Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma [ChIP-seq]
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE59496 | GEO | 2014/07/20
SECONDARY ACCESSION(S): PRJNA255430
REPOSITORIES: GEO
Similar Datasets
Project description:ChIP-Seq analysis of a pediatric human diffuse intrinsic pontine glioma (DIPG) cell line SF8628, harboring the K27M mutation. Goal was to obtain quantitative estimates of K27me3 immunoprecipitation change between vehicle-treated SF8628 cells [dimethyl sulfoxide, (DMSO)] and SF8628 cells incubated with 6 mM GSKJ4 at 24 hours and 72 hours. Three-condition experiment: 72 h GSKJ4-treated cells vs. 24 h GSKJ4-treated cells vs. DMSO-treated cells. Biological replicates: 1 cell line, each with 2 technical replicates per condition.
2014-07-20 | E-GEOD-59496 | biostudies-arrayexpress
Project description:Transcriptional profiling of two pediatric human DIPG cell lines, harboring the K27M mutation. DIPG cell lines were treated with GSKJ4 for 24 and 72 h. The untreated cell lines served as baseline, and expression fold changes in each treated cell line were determined relative to the baseline. Goal was to determine the effects of GSKJ4 treatment on global gene expression in DIPG cells harboring the K27M mutation.
2014-07-14 | GSE59366 | GEO
Project description:Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment and near 100% fatality. The failure of most therapies can be attributed to the delicate location of these tumors and choosing therapies based on assumptions that DIPGs are molecularly similar to adult disease. Recent studies have unraveled the unique genetic make-up of this brain cancer with nearly 80% harboring a K27M-H3.3 or K27M-H3.1 mutation. However, DIPGs are still thought of as one disease with limited understanding of the genetic drivers of these tumors. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling, discovering that DIPGs are three molecularly distinct subgroups (H3-K27M, Silent, MYCN) and uncovering a novel recurrent activating mutation in the activin receptor ACVR1, in 20% of DIPGs. Mutations in ACVR1 were constitutively activating, leading to SMAD phosphorylation and increased expression of downstream activin signaling targets ID1 and ID2. Our results highlight distinct molecular subgroups and novel therapeutic targets for this incurable pediatric cancer. Illumina Infinium 450K arrays were performed according to the manufacturer's directions on bisulfite converted gDNA extracted from fresh frozen biopsy and autopsy brain tissue from DIPG patients. CpG methylation profiling on Illumina Infinium 450K arrays was performed for 28 paediatric DIPG samples.
2014-03-31 | E-GEOD-50022 | biostudies-arrayexpress
Project description:Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment and near 100% fatality. The failure of most therapies can be attributed to the delicate location of these tumors and choosing therapies based on assumptions that DIPGs are molecularly similar to adult disease. Recent studies have unraveled the unique genetic make-up of this brain cancer with nearly 80% harboring a K27M-H3.3 or K27M-H3.1 mutation. However, DIPGs are still thought of as one disease with limited understanding of the genetic drivers of these tumors. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling, discovering that DIPGs are three molecularly distinct subgroups (H3-K27M, Silent, MYCN) and uncovering a novel recurrent activating mutation in the activin receptor ACVR1, in 20% of DIPGs. Mutations in ACVR1 were constitutively activating, leading to SMAD phosphorylation and increased expression of downstream activin signaling targets ID1 and ID2. Our results highlight distinct molecular subgroups and novel therapeutic targets for this incurable pediatric cancer. Illumina HT-12 arrays were performed according to the manufacturer's directions on RNA extracted from FFPE biopsy and autopsy brain tissue from DIPG patients. Gene expression profiling on Illumina HT-12 arrays was performed for 35 paediatric DIPG samples and 10 normal brain samples
2014-03-31 | E-GEOD-50021 | biostudies-arrayexpress
Project description:Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment and near 100% fatality. The failure of most therapies can be attributed to the delicate location of these tumors and choosing therapies based on assumptions that DIPGs are molecularly similar to adult disease. Recent studies have unraveled the unique genetic make-up of this brain cancer with nearly 80% harboring a K27M-H3.3 or K27M-H3.1 mutation. However, DIPGs are still thought of as one disease with limited understanding of the genetic drivers of these tumors. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling, discovering that DIPGs are three molecularly distinct subgroups (H3-K27M, Silent, MYCN) and uncovering a novel recurrent activating mutation in the activin receptor ACVR1, in 20% of DIPGs. Mutations in ACVR1 were constitutively activating, leading to SMAD phosphorylation and increased expression of downstream activin signaling targets ID1 and ID2. Our results highlight distinct molecular subgroups and novel therapeutic targets for this incurable pediatric cancer. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from snap frozen biopsy and autopsy brain tissue from DIPG patients. Copy number analysis on Affymetrix 6.0 SNP arrays was performed for 45 paediatric DIPG samples, 27 matched normal brain samples, and HapMap samples.
