Selection of NPC specific Transcription factors
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE29729 | GEO | 2011/06/07
SECONDARY ACCESSION(S): PRJNA153873
REPOSITORIES: GEO
Similar Datasets
Project description:To construct a candidate pool of NPC specific transcription factor (TF), we selected the genes expressed at relatively high levels in NPCs by comparing them to mixed RNA derived from multiple organs, eliminating housekeeping genes. As result, 160 putative NPC specific TFs were selected. We used three independent NPC lines (NSEB5-2C, NS195R, NS21) established from different ES cell lines (EB5, 195R, 21, respectively). Genes exhibiting relatively higher expression (1.5 fold) in NSEB5-2C and NS195R (or, NSEB5-2C and NS21) were selected by comparing with Mixture (consisting of equal microgram of RNAs from heart, kidney, thymus, spleen, liver, lung, d11 embryo). Gene Ontology (GO) terms ‘DNA binding’ and ‘transcription activity’ were used to select TFs.
2011-06-07 | E-GEOD-29729 | biostudies-arrayexpress
Project description:Induced pluripotent stem cell-derived neural progenitor cells (iPSC-NPCs) are a promising source of tailor-made cell therapy for neurological diseases. However, tumorigenicity and immunogenicity are major obstacles to translational use. Here we demonstrate epidural therapeutics of human iPSC-NPC grafts after experimental ischemic stroke to avoid surgical damage and intracerebral teratomas. We found that human iPSC-NPCs co-cultured trans-membranously with rat cortical cells subjected to oxygen-glucose deprivation, compared with human mesenchymal stem cells from bone marrow and umbilical cord Wharton's jelly, superiorly enhanced neural survival and growth as well as mitigated astrogliosis. Using comparative whole-genome microarrays and cytokine arrays, we identified a neurorestorative secretome from iPSC-NPCs and neutralization of the enriched cytokines potently abolished the neuroprotective effects in the iPSC-NPC co-cultures. Moreover, we implanted the human iPSC-NPCs epidurally using fibrin glue over the peri-infarct cortex at 7 days following permanent middle cerebral artery occlusion in adult rats. The cell-treated rats showed significant improvement in their paretic forelimb usage and grip strength from 10 days post-transplantation (dpt) onwards compared to the vehicle-treated rats, accompanied by ameliorated infarct/atrophy volumes, inflammatory infiltration and astrogliosis, as well as augmented angiogenesis, oligodendrocyte precursor cells and white matter integrity. Some iPSC-NPCs migrated into the peri-infarct cortex but poorly survived by 21 dpt. This proof-of-concept study demonstrates that a less invasive yet effective epidural delivery route of human iPSC-NPCs may promote functional remodeling of the peri-infarct brain predominantly through distinct paracrine effects. cDNA samples from iPSC-NPC were hybridized to the human genome U133 Plus 2.0 GeneChip arrays.
2016-06-02 | E-GEOD-82101 | biostudies-arrayexpress
Project description:Induced pluripotent stem cell-derived neural progenitor cells (iPSC-NPCs) are a promising source of tailor-made cell therapy for neurological diseases. However, tumorigenicity and immunogenicity are major obstacles to translational use. Here we demonstrate epidural therapeutics of human iPSC-NPC grafts after experimental ischemic stroke to avoid surgical damage and intracerebral teratomas. We found that human iPSC-NPCs co-cultured trans-membranously with rat cortical cells subjected to oxygen-glucose deprivation, compared with human mesenchymal stem cells from bone marrow and umbilical cord Wharton's jelly, superiorly enhanced neural survival and growth as well as mitigated astrogliosis. Using comparative whole-genome microarrays and cytokine arrays, we identified a neurorestorative secretome from iPSC-NPCs and neutralization of the enriched cytokines potently abolished the neuroprotective effects in the iPSC-NPC co-cultures. Moreover, we implanted the human iPSC-NPCs epidurally using fibrin glue over the peri-infarct cortex at 7 days following permanent middle cerebral artery occlusion in adult rats. The cell-treated rats showed significant improvement in their paretic forelimb usage and grip strength from 10 days post-transplantation (dpt) onwards compared to the vehicle-treated rats, accompanied by ameliorated infarct/atrophy volumes, inflammatory infiltration and astrogliosis, as well as augmented angiogenesis, oligodendrocyte precursor cells and white matter integrity. Some iPSC-NPCs migrated into the peri-infarct cortex but poorly survived by 21 dpt. This proof-of-concept study demonstrates that a less invasive yet effective epidural delivery route of human iPSC-NPCs may promote functional remodeling of the peri-infarct brain predominantly through distinct paracrine effects.
2016-06-02 | GSE82101 | GEO
Project description:During mitotic exit, thousands of nuclear pore complexes (NPCs) assemble concomitant with the nuclear envelope to build a transport-competent nucleus. Here, we show that Nup50 plays a crucial role in NPC assembly independent of its well-established function in nuclear transport. RNAi-mediated downregulation in cells or immunodepletion of Nup50 protein in Xenopus egg extracts interferes with NPC assembly. We define a conserved central region of 46 residues in Nup50 that is crucial for Nup153 and MEL28/ELYS binding, and for NPC interaction. Surprisingly, neither NPC interaction nor binding of Nup50 to importin /, the GTPase Ran, or chromatin is crucial for its function in the assembly process. Instead, an N-terminal fragment of Nup50 can stimulate the Ran GTPase guanyl-nucleotide exchange factor RCC1 and NPC assembly, indicating that Nup50 acts via the Ran system in NPC reformation at the end of mitosis. In support of this conclusion, Nup50 mutants defective in RCC1 binding and stimulation cannot replace the wild-type protein in in vitro NPC assembly assays, while excess RCC1 can compensate the loss of Nup50.
