in cortical interneurons at the network level and its impact on behavior remain unknown and must be explored to fully understand the disease implications of dysregulated DNMT1 expression and function. To address this, we utilized a conditional knockout mouse model with Dnmt1 deletion in PV interneurons. Our findings reveal that a Dnmt1 deficiency leads to increased spontaneous firing rates of cortical neurons, reduced cortical gamma oscillations, and altered visually evoked neural responses. Despite intact sensory perception, Dnmt1-deficient mice exhibited reduced physical activity, heightened anxiety-like behavior, and signs of anhedonia and apathy, which represent core features of MDD. These results underscore the critical role of DNMT1 in PV interneuron function and identify it as a potential target for MDD research.

neuroscience↗

bioRxiv2024

Harnessing early multimodal motor training to drive motor recovery and brain-wide structural reorganization after stroke

Stroke survivors often suffer from severe motor impairments, highlighting the critical need for effective rehabilitation strategies. In experimental models, extensive task-specific motor training within the first few weeks post-stroke significantly mitigates motor deficits. However, whether more multimodal motor training approaches after stroke can restore task-specific performance in non-trained motor tasks remains largely unknown. Additionally, while stroke itself triggers structural brain reorganization, the influence of early multimodal motor training on this process remains unclear. Here, we employed T2-weighted MRI to investigate brain region-specific volumetric changes over eight weeks in rats subjected to stroke and subsequent early multimodal motor training. We found that this combination not only facilitated task-specific motor function recovery, but also induced dramatic, multi-region, brain-wide volumetric changes. Specifically, over 80 locations within 50 distinct brain regions across both hemispheres exhibited substantial volumetric alterations in a predominantly bilateral symmetric pattern. In contrast, stroke or training alone resulted in changes in 8-15 locations within 7-13 brain regions, with stroke alone primarily affecting the infarcted hemisphere. Analysis of temporal volume changes revealed two distinct trajectories in post-stroke trained rats: one of initial swelling followed by shrinkage, and another of initial shrinkage followed by swelling, suggesting an early and delayed motor learning period. Overall, our findings demonstrate that multimodal motor training early after stroke effectively restores task-specific motor function and profoundly reshapes brain structure on a brain-wide scale, offering vital insights for developing optimized rehabilitation protocols to maximize recovery in stroke patients.

neuroscience↗

bioRxiv2023

Characterization of alternative splicing in high-risk Wilms tumors

The significant heterogeneity of Wilms tumors between different patients is thought to arise from genetic and epigenetic distortions that occur during various stages of fetal kidney development in a way that is poorly understood. To address this, we characterized the heterogeneity of alternative mRNA splicing in Wilms tumors using a publicly available RNAseq dataset of high-risk Wilms tumors and normal kidney samples. Through Pareto task inference and cell deconvolution, we found that the tumors and normal kidney samples are organized according to progressive stages of kidney development within a triangle-shaped region in latent space, whose vertices, or "archetypes," resemble the cap mesenchyme, the nephrogenic stroma, and epithelial tubular structures of the fetal kidney. We identified a set of genes that are alternatively spliced between tumors located in different regions of latent space and found that many of these genes are associated with the Epithelial to Mesenchymal Transition (EMT) and muscle development. Using motif enrichment analysis, we identified putative splicing regulators, some of which are associated with kidney development. Our findings provide new insights into the etiology of Wilms tumors and suggest that specific splicing mechanisms in early stages of development may contribute to tumor development in different patients.

cancer biology↗

bioRxiv2022

Generation of adult hippocampal neural stem cells occurs in the early postnatal dentate gyrus and depends on cyclin D2

In the hippocampus, lifelong neurogenesis is maintained by a pool of multipotent adult neural stem cells (aNSCs) residing in the subgranular zone of the dentate gyrus (DG). Yet, the mechanisms guiding the transition of NSCs from developmental to adult remain unclear. By using nestin-reporter mice deficient for D2, a cyclin expressed mainly postnatally, we show that the aNSC pool is established through D2-dependent proliferation during the first two weeks of life. The absence of D2 allows the normal development of the DG until birth but prevents the postnatal formation of radial glia-like aNSCs. Additionally, retroviral fate mapping demonstrates that aNSCs are born on-site from precursors located in the DG shortly after birth. Altogether, our data suggest that aNSCs are a population distinct from developmental NSCs and thus imply that adult hippocampal neurogenesis is not a mere continuation of development.

neuroscience↗

bioRxiv2022

Characterization of the continuous transcriptional heterogeneity in Wilms tumors using unsupervised machine learning

