Tissue metabolites in diffuse glioma and their modulations by IDH1 mutation, histology and treatment
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE190504 | GEO | 2021/12/09
REPOSITORIES: GEO
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Project description:The discovery of the oncometabolite 2-hydroxyglutarate in isocitrate dehydrogenase 1-mutated (IDH1-mutated) tumor entities affirmed the role of metabolism in cancer. However, large databases with tissue metabolites that are modulated by IDH1 mutation remain an area of development. Here, we present an unprecedented and valuable resource for tissue metabolites in diffuse glioma and their modulations by IDH1 mutation, histology, and tumor treatments in 101 tissue samples from 73 diffuse glioma patients (24 astrocytoma, 17 oligodendroglioma, 32 glioblastoma), investigated by NMR-based metabolomics and supported by RNA-Seq. We discovered comparison-specific metabolites and pathways modulated by IDH1 (IDH1 mutation status cohort) and tumor entity. The Longitudinal investigation cohort provides metabolic profiles of untreated and corresponding treated glioma samples at first progression. Most interestingly, univariate and multivariate cox regressions and Kaplan-Meier analyses revealed that tissue metabolites correlate with progression-free and overall survival. Thus, this study introduces potentially novel candidate prognostic and surrogate metabolite biomarkers for future prospective clinical studies, aiming at further refining patient stratification in diffuse glioma. Furthermore, our data will facilitate the generation of so-far-unanticipated hypotheses for experimental studies to advance our molecular understanding of glioma biology.
2022-09-07 | MTBLS3873 | MetaboLights
Project description:Mutations in the genes encoding isocitrate dehydrogenase 1 and 2 (IDH1/2) occur in a variety of tumor types, resulting in production of the proposed oncometabolite, 2-hydroxyglutarate (2-HG). How mutant IDH and 2-HG alter signaling pathways to promote cancer, though, remains unclear. Additionally, there exist relatively few cell lines with IDH mutations. To examine the effect of endogenous IDH mutations and 2-HG, we created a panel of isogenic epithelial cell lines with either wild-type IDH1/2 or clinically relevant IDH1/2 mutations. Differences were noted in the ability of IDH mutations to cause robust 2-HG accumulation. IDH1/2 mutants that produce high levels of 2-HG cause an epithelial-mesenchymal transition (EMT)-like phenotype, characterized by changes in EMT-related gene expression and cellular morphology. 2-HG is sufficient to recapitulate aspects of this phenotype in the absence of an IDH mutation. In the cells types examined, mutant IDH-induced EMT is dependent on upregulation of the transcription factor ZEB1 and downregulation of the mir-200 family of microRNAs. Furthermore, sustained knockdown of IDH1 in IDH1 R132H mutant cells is sufficient to reverse many characteristics of EMT, demonstrating that continued expression of mutant IDH is required to maintain this phenotype. These results suggest mutant IDH proteins can reversibly deregulate discrete signaling pathways that contribute to tumorigenesis 9 HCT116 isogenic clones with wild-type or IDH1/2 mutations. Samples were analyzed in duplicate.
2012-10-25 | E-GEOD-41802 | biostudies-arrayexpress
Project description:2-hydroxyglutarate (2-HG) is an oncometabolite accumulating in certain cancers and some neurometabolic diseases. In cancers 2-HG accumulation is induced by a gain-of-function mutation in isocitrate dehydrogenase (IDH) genes, leading to conversion of alpha-ketoglutarate (a-KG) into 2-HG
2023-04-15 | E-MTAB-11328 | biostudies-arrayexpress
Project description:Isocitrate dehydrogenase (IDH) mutations, a hallmark of gliomagenesis, result in the production of the oncometabolite R-2-hydroxyglutarate (R-2-HG) which is thought to promote tumorigenesis via DNA methylation. Here we identify an additional immunosuppressive activity of R-2-HG: Tumor cell-derived R-2-HG is taken up by T-cells where it induces a strong and immediate perturbation of calcium- and ATP-dependent signaling events, and polyamine biosynthesis. This results in a profound suppression of antigen-specific T-cell activation and effector cytokine production in experimental mouse and human systems. In a large cohort of WHO grade II and III gliomas, IDH1 mutant tumors display reduced infiltration by T-cells compared to IDH1 wildtype tumors. Spontaneous and induced mutation-specific antitumor immunity to syngeneic IDH1-mutant tumors in MHC-humanized mice is improved by isolated genetic ablation of the neomorphic enzymatic function of mutant IDH1. Taken together, these data attribute a novel, fundamentally non-tumor-cell-autonomous role of an oncometabolite in shaping the tumor immune microenvironment. We investigated the effects of exogenous R-2-HG on primary human T cells.