2014-03-31 | E-GEOD-50024 | biostudies-arrayexpress
Project description:Human diffuse intrinsic pontine gliomas (DIPG) are an aggressive form of pediatric brain tumors that arise in the pons in young children thus resulting in significant morbidity and very poor survival. Recent data suggest that mutations in the histone H3.3 variant are often found in these tumors, though the mechanism of their contribution to oncogenesis remains to be elucidated. Here we report that the combination of constitutive PDGFRA activation and p53 suppression as well as expression of the K27M mutant form of the histone H3.3 variant leads to neoplastic transformation of hPSC-derived neural precursors. Our study demonstrates that human ES cells represent an excellent platform for the modeling of human tumors in vitro and in vivo, which could potentially lead to the elucidation of the molecular mechanisms underlying neoplastic transformation and the identification of novel therapeutic targets. Human ES cells were differentiated to NPCs and lentivirally transduced with a combination of constitutively active PDGFRA (D842V), sh-p53, and WT or K27M mutant form of histone H3.3 variant.
2014-11-21 | E-GEOD-55541 | biostudies-arrayexpress
Project description:Background: The histone variant H3.3 K27M mutation is a defining characteristic of diffuse intrinsic pontine glioma (DIPG)/diffuse midline glioma (DMG). This histone mutation is responsible for major alterations to histone H3 post-translational modification (PTMs) and subsequent aberrant gene expression. However, much less is known about the effect this mutation has on chromatin structure and function, including open versus closed chromatin regions as well as their transcriptomic consequences. Results: Recently, we developed isogenic CRISPR-edited DIPG cell lines that are wild- type for histone H3.3 that can be compared to their matched K27M lines. Here we show via ATAC-seq analysis that H3.3K27M glioma cells have unique accessible chromatin at regions corresponding to neurogenesis, NOTCH, and neuronal development pathways and associated genes that are overexpressed in H3.3K27M compared to our isogenic wild-type cell line. As to mechanisms, accessible enhancers and super-enhancers corresponding to increased gene expression in H3.3K27M cells were also mapped to genes involved in neurogenesis and NOTCH signaling, suggesting that these pathways are key to DIPG tumor maintenance. Motif analysis implicates specific transcription factors as central to the neuro-oncogenic K27M signaling pathway including, in particular, ASCL1 and NEUROD1. Conclusions: Altogether our findings indicate that H3.3K27M causes chromatin to take on a more accessible configuration at key regulatory regions for NOTCH and neurogenesis genes resulting in increased oncogenic gene expression, which is at least partially reversible upon editing K27M back to wild- type.
