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Expression from control subplate neurons with few synapses and cocultured subplate neurons with induced synaptogenesis

ABSTRACT: The transcriptional events accompanying synaptogenesis are largely unknown, or have been studied in systems in which synapse formation occurs gradually over time. With a system in which synaptogenesis is synchronized and controllable, molecular or biochemical techniques can be used to examine cellular events across cultures on a wide scale, as synapses develop. Here, we have triggered synaptogenesis in immunopurified subplate neurons by coculturing with cortical feeder layers and have used microarrays to investigate the transcriptional events occuring in this more defined and controllable system. Keywords: treatment type comparison, time course

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE8318 | GEO | 2008/11/24

SECONDARY ACCESSION(S): PRJNA101299

REPOSITORIES: GEO

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Transcription profiling of rat control subplate neurons with few synapses and cocultured subplate neurons with induced synaptogenesis

Project description:The transcriptional events accompanying synaptogenesis are largely unknown, or have been studied in systems in which synapse formation occurs gradually over time. With a system in which synaptogenesis is synchronized and controllable, molecular or biochemical techniques can be used to examine cellular events across cultures on a wide scale, as synapses develop. Here, we have triggered synaptogenesis in immunopurified subplate neurons by coculturing with cortical feeder layers and have used microarrays to investigate the transcriptional events occuring in this more defined and controllable system. Experiment Overall Design: Affymetrix rat GeneChip microarrays were used to assess whether coculturing induces transcriptional changes in subplate neurons. Subplate synapses develop rapidly following coculturing; an exposure to the feeder layer of only 48 hours is sufficient to detect a significant increase in the density of synapses, and is as effective as longer durations. Within the first few minutes or hours of a cell's response to an exogenous signal, any primary transcriptional events are expected to involve activation of immediate early genes (IEGs), often transcription factors themselves, which may then turn on downstream target response genes encoding factors to be delivered to sites of action, such as synapses. With the aim of searching for such downstream genes, microarrays were performed after 24 hours of coculturing, an intermediate timepoint between the likely phase of IEG transcription and the large wave of synaptogenesis seen between 24 and 48 hours of coculturing. Additional microarrays were also performed after 96 hours of coculturing to assess transcriptional changes that might occur over longer timescales. Five biological replicates of control and cocultured neurons at 24 and 96 hours were used, for a total of 20 microarrays.

2008-11-29 | E-GEOD-8318 | biostudies-arrayexpress

Rattus norvegicus

Project description:Expression from control subplate neurons with few synapses and cocultured subplate neurons with induced synaptogenesis

| PRJNA101299 | ENA

Gene chip analysis of NPCs with and without cocultured with ASCs

Project description:We used microarrays to detail the global programme of gene expression underlying the coculturing of degenerate NPCs and ASCs and identified distinct classes of altered genes and ncRNAs during this process.

2018-03-23 | GSE112216 | GEO

Gene chip analysis of ASCs with and without cocultured with NPCs

Project description:We used microarrays to detail the global programme of gene expression underlying the coculturing of ASCs and degenerative NPCs and identified distinct classes of altered genes and ncRNAs during this process.

2019-08-31 | GSE118927 | GEO

Disruption of human-specific synaptogenesis program in autism [RNA-seq]

Project description:To test the connection between the molecular mechanisms underlying autistic disorder and human cognitive evolution, we analyzed the gene expression changes taking place during prefrontal cortex development in autism patients and healthy controls, as well as non-human primates. We found the genes with expression changes in autism are significantly overlapped with genes showing human-specific developmental profile. A major pattern of the overlapped genes reflects the aberrant acceleration of synaptogenesis and synaptic maturation followed by premature synaptic pruning in the prefrontal cortex of autism patients. This pattern involves the same developmental program that controls human-specific extension of cortical synaptogenesis in healthy individuals. Taken together, these findings shed light on the molecular mechanisms underlying autistic phenotype and provide potential targets for clinical intervention.