Wilms tumors are pediatric malignancies that are thought to arise from faulty kidney development. To date, the course of treatment depends on manual histopathological classification which is difficult since the tumors differ between patients in a continuous manner. Here, we used three computational approaches to characterize the continuous heterogeneity of Wilms tumors. We first chose a published dataset of microarray gene expression measurements from high-risk blastemal-type Wilms tumors. Then, we used Pareto Task Inference to show that the tumors form a triangle-shaped continuum in latent space that is bounded by three tumor archetypes with "stromal", "epithelial", and "blastemal" characteristics, that resemble the un-induced mesenchyme, the Cap mesenchyme, and early epithelial structures of the fetal kidney. We confirmed this by fitting a generative probabilistic "grade of membership" model whereby each tumor is represented as a unique mixture of three hidden "topics" with blastemal, stromal, and epithelial characteristics. Finally, we used cellular deconvolution to show that each tumor is composed of a unique mixture of cell populations resembling the un-induced mesenchyme, the cap mesenchyme, and the early epithelial structures of the fetal kidney. We anticipate that these methodologies will pave the way for more quantitative strategies for tumor stratification and classification.

cancer biology↗

bioRxiv2021

Arc rescues defective synaptic plasticity and cognitive dysfunction in sepsis-associated encephalopathy

Sepsis-associated encephalopathy (SAE) is a frequent complication in patients with severe systemic infection resulting in acute brain dysfunction and incapacitating long-term sequelae. SAE includes delirium, premature death, post-traumatic stress disorder, and major long-term cognitive impairment. The underlying pathophysiology of SAE is largely unresolved and specific treatment options are missing. We induced the peritoneal contamination and infection (PCI) sepsis model in 769 mice and compared these with 259 control mice. We found that experimental sepsis causes synaptic pathology in the brain characterized by severely disordered synaptic plasticity with reduced long-term potentiation, changes in CA1 pyramidal neuron dendritic spines, and behavioral abnormalities indicating cognitive dysfunction. Using electrophysiology, we found reduced frequency of quantal and spontaneous excitatory postsynaptic currents whereas amplitudes of miniature, spontaneous, and evoked excitatory currents were increased, pointing towards a homeostatic synaptic scaling mechanism. Corresponding to dysfunctional excitatory synaptic function we discovered downregulation of genes related to neuronal and synaptic signaling in the brain, including the gene for activity-regulated cytoskeleton-associated protein (Arc/Arg3.1), members of the transcription-regulatory EGR gene family, and the gene for dual-specificity phosphatase 6 (Dusp6). At the protein level, ARC expression and MAP kinase signaling in the brain were affected. For targeted rescue of dysfunctional synaptic signaling and plasticity, we overexpressed ARC in the hippocampus by microinjection of an adeno-associated virus containing a neuron-specific plasmid of the ARC transgene. Hereby we achieved recovery of defective synaptic plasticity in the hippocampal Schaffer collateral-CA1 pathway and improvement of memory dysfunction. Using a different rescue paradigm, PCI mice were subjected to enriched environment providing multiple activating stimuli. Enriched environment led to restoration of disordered long-term potentiation and memory, thus demonstrating the potential for activity-induced improvement. Together, we identified synaptic pathomechanisms of SAE after severe systemic infection and provide a conceptual approach to treat SAE-related disease mechanisms which may be applicable to patients afflicted with SAE.

neuroscience↗

bioRxiv2020

Experience-dependent structural plasticity in the adult brain: How the learning brain grows.

Volumetric magnetic resonance imaging studies have shown that intense learning can be associated with grey matter volume increases in the adult brain. The underlying mechanisms are poorly understood. Here we used monocular deprivation in rats to analyze the mechanisms underlying use-dependent grey matter increases. Optometry for quantification of visual acuity was combined with volumetric magnetic resonance imaging and microscopic techniques in longitudinal and cross-sectional studies. We found an increased spatial vision of the open eye which was associated with a transient increase in the volumes of the contralateral visual and lateral entorhinal cortex. In these brain areas dendrites of neurons elongated, and there was a strong increase in the number of spines, the targets of synapses, which was followed by spine maturation and partial pruning. Astrocytes displayed a transient pronounced swelling and underwent a reorganization of their processes. The use-dependent increase in grey matter corresponded predominantly to the swelling of the astrocytes. Experience-dependent increase in brain grey matter volume indicates a gain of structure plasticity with both synaptic and astrocyte remodeling. HighlightsO_LIPerception learning causes a transient increase in brain grey matter volume detectable by MRI. C_LIO_LIThis learning results in pronounced changes of neuronal dendrites and an increase in the number of dendritic spines. C_LIO_LIStructural neuronal plasticity is associated with a reorganization and transient swelling of astrocytes. C_LIO_LIBrain volume and astrocyte volume return to baseline post-learning, with a persistent increase in the number of mature spines. C_LI

neuroscience↗

bioRxiv2020

Intraneuronal chloride accumulation via NKCC1 is not essential for hippocampal network development in vivo