2022-04-24 | GSE201265 | GEO
Project description:Diffuse intrinsic pontine gliomas (DIPGs) are highly lethal childhood brain tumors. Their unique genetic makeup, pathological heterogeneity, and brainstem location all present challenges to treatment. Developing mouse models that accurately reflect each of these distinct features will be critical to advance our understanding of DIPG development, progression, and therapeutic resistance. The aim of this study was to generate new mouse models of DIPG, and characterize the role of specific oncogenic combinations in DIPG pathogenesis. We used in utero electroporation (IUE) to transfect neural stem cells in the developing brainstem with PiggyBac DNA transposon plasmids. Combinations of PDGFB or PdgfraD842V, dominant negative Trp53 (DNp53), and H3.3K27M expression induced fully penetrant brainstem gliomas. IUE enabled the targeted transfection of brainstem neural stem cells. PDGFB + DNp53 induced the rapid development of grade-IV gliomas. PdgfraD842V + DNp53 produced slower forming grade-III gliomas. Addition of H3.3K27M only significantly accelerated PdgfraD842V DIPG development. Glioma subgroup molecular signatures were associated with differences in bulk PDGFB and PdgfraD842V tumor composition. H3.3K27M induced both overlapping and unique gene expression changes in PDGFB and PdgfraD842V tumors. Paracrine effects of PDGFB promote disruption of pericyte-endothelial interactions and angiogenesis in PDGFB DIPG mouse models. Brainstem targeted in utero electroporation provides a rapid and flexible system to generate diverse DIPG mouse models. Using IUE to investigate mutation and pathohistological heterogeneity of DIPG will provide a valuable tool for future genetic and preclinical studies.
2019-11-14 | GSE128807 | GEO
Project description:We studied the effect of BMI1 inhibition in diffuse intrinsic pontine glioma cells (DIPG). We reported the application of chromatin immunoprecipitation sequencing for high-thoughput profiling of BMI1 and H2AK119ub in diffuse intrinsic pontine glioma cells (DIPG) in response to BMI1 inhibition. We also performed bulk RNA sequencing of DIPG cells in response to pharmacological inhibition or knockdown of BMI1.
2020-10-22 | GSE140768 | GEO
Project description:Diffuse intrinsic pontine glioma (DIPG) is an aggressive childhood tumor of the brainstem with currently no curative treatment available. The vast majority of DIPGs carry a mutation in histone H3 leading to a lysine 27-to-methionine exchange (H3K27M). The H3K27M mutation has been shown to inhibit EZH2, the catalytic subunit of the polycomb repressive complex 2, which presumably leads to global reduction of H3K27 trimethylation and upregulation of tumor-driving genes. However, the exact pathomechanism and cellular context remain elusive. Recent single cell transcriptome data suggested the DIPG cell of origin to be of oligodendroglial lineage, whereas in vivo studies demonstrated neural stem or progenitor cells (NPCs, NSCs) to be susceptible for malignant transformation upon H3K27M expression. Here, we used targeted human induced pluripotent stem cells (iPSCs) carrying an inducible H3.3-K27M allele in the endogenous H3F3A locus together with specific differentiation methods to study the effects of the mutation in disease-relevant cell identities of the neural lineage. Phenotypic, transcriptomic, and chromatin immunoprecipitation sequencing (ChIP-seq) analyses revealed a distinct role of H3.3-K27M for deregulating bivalent promoter-associated developmental genes producing diverse outcomes in different cell types. While being fatal for iPSCs, H3.3-K27M increased proliferation in NSCs and to a lesser extent in oligodendroglial progenitor cells (OPCs) but not in astroglial-restricted precursors. Importantly, we demonstrated that only NSCs but not OPCs gave rise to tumors upon induction of the H3.3-K27M and TP53 inactivation in an orthotopic xenograft model faithfully recapitulating human DIPGs. Thus, we provide evidence that indeed only NSCs can develop H3.3-K27M-driven DIPG-like tumors but that the mutation actively drives acquisition of oligodendroglial characteristics, thus explaining the different observations of cell identity. Identification of the originating cell type may help to determine specific vulnerabilities of this tumor for developing targeted therapies.
2021-02-09 | GSE133153 | GEO