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CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [HumanMethylation850 BeadChip]

ABSTRACT: CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [HumanMethylation850 BeadChip]

PROVIDER: PRJNA490591 | ENA |

REPOSITORIES: ENA

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CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA

Project description:CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA

| PRJNA490433 | ENA

CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [ChIP-Seq]

Project description:CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [ChIP-Seq]

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CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [RNA-Seq]

Project description:CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [RNA-Seq]

| PRJNA490436 | ENA

CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [HumanMethylation850 BeadChip]

Project description:Glioblastoma is an incurable brain cancer characterized by high genetic and pathological heterogeneity. Here we mapped active chromatin landscapes with gene expression, whole-exomes, copy number profiles, and DNA methylomes across 44 glioblastoma stem cell (GSCs) models, 50 primary glioblastomas, and 10 neural stem cells (NSCs) with the goal of identifying essential super enhancer (SE)-associated genes and the core transcription factors that establish them and glioblastoma identity. Glioblastomas segregate with two dominant enhancer profiles that coopt unique developmental transcription factor regulatory programs to enforce tumor identity. From group specific enhancer profiles, we inferred core transcription factors that define subgroup identity. These transcription factors show higher activity in glioblastomas versus normal neural stem cells, are associated with poor clinical outcomes, and are required for glioblastoma growth in vitro and in vivo. Given challenges with genetically-defined targeted therapies for glioblastoma, we propose targeting underlying transcriptional identity may serve as an important therapeutic strategy.

2019-03-18 | GSE119774 | GEO

CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [RNA-Seq]

2019-03-18 | GSE119834 | GEO

CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [ChIP-Seq]

2019-03-18 | GSE119755 | GEO

Chromatin landscapes reveal developmentally encoded transcriptional states that define human glioblastoma.

Project description:Glioblastoma is an incurable brain cancer characterized by high genetic and pathological heterogeneity. Here, we mapped active chromatin landscapes with gene expression, whole exomes, copy number profiles, and DNA methylomes across 44 patient-derived glioblastoma stem cells (GSCs), 50 primary tumors, and 10 neural stem cells (NSCs) to identify essential super-enhancer (SE)-associated genes and the core transcription factors that establish SEs and maintain GSC identity. GSCs segregate into two groups dominated by distinct enhancer profiles and unique developmental core transcription factor regulatory programs. Group-specific transcription factors enforce GSC identity; they exhibit higher activity in glioblastomas versus NSCs, are associated with poor clinical outcomes, and are required for glioblastoma growth in vivo. Although transcription factors are commonly considered undruggable, group-specific enhancer regulation of the MAPK/ERK pathway predicts sensitivity to MEK inhibition. These data demonstrate that transcriptional identity can be leveraged to identify novel dependencies and therapeutic approaches.

| S-EPMC6504206 | biostudies-literature

CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-03-18 | GSE119776 | GEO

Physical and molecular landscapes of mouse glioma extracellular vesicles define heterogeneity

Project description:Physical and molecular landscapes of mouse glioma extracellular vesicles define heterogeneity

| PRJNA508725 | ENA

A short ORF-encoded transcriptional regulator

Project description:Recent technological advances have expanded the annotated protein coding content of mammalian genomes, as hundreds of previously unidentified, short open reading frame (ORF)-encoded peptides (SEPs) have now been found to be translated. Although several studies have identified important physiological roles for this emerging protein class, a general method to define their interactomes is lacking. Here, we demonstrate that genetic incorporation of the photo-crosslinking noncanonical amino acid AbK into SEP transgenes allows for the facile identification of SEP cellular interaction partners using affinity-based methods. From a survey of seven SEPs, we report the discovery of short ORF-encoded histone binding protein (SEHBP), a conserved microprotein that interacts with chromatin-associated proteins, localizes to discrete genomic loci, and induces a robust transcriptional program when overexpressed in human cells. This work affords a straightforward method to help define the physiological roles of SEPs and demonstrates its utility by identifying SEHBP as a short ORF-encoded transcription factor.

2021-01-11 | GSE164239 | GEO

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