Transcriptomic profiling of IDH-wt-hGICs-MGT#4-dEGFP cells upon overexpression of CRISPRa-screen predicted pro-mesenchymal phenotypic drivers.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE236153 | GEO | 2023/11/27
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptomic profiling of IDH-wt-hGICs-MGT#4-dEGFP cells upon overexpression of CRISPRa-screen predicted pro-mesenchymal phenotypic drivers.
| PRJNA989141 | ENA
Project description:To analyze the gene expression proflies of oligodendrocyte lineage in IDH-mutant glioma cells, we profiled more than 70000 cells from 16 IDH-mutant glioma samples by single cell RNA-seq.
2023-03-25 | GSE227718 | GEO
Project description:IDH mutant cells are deficient in retinoic acid production, which impacts downstream gene expression and pathways. We looked at the effect of supplementing IDH mutant glioma cells with ATRA on gene expression and downstream pathways. We compared gene expression changes with IDH WT cells that were also treated with ATRA
2019-12-11 | GSE141789 | GEO
Project description:Gain-of-function IDH mutations define major clinical and prognostic classes of gliomas. Mutant IDH protein produces a novel onco-metabolite, 2-hydroxyglutarate (2-HG), that interferes with iron-dependent hydroxylase enzymes, including the TET family of 5'-methylcytosine hydroxylases. TET enzymes are critical for the dynamic regulation of DNA methylation. IDH mutant gliomas thus manifest a CpG island methylator phenotype (G-CIMP), though the functional significance of this altered epigenetic state remains unclear. Here we show that IDH1 mutant gliomas exhibit hyper-methylation at CTCF binding sites, leading to reduced binding of this methylation-sensitive insulator protein. Loss of CTCF binding is associated with a loss of insulation between topological domains and aberrant gene activation. We specifically demonstrate that loss of CTCF at a domain boundary permits a constitutive enhancer to aberrantly interact with the receptor tyrosine kinase gene PDGFRA, a prominent glioma oncogene. Treatment of IDH mutant gliomaspheres with demethylating agent partially restores insulator function and reduces PDGFRA expression. Conversely, CRISPR-mediated disruption of the CTCF binding sequence in IDH wildtype gliomaspheres induces PDGFRA expression and increases proliferation. Our study suggests that IDH mutations promote gliomagenesis by disrupting chromosomal topology and allowing aberrant regulatory interactions that induce oncogene expression. CTCF occupancy characterization and histone H3K27 acetylation profiling in IDH1 mutant and wild-type glioma patient specimens and culture models. ChIP-seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns.
2015-12-23 | E-GEOD-70991 | biostudies-arrayexpress
Project description:RNA-sequencing for myeloid inflammation-related genes was conducted on primary tumor samples from patients with IDH-wildtype glioblastoma (GBM) and grade 4 IDH-mutant astrocytoma (G4IMA). In addition, the IDH-wildtype murine glioma cell line GL261 and a strain of IDH-mutant GL261 were also sequenced using the murine counterpart of the RNA-sequencing myeloid innate immunity panel.
2024-05-29 | GSE268118 | GEO
Project description:Background: Dystrophic epidermolysis bullosa (DEB) is a skin blistering disease caused by mutations in COL7A1, which encodes type VII collagen (C7). There is no cure for DEB, but previous work has shown potential therapeutic benefit in increasing production of even partially functional C7. Genome-wide screens using CRISPR-Cas9 have enabled the identification of genes involved in cancer development, drug resistance, and other genetic diseases, suggesting that they could be used to identify novel drivers of C7 production. Methods: A keratinocyte C7 reporter cell line was created by integrating a tdTomato fluorescent marker into the last exon of the endogenous COL7A1 gene. A genome-wide CRISPR activation (CRISPRa) screen was performed with the C7_tdTomato reporter to identify genes and pathways that increase C7 expression. High tdTomato-expressing cells were sorted and sequenced to identify the single guide RNAs (sgRNAs) that became enriched relative to the starting material. Pathway analysis was performed on the corresponding genes to identify regulators and pathways that influence C7 expression. A targeted drug screen was performed in three different keratinocyte cell lines based on the CRISPRa screen results, and C7 upregulation was evaluated. Results: The C7_tdTomato cell line was validated as an effective reporter cell line for detection of C7 upregulation. The CRISPRa screen identified two genes, DENND4B and TYROBP as top hits based on enrichment in the high fluorescence population and representation with multiple sgRNAs. Pathway analysis of the CRISPRa screen showed enrichment of toll-like receptor and interferon-related upstream regulators and functions related to calcium uptake and immune signaling. Several compounds in the targeted drug screen increased C7 expression in at least one keratinocyte line, but only kaempferol, a plant flavonoid, significantly increased C7 mRNA and protein in a DEB patient line. Conclusions: The novel C7_tdTomato reporter cell line can be used to screen compounds for increased C7 expression. The CRISPRa screen combined with a fluorescent reporter cell line can be used to reveal mechanistic regulators of gene expression and therapeutic targets for rare genetic diseases. Kaempferol has shown promising results in increasing C7 production and should be further evaluated as a potential therapeutic for DEB patients.