2016-07-27 | E-GEOD-84849 | biostudies-arrayexpress
Project description:Mutations in isocitrate dehydrogenase (IDH) genes occur in various malignant tumors including chondrosarcoma. IDH mutations contribute to malignant transformation by catalyzing the production of 2-hydroxyglutarate (2-HG), a competitive inhibitor of α-ketoglutarate-dependent dioxygenases. Mutant IDH inhibitors are therefore potential novel anticancer drugs in IDH mutant tumors. Here, we examined the efficacy of the inhibition of mutant IDH1 as an antitumor approach in chondrosarcoma cells in vitro and in vivo, and investigated the association between the IDH mutation and chondrosarcoma cells.
2021-11-06 | GSE122202 | GEO
Project description:Malignant gliomas are heterogeneous tumors arising in the central nervous system (CNS) driven by epigenetic and metabolic aberrations. Mutations in Isocitrate DeHydrogenase (IDH1/2) enzymes, highly frequent in adult gliomas, confer a gain-of-function activity that favors the conversion of a-ketoglutarate (α-KG) to the oncometabolite 2-hydroxyglutarate (2-HG), a competitive inhibitor of α-KG-dependent enzymes. These include DNA and histone lysine demethylases, resulting in an aberrant hypermethylation phenotype in mutant-IDH-expressing cells. Leveraging epigenetic-focused cytometry by time-of-flight (CyTOF) analysis, we profiled the effect of mutant-IDH1 expression on a broad panel of histone modifications. This analysis revealed extensive remodeling of chromatin patterns by mutant-IDH, with a global reduction in histone acetylation being the most prominent alteration. The loss of histone acetylation occurs rapidly following mutant-IDH1 induction and affects acetylation patterns over enhancers and intergenic regions. Furthermore, cells expressing mutant-IDH1 showed higher epigenetic heterogeneity, which may support the tumorigenic potential of these cells. Our study underscores the tight interaction between chromatin and metabolism dysregulation in glioma, highlighting novel epigenetic pathways affected by mutant-IDH1-driven metabolic rewiring.
2024-12-13 | GSE276663 | GEO
Project description:Malignant gliomas are heterogeneous tumors arising in the central nervous system (CNS) driven by epigenetic and metabolic aberrations. Mutations in Isocitrate DeHydrogenase (IDH1/2) enzymes, highly frequent in adult gliomas, confer a gain-of-function activity that favors the conversion of a-ketoglutarate (α-KG) to the oncometabolite 2-hydroxyglutarate (2-HG), a competitive inhibitor of α-KG-dependent enzymes. These include DNA and histone lysine demethylases, resulting in an aberrant hypermethylation phenotype in mutant-IDH-expressing cells. Leveraging epigenetic-focused cytometry by time-of-flight (CyTOF) analysis, we profiled the effect of mutant-IDH1 expression on a broad panel of histone modifications. This analysis revealed extensive remodeling of chromatin patterns by mutant-IDH, with a global reduction in histone acetylation being the most prominent alteration. The loss of histone acetylation occurs rapidly following mutant-IDH1 induction and affects acetylation patterns over enhancers and intergenic regions. Furthermore, cells expressing mutant-IDH1 showed higher epigenetic heterogeneity, which may support the tumorigenic potential of these cells. Our study underscores the tight interaction between chromatin and metabolism dysregulation in glioma, highlighting novel epigenetic pathways affected by mutant-IDH1-driven metabolic rewiring.