NKCC1 is the primary transporter mediating chloride uptake in immature principal neurons, but its role in the development of in vivo network dynamics and cognitive abilities remains unknown. Here, we address the function of NKCC1 in developing mice using electrophysiological, optical and behavioral approaches. We report that NKCC1 deletion from telencephalic glutamatergic neurons decreases in-vitro excitatory GABA actions and impairs neuronal synchrony in neonatal hippocampal brain slices. In vivo, it has a minor impact on correlated spontaneous activity in the hippocampus and does not affect network activity in the intact visual cortex. Moreover, long-term effects of the developmental NKCC1 deletion on synaptic maturation, network dynamics and behavioral performance are subtle. Our data reveal a neural network function of depolarizing GABA in the hippocampus in vivo, but challenge the hypothesis that NKCC1 is essential for major aspects of hippocampal development.

neuroscience↗

bioRxiv2020

DNA methyltransferase 1 (DNMT1) function is implicated in the age-related loss of cortical interneurons

Increased life expectancy in modern society comes at the cost of age-associated disabilities and diseases. Aged brains not only show reduced excitability and plasticity, but also a decline in inhibition. Age-associated defects in inhibitory circuits likely contribute to cognitive decline and age-related disorders. Molecular mechanisms that exert epigenetic control of gene expression, contribute to age-associated neuronal impairments. Both DNA methylation, mediated by DNA methyltransferases (DNMTs), and histone modifications maintain neuronal function throughout lifespan. Here we provide evidence that DNMT1 function is implicated in the age-related loss of cortical inhibitory interneurons. Deletion of Dnmt1 in parvalbumin-positive interneurons attenuates their age-related decline in the cerebral cortex. Moreover, DNMT1-deficient mice show improved somatomotor performance and reduced aging-associated transcriptional changes. A decline in the proteostasis network, responsible for the proper degradation and removal of defective proteins, is suggested to be essentially implicated in age- and disease-related neurodegeneration. Our data suggest that DNMT1 acts indirectly on interneuron survival in aged mice by modulating the proteostasis network during life-time.

neuroscience↗

bioRxiv2019

Characterization of splice isoform switching during human kidney development

Nephrons are the functional units of the kidney. During kidney development, cells from the cap mesenchyme - a transient kidney-specific progenitor state - undergo a mesenchymal to epithelial transition (MET) and subsequently differentiate into the various epithelial cell types that create the tubular structures of the nephron. Faults in this transition can lead to a pediatric malignancy of the kidney called Wilms tumor that mimics normal kidney development. While kidney development has been characterized at the gene expression level, a comprehensive characterization of alternative splicing is lacking. We therefore performed RNA sequencing on cell populations representing early, intermediate, and late developmental stages of the human fetal kidney, as well as three blastemal-predominant Wilms tumor patient-derived xenografts. We identified a set of transcripts that are alternatively spliced between the different developmental stages. Moreover, we found that cells from the earliest developmental stage have a mesenchymal splice-isoform profile that is similar to that of blastemal-predominant Wilms tumors. RNA binding motif enrichment analysis suggests that the mRNA binding proteins ESRP1, ESRP2, RBFOX2, and QKI regulate mRNA splice isoform switching during human kidney development. These findings illuminate new molecular mechanisms involved in kidney development and pediatric kidney tumors.\n\nHIGHLIGHTSO_LIDuring fetal kidney development, kidney progenitor cells undergo a mesenchymal to epithelial transition (MET) and subsequently differentiate into the various epithelial cell types that create the tubular structures of the nephron.\nC_LIO_LIRNA sequencing identifies a set of transcripts that undergo splice isoform switching during the mesenchymal to epithelial transition (MET) that occurs in the course of human fetal kidney development.\nC_LIO_LICells in the early stages of kidney development have a mesenchymal splice-isoform profile that is similar to that observed in blastemal-predominant Wilms tumor patient-derived xenografts (WT-PDX) that represent an aggressive subtype of Wilms tumors.\nC_LIO_LIRNA binding motif enrichment analysis indicates that the mRNA binding proteins ESRP1, ESRP2, RBFOX2, and QKI regulate splice isoform switching during human kidney development.\nC_LI

genomics↗

bioRxiv2019

Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development

During mammalian kidney development, nephron progenitors undergo a mesenchymal to epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, the different cell types in the developing kidney were characterized using the Dropseq single cell RNA sequencing technology for measuring gene expression from thousands of individual cells. However, many genes can also be alternatively spliced and this creates an additional layer of heterogeneity. We therefore used full transcript length single-cell RNA sequencing to obtain the transcriptomes of 544 individual cells from mouse embryonic kidneys. We first used gene expression levels to identify each cell type. Then, we comprehensively characterized the splice isoform switching that occurs during the transition between mesenchymal and epithelial cellular states and identified several putative splicing regulators, including the genes Esrp1/2 and Rbfox1/2. We anticipate that these results will improve our understanding of the molecular mechanisms involved in kidney development.

genomics↗