Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin states in glioblastoma stem cell [ChIP-seq]

ABSTRACT: In human, the 39 coding HOX genes and 18 referenced non-coding antisense transcripts are arranged in four genomic clusters named HOXA, B, C, and D. This highly conserved family belongs to the homeobox class of genes that encode transcription factors required for normal development. Therefore, HOX gene deregulation might contribute to the development of many cancer types. Here, we study HOX gene deregulation in adult glioma, a common type of primary brain tumor. We performed extensive molecular analysis of tumor samples, classified according to their isocitrate dehydrogenase (IDH1) gene mutation status, and of glioma stem cells. We found widespread expression of sense and antisense HOX transcripts only in aggressive (IDHwt) glioma samples, although the four HOX clusters displayed DNA hypermethylation. Integrative analysis of expression-, DNA methylation- and histone modification signatures along the clusters revealed that HOX gene upregulation relies on canonical and alternative bivalent CpG island promoters that escape hypermethylation. H3K27me3 loss at these promoters emerges as the main cause of widespread HOX gene upregulation in IDHwt glioma cell lines and tumors. Our study provides the first comprehensive description of the epigenetic changes at HOX clusters and their contribution to the transcriptional changes observed in adult glioma. It also identified putative "master" HOX proteins that might contribute to the tumorigenic potential of glioma stem cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE161436 | GEO | 2021/03/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

CNV analysis of normal brain and glioma samples II

Project description:In human, the 39 coding HOX genes and 18 referenced non-coding antisense transcripts are arranged in four genomic clusters named HOXA, B, C, and D. This highly conserved family belongs to the homeobox class of genes that encode transcription factors required for normal development. Therefore, HOX gene deregulation might contribute to the development of many cancer types. Here, we study HOX gene deregulation in adult glioma, a common type of primary brain tumor. We performed extensive molecular analysis of tumor samples, classified according to their isocitrate dehydrogenase (IDH1) gene mutation status, and of glioma stem cells. We found widespread expression of sense and antisense HOX transcripts only in aggressive (IDHwt) glioma samples, although the four HOX clusters displayed DNA hypermethylation. Integrative analysis of expression-, DNA methylation- and histone modification signatures along the clusters revealed that HOX gene upregulation relies on canonical and alternative bivalent CpG island promoters that escape hypermethylation. H3K27me3 loss at these promoters emerges as the main cause of widespread HOX gene upregulation in IDHwt glioma cell lines and tumors. Our study provides the first comprehensive description of the epigenetic changes at HOX clusters and their contribution to the transcriptional changes observed in adult glioma. It also identified putative "master" HOX proteins that might contribute to the tumorigenic potential of glioma stem cells.

2021-03-09 | GSE161275 | GEO

EPIC-based DNA methylation analysis of glioblastoma stem cells.

2021-03-09 | GSE161175 | GEO

Stranded RNA-seq were performed on total RNA following ribosomal RNAs depletion (Ribo-zero removal kit, illumina) for glioblastoma stem cell

2021-03-09 | GSE161438 | GEO

Transcriptome of glioblastoma stem cells.

2021-03-09 | GSE161437 | GEO

Postoperative risk of IDH mutant glioma-associated seizures and their potential management with IDH mutant inhibitors

Project description:To investigate the peri-tumoral effect of IDHmut vs IDHwt glioma, we engrafted IDHmut or IDHwt mouse glioma intracranially in C57BL/6 mice.

2024-04-21 | GSE227995 | GEO

Stranded RNA-seq were performed on total RNA following ribosomal RNAs depletion (Ribo-zero removal kit, illumina) for 3 brain , 8 IDHwt and 5 IDHmut glioma samples.

Project description:Aberrant DNA methylation is a well-defined feature of cancer cells that is commonly associated to transcriptional alteration. Nonetheless, a primary role of this defect in genome-wide cancer-associated gene misregulation is still being questioned. Here, we used adult glioma, a widespread type of brain tumor, to evaluate the relative contribution of DNA methylation-dependent and -independent mechanisms on transcriptional alteration at CpG-island/promoter-associated genes in cancer cells. By extensive molecular analyses conducted in both IDH wild-type (IDHwt) and IDH mutated (IDHmut) samples, we show that DNA hypermethylation affects only a minority of genes that show a loss or a gain of expression. In IDHwt samples, for instance, more than 75% of aberrantly repressed genes do not display DNA methylation defect at their CpG-island promoter. Rather, an alteration in the H3K27me3 signature is the predominant molecular defect at misregulated genes. We also observed that a bivalent chromatin signature in stem cell might not only predispose genes to hypermethylation, as widely documented, but more generally to all type of transcriptional alterations. In addition, we evidenced that transcriptional strength in healthy brain influences the choice between DNA methylation- or H3K27me3- associated silencing pathway at repressed genes in glioma. Combined our study supports a model whereby the altered developmental control of H3K27me3 dynamics, and more specifically defects in the interplay between polycomb protein complexes and brain-specific transcriptional machinery, is the main cause of transcriptional alteration in glioma cells. Together our study provides a comprehensive and revisited picture of epigenetic gene deregulations in cancer. Our observations are also of importance for the design of drugs that aims to target cancer epigenetic defects.

2019-09-09 | GSE123892 | GEO

CNV analysis of normal brain and glioma samples

2019-09-09 | GSE123682 | GEO

HM450K-based DNA methylation analysis of normal brain and glioma samples

2019-09-09 | GSE123678 | GEO

The epigenetic evolution of glioma is determined by the IDH1 mutation status and treatment regimen

Project description:Tumor adaptation or selection is thought to underlie therapy resistance in glioma. To investigate longitudinal epigenetic evolution of gliomas in response to therapeutic pressure, we performed an epigenomic analysis of 132 matched initial and recurrent tumors from patients with IDH-wildtype (IDHwt) and IDH-mutant (IDHmut) glioma. IDHwt gliomas showed a stable epigenome over time with relatively low levels of global methylation. The epigenome of IDHmut gliomas showed initial high levels of genome-wide DNA methylation that was progressively reduced to levels similar to those of IDHwt tumors. Integration of epigenomics, gene expression, and functional genomics identified HOXD13 as a master regulator of IDHmut astrocytoma evolution. Furthermore, relapse of IDHmut tumors was accompanied by histological progression that was associated with survival, as validated in an independent cohort. Finally, the initial cell composition of the tumor microenvironment varied between IDHwt and IDHmut tumors and changed differentially following treatment, suggesting increased neo-angiogenesis and T-cell infiltration upon treatment of IDHmut gliomas. This study provides one of the largest cohorts of paired longitudinal glioma samples with epigenomic, transcriptomic, and genomic profiling and suggests that treatment of IDHmut glioma is associated with epigenomic evolution towards an IDHwt-like phenotype.

2023-12-13 | GSE248471 | GEO