2024-12-13 | GSE238105 | GEO
Project description:Malignant gliomas are heterogeneous tumors arising in the central nervous system (CNS) driven by epigenetic and metabolic aberrations. Mutations in Isocitrate DeHydrogenase (IDH1/2) enzymes, highly frequent in adult gliomas, confer a gain-of-function activity that favors the conversion of a-ketoglutarate (α-KG) to the oncometabolite 2-hydroxyglutarate (2-HG), a competitive inhibitor of α-KG-dependent enzymes. These include DNA and histone lysine demethylases, resulting in an aberrant hypermethylation phenotype in mutant-IDH-expressing cells. Leveraging epigenetic-focused cytometry by time-of-flight (CyTOF) analysis, we profiled the effect of mutant-IDH1 expression on a broad panel of histone modifications. This analysis revealed extensive remodeling of chromatin patterns by mutant-IDH, with a global reduction in histone acetylation being the most prominent alteration. The loss of histone acetylation occurs rapidly following mutant-IDH1 induction and affects acetylation patterns over enhancers and intergenic regions. Furthermore, cells expressing mutant-IDH1 showed higher epigenetic heterogeneity, which may support the tumorigenic potential of these cells. Our study underscores the tight interaction between chromatin and metabolism dysregulation in glioma, highlighting novel epigenetic pathways affected by mutant-IDH1-driven metabolic rewiring.
2024-12-13 | GSE238104 | GEO
Project description:Human astrocytomas and oligodendrogliomas are defined by mutations in the metabolic enzyme isocitrate dehydrogenase (IDH) 1 or 2. Mutant IDH1 causes the production and accumulation of the metabolite 2 hydroxyglutarate, which induces genome-wide hypermethylation, and is thought to be a driver mutation of these tumours. However, there are multiple contradictory effects of mutant IDH1 in cell lines and in vivo models, prompting us to study the effect of mutant IDH1 on cell differentiation, proliferation, and apoptosis. Here we established mouse glioma initiating cells (GIC) by inactivating the tumour suppressor genes Pten and p53 in the neural stem/progenitor cell population of the forebrain, and compared these GIC with triple mutant tumours expressing in addition the Idh1 R132H mutation. We found that Idh1 mutant cells proliferate less in vitro and mice with Idh1 mutant tumour survived significantly longer than their Idh1 wild type counterparts. By comparing the RNA expression profiles of Idh wild-type and Idh mutant cells and tumours we identified endoplasmic reticulum stress pathways were significantly associated with Idh1 mutation.
2019-08-22 | GSE119741 | GEO
Project description:Human astrocytomas and oligodendrogliomas are defined by mutations in the metabolic enzyme isocitrate dehydrogenase (IDH) 1 or 2. Mutant IDH1 causes the production and accumulation of the metabolite 2 hydroxyglutarate, which induces genome-wide hypermethylation, and is thought to be a driver mutation of these tumours. However, there are multiple contradictory effects of mutant IDH1 in cell lines and in vivo models, prompting us to study the effect of mutant IDH1 on cell differentiation, proliferation, and apoptosis. Here we established mouse glioma initiating cells (GIC) by inactivating the tumour suppressor genes Pten and p53 in the neural stem/progenitor cell population of the forebrain, and compared these GIC with triple mutant tumours expressing in addition the Idh1 R132H mutation. We found that Idh1 mutant cells proliferate less in vitro and mice with Idh1 mutant tumour survived significantly longer than their Idh1 wild type counterparts. By comparing the miRNA expression profiles of Idh wild-type and Idh mutant cells and tumours we identified miR-183-5p as a differentially expressed miRNA.
2019-08-22 | GSE119740 | GEO