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Identification of activity-dependent gene expression profiles in cultured rat cortical neurons

ABSTRACT: We report a genome-wide expression analysis of cultured rat cortical neurons treated with specific pharmacological agents, a model with alterations in neuronal activity. Using the microarray approach in combination with microelectrode array (MEA) technology, we ascertained out of approximately 27,000 genes 248 activity-dependent genes, which encompass a large number of members of distinct families, including synaptic vesicle proteins, ion channels, signal transduction molecules, synaptic growth regulators, and others. These genes were further confirmed to be Ca2+-sensitive, largely regulated by Ca2+ influx through N-methyl-D-aspartate (NMDA) receptors, and partly through L-type voltage-gated Ca2+ channels (VGCCs). In addition, the dynamics of gene expression cascades, specifically and temporally regulated, and the pools of those downstream genes, selectively responded to particular routes of Ca2+ entry, were also elucidated, as well as the functional consequences of candidate genes associated with synaptic plasticity. Keywords: pharmacological agents, cortical neurons

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE6254 | GEO | 2006/11/25

SECONDARY ACCESSION(S): PRJNA99685

REPOSITORIES: GEO

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Project description:Kabuki Syndrome (KS) is a multisystemic rare disorder, characterized by growth delay, distinctive facial features, intellectual disability, and rarely autism spectrum disorder. This condition is mostly caused by de novo mutations of KMT2D, encoding a catalytic subunit of the COMPASS complex involved in enhancer regulation. KMT2D catalyzes the deposition of histone-3-lysine-4 mono-methyl (H3K4Me1) that marks active and poised enhancers. To assess the impact of KMT2D mutations in the chromatin landscape of KS tissues, we have generated patient-derived induced pluripotent stem cells (iPSC), which we further differentiated into neural crest stem cells (NCSC), mesenchymal stem cells (MSC) and cortical neurons (iN). In addition, we further collected blood samples from 5 additional KS patients. To complete our disease modeling cohort we generated an isogenic KMT2D mutant line from human embryonic stem cells, which we differentiated into neural precursor and mature neurons. Micro-electrode-array (MEA)-based neural network analysis of KS iNs revealed an altered pattern of spontaneous network-bursts in a Kabuki-specific pattern. RNA-seq profiling was performed to relate this aberrant MEA pattern to transcriptional dysregulations, revealing that dysregulated genes were enriched for neuronal functions, such as ion channels, synapse activity, and electrophysiological activity. Here we show that KMT2D haploinsufficiency tends to heavily affect the transcriptome of cortical neurons and differentiated tissues while sparing multipotent states, suggesting that KMT2D has a most prevalent role in terminally differentiated cell and activate transcriptional circuitry unique to each cell type. Moreover, thorough profiling of H3K4Me1 unveiled the almost complete uncoupling between this chromatin mark and the regulatory effects of KMT2D on transcription, which is instead reflected by a defect of H3K27Ac. By integrating RNA-seq with ChIP-seq data we defined TEAD and REST as the master effectors of KMT2D haploinsufficiency. Also, we identified a subset of genes whose regulation is controlled by the balance between KMT2D and EZH2 dosage. Finally, we identified the bona fide direct targets of KMT2D in healthy and KS mature cortical neurons and TEAD2 as the main proxy of KMT2D dysregulation in KS. Overall, our study provides the transcriptional and epigenomic characterization of patient-derived tissues as well as iPSCs and differentiated disease-relevant cell types, as well as the identification of KMT2D direct target in cortical neurons, together with the identification of a neuronal phenotype of the spontaneous electrical activity.

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Identification of activity-dependent gene expression profiles in cultured rat cortical neurons

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