2022-01-31 | GSE163024 | GEO
Project description:Oligoastrocytoma (OA) was formerly defined as a mixed glioma exhibiting histological features of both astrocytoma and oligodendroglioma. However, OA has been shown to be attributable to either glioma-type based on its molecular characteristics and was excluded from the glioma classification with the introduction of the integrated diagnosis. Nevertheless, some cases showing genetic features of both oligodendroglioma and astrocytoma have been reported since the integrated diagnosis era, and whether OA exists as a glioma-type remains controversial. All previously reported cases were mixed gliomas with and without 1p/19q-codeletion in the lineage of isocitrate dehydrogenase (IDH) mutant gliomas. Herein, we described a 33-year-old man with a progressive headache. Magnetic resonance imaging showed a large left frontal lobe tumor composed of a cystic component with contrast-enhancing walls and a non-contrast-enhancing solid component. The patient underwent a gross total removal of the tumor. Histologically, the cystic and solid components showed oligodendroglioma and astrocytoma morphology, respectively. Immunohistochemically, IDH1-R132H staining was positive in the cystic component and negative in the solid component. Sanger sequencing confirmed the IDH1-R132H mutation and the C228T mutation in the telomerase reverse transcriptase promoter (TERTp) region in the cystic component, while both IDH1/2 and TERTp were wildtype in the solid component. Fluorescence in situ hybridization revealed 1p/19q-codeletion in both areas. The integrated diagnosis led to the diagnosis of oligoastrocytoma consisting of IDH-mutant 1p/19q-codeleted oligodendroglioma and IDH-wildtype astrocytoma. Furthermore, deoxyribonucleic acid (DNA) extracted separately from each area of formalin-fixed paraffin-embedded specimen revealed a distinct methylation profile. On the other hand, the global DNA copy-number analysis derived from the microarray data showed similar copy-number profiles including 1p/19q-codeletion for both sites. This is the first report of a dual-genotype oligoastrocytoma with IDH-mutant 1p/19q-codeleted oligodendroglioma and IDH-wildtype astrocytoma. This extremely rare case provides profound insight into the process of acquiring genetic abnormalities in the development of glioma.
2025-10-31 | GSE280730 | GEO
Project description:Recent single-cell transcriptomic studies report that IDH-mutant gliomas share a common hierarchy of cellular phenotypes, independent of genetic subtype. However, the genetic differences between IDH-mutant glioma subtypes are prognostic, predictive of response to chemotherapy, and correlate with distinct tumor microenvironments. To reconcile these findings, we profiled 22 human IDH-mutant gliomas via single-cell assay for transposase-accessible chromatin (scATAC-seq). We determined the cell-type specific differences in transcription-factor expression and associated regulatory grammars between IDH-mutant glioma subtypes. We find that while IDH-mutant gliomas do share a common distribution of cell types, there are significant differences in the expression and targeting of transcription factors that regulate glial identity and cytokine elaboration. We knocked out the chromatin-remodeler ATRX, which suffers loss-of-function alterations in most IDH-mutant astrocytomas, in an IDH-mutant immunocompetent intracranial murine model. We find that both human ATRX-mutant gliomas and murine ATRX-knockout gliomas are more heavily infiltrated by immunosuppressive monocytic-lineage cells derived from circulation than ATRX-intact gliomas, in an IDH-mutant background. ATRX knockout in murine glioma recapitulates gene expression and open-chromatin signatures that are specific to human ATRX-mutant astrocytomas, including drivers of astrocytic lineage and immune-cell chemotaxis. ATRX knockout in murine glioma recapitulates gene expression and open chromatin signatures that are specific to human ATRX-mutant astrocytomas, including drivers of astrocytic lineage and immune-cell chemotaxis. Through single-cell cleavage under targets and tagmentation assays and meta-analysis of public data, we show that ATRX loss leads to a global depletion in CCCTC-binding factor association with DNA, gene dysregulation along associated chromatin loops, and protection from therapy-induced senescence.
2021-10-20 | GSE155430 | GEO
Project description:Identification of IDH mutations has uncovered the crucial role played by metabolism in glioma-genesis. Oncolytic herpes virus (oHSV) therapy initiates direct tumor debulking by tumor lysis and also activates antitumor immunity however little is known about the role of glioma metabolism in determining oHSV efficacy. Here we identified that oHSV therapy rewired central carbon metabolism with increased glucose utilization towards oxidative phosphorylation and shuttled glutamine towards reductive carboxylation in IDH wildtype (wt) glioma. The switch in metabolism resulted in increased lipid synthesis, and cellular ROS. PKC induced ACSL4 in oHSV treated cells led to lipid peroxidation and ferroptosis. Ferroptosis was critical to launch an antitumor immune response important for efficacy. Mutant IDH (IDHR132H) gliomas are incapable of reductive carboxylation and hence ferroptosis. Pharmacological blockade of IDHR132H induced ferroptosis and antitumor immunity. This study provides a rationale to treat high grade IDHR132H glioma patients under oHSV treatment with IDHR132H inhibitor.
2025-04-02 | GSE289317 | GEO
Project description:Glioblastoma (GBM) is the most frequent and most aggressive form of diffuse glioma. The prognosis is very poor, with a median overall survival of 15 months after maximum safe resection and radiochemotherapy.GBM is one of the most genetically unstable cancers. It is characterized by numerous chromosome (chr) copy number alterations (CNA), such as chr 7 gain, chr 9p loss, and chr 10 loss, along with CDKN2A homozygous deletion (chr 9p21) and EGFR amplification (chr 7p11).Chromosome instability (CIN) may be the cause or the consequence of GBM development. In high-grade diffuse gliomas (HGG), CIN may initiate tumorigenesis. To identify recurrent genomic abnormalities in IDH WT glioblastomas, SNP arrays (Illumina 850K CytoSNP) were analyzed for 123 IDH WT GBM cases.
2018-02-27 | E-MTAB-6371 | biostudies-arrayexpress