Mus musculus
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ABSTRACT:
PROVIDER: PRJNA106639 | ENA |
REPOSITORIES: ENA
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Project description:XBP1 is a transcription factor that is induced by unconventional splicing associated with endoplasmic reticulum stress and plays a role in development of liver and plasma cells. We previously reported that brain derived neurotrophic factor (BDNF) leads to splicing of XBP1 mRNA in neurites, and that XBP1 is required for BDNF-induced neurite extension and branching. To search for the molecular mechanisms of how XBP1 plays a role in neural development, comprehensive gene expression analysis was performed in primary telencephalic neurons obtained from Xbp1 knockout mice at embryonic day 12.5. By searching for the genes induced by BDNF in wild type neurons but this induction was reduced in Xbp1 knockout mice, we found that upregulation of three GABAergic markers, somatostatin (Sst), neuropeptide Y (Npy), and calbindin (Calb1), were compromised in Xbp1 knockout neurons. Attenuated induction of Npy and Calb1 was confirmed by quantitative RT-PCR. In neurons lacking in Xbp1, upregulation of GABAergic markers was attenuated. Impaired BDNF-induced neurite extension in Xbp1 knockout neurons might be mediated by disturbed BDNF-induced differentiation of GABAergic interneurons. Keywords: time-cource, genetic modification
2008-09-25 | GSE11322 | GEO
Project description:XBP1 is a transcription factor that is induced by unconventional splicing associated with endoplasmic reticulum stress and plays a role in development of liver and plasma cells. We previously reported that brain derived neurotrophic factor (BDNF) leads to splicing of XBP1 mRNA in neurites, and that XBP1 is required for BDNF-induced neurite extension and branching. To search for the molecular mechanisms of how XBP1 plays a role in neural development, comprehensive gene expression analysis was performed in primary telencephalic neurons obtained from Xbp1 knockout mice at embryonic day 12.5. By searching for the genes induced by BDNF in wild type neurons but this induction was reduced in Xbp1 knockout mice, we found that upregulation of three GABAergic markers, somatostatin (Sst), neuropeptide Y (Npy), and calbindin (Calb1), were compromised in Xbp1 knockout neurons. Attenuated induction of Npy and Calb1 was confirmed by quantitative RT-PCR. In neurons lacking in Xbp1, upregulation of GABAergic markers was attenuated. Impaired BDNF-induced neurite extension in Xbp1 knockout neurons might be mediated by disturbed BDNF-induced differentiation of GABAergic interneurons. Experiment Overall Design: Brain derived neurotrophic factor (BDNF) effect examined in telencephalon primary cultures from Xbp1 knockouts and wild-type controls. Experiment Overall Design: Two female Xbp1 +/- mice were mated with male Xbp1 +/- mice, and at embryonic day 12.5 (E12.5) the embryos were dissected. Among the 25 embryos obtained from the 2 pregnant female mice, 6 were genotyped as Xbp1 -/- and 4 were Xbp1 +/+ by a rapid PCR assay using Z-Taq. Telencephalon was dissected from each embryo, and treated with collagenase and trypsin. Six Xbp1 -/- telencephalon samples and 4 Xbp1 +/+ samples were collected together, respectively. Each sample was divided into 15 aliquots, and the cells were subject to low density culture on plastic culture dishes. The neurons were maintained in a serum-free medium (Neurobasal medium supplemented with 0.5 mM glutamine and B27 supplement [Invitrogen]). On the third day in vitro (3 DIV) , neurons in 10 of 15 dishes in each group were stimulated with BDNF (100 ng/ml). On 4 DIV, neurons in 5 dishes stimulated with BDNF (24 hours BDNF treatment) and 5 dishes with no stimulation (0 hour) were lysed to extract total RNA. On 5 DIV, neurons in 5 dishes stimulated with BDNF (48 hours BDNF treatment) were lysed. Experiment Overall Design: Total RNA was extracted using RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to the protocol provided by the manufacturer. The quantity and quality of RNA were measured using NanoDrop ND-1000. Biotin-labeled cRNA for DNA microarray analysis was synthesized using Two Cycle cDNA Synthesis and IVT labeling Kit. The integrity of the cRNA samples was verified using Test3 Array. Each biotin-labeled cRNA sample from one dish was hybridized to a single Affymetrix GeneChip Mouse Genome 430A 2.0 Array, and totally 30 arrays were used. The hybridization signal on the chip was scanned using an HP GeneArray scanner and processed by MAS5. After imported into GeneSpring software, data normalization was performed by dividing each microarray data set by its median value. Probes called as present in at least half of the 30 samples were selected.
