BACKGROUND: (blind field). METHODS: Multidimensional molecular profiles of 70 gliobalstoma and 4 non-tumoral brain samples were obtained, comprising gene expression, DNA methylation, and gene copy number alterations. Validation datasets were downloaded from the public domain including The Cancer Genome Atlas (TCGA) Project. For 4 glioma-derived sphere lines marks for active and inactive chromatin were sought by ChIP-PCR. RESULTS: Prominent DNA methylation was observed in the HOXA gene cluster in glioblastoma and respective glioma-derived spheres, in contrast to non tumoral brain. High concordance of correlations between CpG methylation in the HOXA cluster and expression of the HOX-signature was observed with external datasets (RV 0.68 and 0.84). In search of the regulatory region explaining the overexpression of the HOX signature we identified a CpG island encompassing a promoter region in the HOXA locus with strong negative correlation of CpG methylation and expression. A model was constructed explaining the probability of HOX-high in glioblastoma by combining information on gene dosage and methylation at the CpGs identified. The model was successful validated in external datasets. Further experimental evidence supportive for the relevance of epigenetic modulation at this site came from concordance between the methylation status and the presence of marks for active or inactive chromatin, respectively, in HOX-high versus HOX-low sphere lines. CONCLUSIONS: The acquired overexpression of the stem-cell related HOX signature in glioblastoma is in accordance with aberrant de-repression of HOX genes mediated at least in part by increased gene dosage attenuated by DNA methylation. SECONDARY CATEGORY: Tumor Biology.