2021-11-03 | PXD028701 | Pride
Project description:Primary astrocytomas of high histopathological grade (HG-astrocytomas) are largely restricted to older patients and are almost invariably fatal despite multimodal therapy. Here, we show that the young brain has an endogenous defense mechanisms against HG-astrocytomas. Neural precursor cells (NPCs) migrate to HG-astrocytomas, reduce glioma expansion and prolong survival by releasing a group of fatty-acid ethanolamides that have agonistic activity on the vanilloid receptor (transient receptor potential vanilloid subfamily member-1; TRPV1). TRPV1 expression is much higher in HG-astrocytomas than in the tumor-free brain and TRPV1 stimulation triggers tumor cell-death via the activating transcription factor-3 (ATF3) controlled branch of the ER-stress pathway. The anti-tumourigenic response of NPCs is lost with aging. NPC-mediated tumor suppression can be mimicked in the old brain by systemic administration of the synthetic vanilloid Arvanil, indicating that TRPV1 agonists hold potential as new HG-astrocytoma therapeutics. The goal of this microarray study was understand how neural stem / precursor cell (NPC) induced high grade astrocytoma cell-death is controlled by changes in gene expression. We investigated the gene-expression pattern in mouse high grade astrocytoma GL261 cells after incubation with NPC non-conditioned medium (controls) or NPC-conditioned medium by microarrays and found that endoplasmic reticulum stress genes like the activating transcription factor-3 (ATF3) were robustly up-regulated in NPC-conditioned medium treated mouse high grade astrocytoma cells, compared to controls. Comparison of two experimental groups (conditioned medium treated versus non-conditioned medium treated) in three dye swap experiments (6 arrays used in total).
2012-04-30 | E-GEOD-37671 | biostudies-arrayexpress
Project description:Analysis of differential expression between NPC and non-NPC tissues at miRNA expression level. We used a miRNA microarray platform to investigate the profile between NPC tissues and normal nasopharyngeal tissues to evaluate the relationship between miRNA expression and NPC. Recognition of the aberrant miRNAs and enrichment pathway analysis of predicted target gene may provide some clues to estimate the mechanism of miRNA effects on NPC carcinogenesis mediated by miRNA-mRNA regulation. Total RNA was extracted from 8 NPC tissues compared to 4 nasopharyngeal tissues. We peformed the Illumina miRNA microarray to identify the differentially expressed miRNA between NPC tissues and normal nasopharyngeal tissues.
2013-06-25 | E-GEOD-22587 | biostudies-arrayexpress
Project description:<p>Nasopharyngeal carcinoma (NPC) is an aggressive head and neck cancer characterized by Epstein-Barr virus (EBV) infection and dense lymphocyte infiltration. The scarcity of NPC genomic data hinders the understanding of NPC biology, disease progression, and rational therapy design. Here, we performed whole-exome sequencing (WES) on 111 micro-dissected EBV-positive NPCs, with 15 cases subjected to further whole-genome sequencing (WGS), to determine its mutational landscape. We identified enrichment for genomic aberrations of multiple negative regulators of the NF-kB pathway in a total of 41% of cases including CYLD, TRAF3, NFKBIA and NLRC5. Functional analysis confirmed novel inactivating CYLD mutations as drivers for NPC cell growth. The EBV oncoprotein latent member protein 1 (LMP1) functions to constitutively activate NF-kB signaling, and we observed mutual exclusivity among somatic NF-kB pathway aberrations and LMP1-overexpression, suggesting that NF-kB activation is selected for by both somatic and viral events during NPC pathogenesis.</p>
| phs001244 | dbGaP
Project description:Analysis of differential expression between NPC and non-NPC tissues at miRNA expression level. We used a miRNA microarray platform to investigate the profile between NPC tissues and normal nasopharyngeal tissues to evaluate the relationship between miRNA expression and NPC. Recognition of the aberrant miRNAs and enrichment pathway analysis of predicted target gene may provide some clues to estimate the mechanism of miRNA effects on NPC carcinogenesis mediated by miRNA-mRNA regulation.
2013-06-25 | GSE22587 | GEO
Project description:CRISPR-Cas9 screen was done to identify genes required for NPC differentiation. Sox1 is an established NPC marker. Human ESCs were infected with GecKO v2 library, selected with puromycin and then allowed to differentiate into Neural progenitor cells (NPC) using StemDiff monolayer protocol (Stem cell Technologies). Day 7 NPCs were collected and FACS sorted to obtain bottom 1% of Sox1 expressing cells. NGS was used to identify guide sequences in cell population and determine the genes required for Sox1 expression during NPC differentiation.
2022-02-16 | GSE168585 | GEO