2016-08-12 | GSE59288 | GEO

LC-MS/MS - NS-NE - Zika Virus Impairs Neurogenesis and Synaptogenesis Pathways in Human Neural Stem Cells and Neurons

Project description:Growing evidences have associated Zika virus infection with congenital malformations, including microcephaly. Nonetheless, signaling mechanisms that promote the disease outcome are far from being understood, affecting the development of suitable therapeutics. In this study, we applied shotgun mass spectrometry-based proteomics combined with cell biology approaches to characterize altered molecular pathways on neurons and NPCs infected by ZIKV-BR, strain obtained from the 2015 Brazilian outbreak. Assessment of neurons differentiated from iPSC from different donors shows the importance of the host genetic background to the susceptibility of ZIKV infection, also confirmed by cytokine fingerprinting. Additionally, infected cells presented an impairment of neurogenesis and synaptogenesis processes. Moreover, ZIKV-BR infected NPCs showed unique alteration of pathways involved in neurological diseases, cell death and survival and embryonic development compared to ZIKV-AF, showing a human adaptation of the Brazilian viral strain. Taken together, these data explain CNS developmental arrest observed in Congenital Zika Virus syndrome is beyond neuronal cell death.

2019-11-12 | PXD009293 | Pride

Synaptogenesis in purified cortical subplate neurons.

Project description: Not available

| S-EPMC2705692 | biostudies-literature

Disruption of human-specific synaptogenesis program in autism [RNA-seq]

Project description:Disruption of human-specific synaptogenesis program in autism [RNA-seq]

| PRJNA254971 | ENA

Neuronal activation modulates enhancer activity of genes for excitatory synaptogenesis through de novo DNA methylation

Project description:Post-mitotic neurons exhibit DNA methylation changes, contrary to the longstanding belief that the epigenetic pattern in terminally differentiated cells is essentially unchanging. While the mechanism and physiological significance of DNA demethylation in neurons have been extensively elucidated, occurrence of de novo DNA methylation and its impacts have been much less investigated. Here we show that neuronal activation induces global de novo DNA methylation at enhancer regions that can repress target genes in primary cultured hippocampal neurons. The functional significance of this de novo DNA methylation was underpinned by the demonstration that inhibition of DNA methyltransferase (DNMT) activity decreased neuronal activity-induced excitatory synaptogenesis. Overexpression of WW and C2 Domain containing 1 (Wwc1), a representative target gene of de novo DNA methylation, could phenocopy this DNMT inhibition-induced decrease in the synaptogenesis. We found that both DNMT1 and DNMT3a were required for the neuronal activity-induced de novo DNA methylation of Wwc1 enhancer. Taking these findings altogether, we concluded that activity-induced de novo DNA methylation affecting gene expression has impacts on neuronal physiology comparable to those of DNA demethylation.

2020-04-26 | GSE149342 | GEO

Caco-2 cocultured with THP-1, time course

Project description:Previously, we constructed a coculture model to analyze the effect of macrophages on intestinal epithelial cells, and found that TNF-a secreted from human macrophage-like THP-1 cells induced cell damage to intestinal epithelial Caco-2 cells (Exp.Cell.Res. 2006, 312(19):3909-19). In this study, we present activation of NF-kB in Caco-2 cells within 15 min after coculturing. To reveal how TNF-a secreted from THP-1 cells affects Caco-2 cells in an early stage of coculture, we exhaustively analyzed the changes of gene expression in Caco-2 cells cocultured with THP-1 cells over the time periods of 0, 1, 3, 6, 24, and 48 h by using a DNA microarray. Differentially expressed genes extracted with maSigPro demonstrated that IEX-1 was the lowest p-value gene, that is, the most significantly changed gene among the up-regulated genes. The genes expressed in a similar pattern to IEX-1 involved immunity, apoptosis, and protein kinase cascade. These findings suggest that the stimuli of TNF-a from THP-1 cells activates NF-kB, leading induction of various gene expression. This pattern of gene expression indicates that not only early defense response but also cell death occurs at the same time, causing inflammatory condition. Caco-2 cells were cultured for 14 days on a semi-permeable support, and THP-1 cells were differentiated with phorbol myristate acetate (PMA) for 4 days in 12-well plates. Then, the semi-permeable support membrane in which Caco-2 cells had been cultured was placed on the 12-well plates on which THP-1 has been cultured.

2010-04-06 | E-GEOD-17625 | biostudies-arrayexpress

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