Dataset: Gene expression data from glioblastoma tumor samples

Glioblastoma (GBM) is an incurable brain tumor carrying a dismal prognosis, which displays considerable heterogeneity. We have recently...

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Glioblastoma (GBM) is an incurable brain tumor carrying a dismal prognosis, which displays considerable heterogeneity. We have recently identified recurrent H3F3A mutations affecting two critical positions of histone H3.3 (K27, G34) in one-third of pediatric GBM. Here we show that each of these H3F3A mutations defines an epigenetic subgroup of GBM with a distinct global methylation pattern, and are mutually exclusive with IDH1 mutation (characterizing a CpG-Island Methylator Phenotype (CIMP) subgroup). Three further epigenetic subgroups were enriched for hallmark genetic events of adult GBM (EGFR amplification, CDKN2A/B deletion) and/or known transcriptomic signatures. We also demonstrate that the two H3F3A mutations give rise to GBMs in separate anatomic compartments, with differential regulation of OLIG1/2 and FOXG1, possibly reflecting different cellular origins. To further dissect the biological differences between epigenetic glioblastoma subgroups, we looked at the transcriptomic profiles of glioblastoma samples. 46 glioblastoma samples from patients of various ages were selected for RNA extraction and hybridization on Affymetrix Affymetrix Human Genome U133 Plus 2.0 Arrays.

Species:: human
Samples:: 46
Source:: E-GEOD-36245
Updated:: Dec.12, 2014
Registered:: Sep.19, 2014

Factors: (via ArrayExpress)

Sample	H3F3A STATUS	TUMOR LOCATION	AGE AT DIAGNOSIS YEARS	SEX	IDH1 STATUS	SUBGROUP
GSM884997	K27M	ventricular	10	female	WT	K27
GSM884998	WT	frontal lobe	10	female	WT	RTK I
GSM884999	G34R	temporal lobe	9	male	WT	G34
GSM885000	K27M	thalamic	11	female	WT	K27
GSM88500	WT	frontal lobe	13	female	WT	Mesenchymal
GSM885002	WT	nan	38	male	WT	RTK II
GSM885003	WT	nan	40	female	MUT	IDH
GSM885004	WT	nan	32	female	MUT	IDH
GSM885005	WT	nan	46	female	WT	Mesenchymal
GSM885006	WT	nan	34	male	MUT	Mesenchymal
GSM885007	WT	frontal/temporal	20	female	WT	RTK I
GSM885008	WT	nan	36	male	WT	RTK I
GSM885009	WT	parietal lobe	19	male	WT	RTK I
GSM885010	WT	nan	36	male	WT	Mesenchymal
GSM8850	K27M	thalamic	23	female	WT	K27
GSM885012	WT	nan	33	male	MUT	IDH
GSM885013	WT	Cerebellar	20	female	WT	RTK I
GSM885014	WT	nan	38	male	WT	Mesenchymal
GSM885015	WT	nan	48	male	MUT	IDH
GSM885016	G34R	temporal lobe	42	female	WT	G34
GSM885017	WT	nan	33	male	WT	RTK I
GSM885018	WT	nan	40	male	WT	RTK II
GSM885019	WT	nan	25	female	MUT	IDH
GSM885020	WT	nan	38	male	MUT	IDH
GSM88502	WT	frontal lobe	18	male	MUT	IDH
GSM885022	WT	nan	36	male	WT	RTK II
GSM885023	K27M	nan	10	male	WT	nan
GSM885024	WT	nan	not specified	female	nan	nan
GSM885025	WT	nan	not specified	male	nan	nan
GSM885026	nan	hemispheric	nan	female	nan	nan
GSM885027	nan	nan	nan	male	nan	nan
GSM885028	WT	hemispheric	1	male	MUT	nan
GSM885029	G34V	parieto-occipital	19	female	nan	nan
GSM885030	G34R	temporo-parietal	14	male	nan	nan
GSM885025	WT	nan	not specified	male	nan	nan
GSM958490	K27M	thalamic	7	female	WT	K27
GSM95849	G34R	frontal lobe	17	female	WT	G34
GSM958492	G34R	nan	12	female	WT	G34
GSM958493	K27M	pons	6	female	WT	K27
GSM958494	WT	temporal lobe	5	male	WT	nan
GSM958495	WT	central region	14	female	WT	nan
GSM958494	WT	temporal lobe	5	male	WT	nan
GSM958497	K27M	nan	9	female	WT	nan
GSM958498	G34R	parietal lobe	14	male	WT	nan
GSM958499	WT	temporal lobe	19	female	MUT	nan
GSM958500	WT	frontal lobe	14	female	WT	nan