2008-10-26 | E-GEOD-11322 | biostudies-arrayexpress
Project description:Induction of cells expressing markers of GABAergic neurons by transcription factors (miRNA)
| PRJNA314495 | ENA
Project description:Induction of cells expressing markers of GABAergic neurons by transcription factors (mRNA)
| PRJNA314496 | ENA
Project description:Febrile seizures (FS) are a common childhood neurological condition triggered by fever in children without prior neurological disorders. While generally benign, some individuals, particularly those with complex FS or genetic predispositions, may develop epilepsy or other neurological comorbidities. The mechanisms underlying this transition remain unclear. Mutations in SCN1A, encoding the NaV1.1 sodium channel α-subunit, have been linked to several epilepsy syndromes associated with FS. This study examines phenotypic variability in individuals carrying the same SCN1A c.434T>C mutation, using induced pluripotent stem cell (iPSC)-derived neurons from two siblings with FS. Despite sharing the mutation, only the older sibling developed temporal lobe epilepsy (TLE). Transcriptomic analysis revealed downregulation of GABAergic pathway genes in both siblings’ neurons, aligning with SCN1A-associated epilepsy. However, neurons from the sibling with TLE exhibited additional abnormalities, including altered AMPA receptor subunit composition, changes in GABAA receptor subunit and chloride cotransporter expression, and reduced brain-derived neurotrophic factor (BDNF) levels, indicative of developmental immaturity. Voltage-clamp recordings confirmed impaired GABAergic and AMPA receptor-mediated synaptic activity. These findings suggest that combined GABAergic dysfunction, aberrant AMPA receptor composition, and reduced BDNF signaling contribute to the more severe phenotype and increased epilepsy susceptibility. These findings suggest that combined GABAergic dysfunction, aberrant AMPA receptor composition, and reduced BDNF signaling may underlie the more severe phenotype and increase epilepsy susceptibility in this individual.
2025-06-30 | GSE289689 | GEO
Project description:RNAseq data indicate that in the human brain, most neurons co-express the brain-derived neurotrophic factor (BDNF) receptor TrkB and the Neurotrophin-3 (NT3) receptor TrkC. Because NT3 can also activate TrkB and TrkB is expressed at higher levels compared with TrkC, it has been difficult thus far to explore TrkC-mediated signaling. To this end, neurons were generated from human embryonic stem cells lacking the BDNF receptor TrkB using CRISPR/Cas9. These neurons were found to respond to very low concentrations of NT3, lower than the concentrations of BDNF needed to activate TrkB. In order to compare the transcriptional changes following treatment with NT3 RNA-seq analysis was performed and the results compared with those previously obtained following treatment of wild-type neurons with BDNF Merkouris et al. PMID: 29987039. The results indicate that downstream of TrkC activation, most of the changes in gene expression are similar to those seen after TrkB activation. The results also show that exposure to sub-saturating concentrations of either BDNF or NT3 does not cause receptor downregulation as seen with saturating ligand concentrations and that the receptors can be re-activated.
2022-03-22 | E-MTAB-11566 | biostudies-arrayexpress
Project description:A crucial step in understanding the sleep-control mechanism is to identify sleep neurons. In principle, a neuron could promote sleep by inhibiting wake-promoting neurons. Using rabies virus (RV)-mediated transsynaptic tracing, we identified several brain regions with GABAergic neurons that broadly inhibit multiple wake-promoting neuronal populations, and the most prominent source of GABAergic inputs was found in a posterior part of the CeA. The CeA is known to contain multiple subtypes of GABAergic neurons with distinct molecular markers, projection targets, and functional properties. Using translating ribosome affinity purification (TRAP) RNA-Seq, we identified molecular markers for the canditate sleep-promoting neurons in CeA.
2020-04-06 | GSE121888 | GEO
Project description:The progressive loss of dopaminergic identity in midbrain neurons is a hallmark of Parkinson’s disease (PD), contributing to synaptic dysfunction and neurodegeneration. However, the molecular mechanisms linking disease-specific stress to dopaminergic transcriptional failure remain poorly understood. Here, we used human induced pluripotent stem cell (hiPSC)-derived midbrain dopaminergic neurons (mDAs) from sporadic PD patients to investigate early alterations in neuronal identity, plasticity, and survival. We found that PD-derived mDAs exhibit upregulation of phosphorylated α-synuclein, marked reductions in dopaminergic markers (TH, NURR1), deficient dopamine handling and impaired synaptogenesis. Transcriptomic and protein analyses revealed sustained activation of apoptotic caspases (caspase-3, -7) and downregulation of the PKA–CREB–BDNF signaling axis, which underpins dopaminergic differentiation and synaptic maturation. Pharmacological inhibition of caspases with Q-VD-OPh restored pCREB, BDNF, and downstream dopaminergic markers, leading to morphological recovery and functional synaptic rescue. Inhibition of PKA with H89 abrogated these effects, positioning the caspase–PKA–CREB cascade as a critical regulator of dopaminergic identity in PD neurons. These findings define a novel non-apoptotic role for caspases in disrupting the transcriptional program of mDAs and identify a druggable pathway capable of rescuing key aspects of dopaminergic function in a patient-derived cellular model. This work provides a mechanistic rationale for targeting caspase signaling in early-stage PD.
2026-06-08 | PXD066765 | Pride
Project description:MicroRNA (miRNA) dysfunctions are implicated in neurodegenerative disorders, with microglial miR155 dysregulation extensively linked to neuroinflammation in Alzheimer's disease (AD). However, its role in other neural cell types remains unclear. Expanding on previous studies showing miR155 upregulation in hippocampal neurons of both AD model mice and AD patients, we found that in human induced pluripotent stem cell (hiPSC)-derived neural stem cells (NSCs), MIR155 regulates NSC proliferation, with MIR155 deletion increasing NSC numbers and overexpression downregulating NSC markers. In cortical neurons, MIR155 deletion is associated with increased neuronal outgrowth and GABAergic interneuron generation. In cortical organoids, MIR155 deletion promotes ventral patterning and increases GABAergic interneuron formation. Deleting miR155 in an AD mouse model induced the expansion of hippocampal NSCs in the sub-granular zone (SGZ) and the hilus, and promoted an increase in the number of hippocampal GABAergic interneurons, highlighting the novel role of miR155 in adult hippocampal neurogenesis and GABAergic interneuron signaling.
2026-08-12 | GSE277200 | GEO
Project description:MicroRNA (miRNA) dysfunctions are implicated in neurodegenerative disorders, with microglial miR155 dysregulation extensively linked to neuroinflammation in Alzheimer's disease (AD). However, its role in other neural cell types remains unclear. Expanding on previous studies showing miR155 upregulation in hippocampal neurons of both AD model mice and AD patients, we found that in human induced pluripotent stem cell (hiPSC)-derived neural stem cells (NSCs), MIR155 regulates NSC proliferation, with MIR155 deletion increasing NSC numbers and overexpression downregulating NSC markers. In cortical neurons, MIR155 deletion is associated with increased neuronal outgrowth and GABAergic interneuron generation. In cortical organoids, MIR155 deletion promotes ventral patterning and increases GABAergic interneuron formation. Deleting miR155 in an AD mouse model induced the expansion of hippocampal NSCs in the sub-granular zone (SGZ) and the hilus, and promoted an increase in the number of hippocampal GABAergic interneurons, highlighting the novel role of miR155 in adult hippocampal neurogenesis and GABAergic interneuron signaling.
2026-08-12 | GSE277199 | GEO