Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms

Abstract

In cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution of DNA methylation-dependent and -independent mechanisms to transcriptional alterations at CpG island/promoter-associated genes in cancer, we studied 70 samples of adult glioma, a widespread type of brain tumor, classified according to their isocitrate dehydrogenase (IDH1) mutation status. We found that most transcriptional alterations in tumor samples were DNA methylation-independent. Instead, altered histone H3 trimethylation at lysine 27 (H3K27me3) was the predominant molecular defect at deregulated genes. Our results also suggest that the presence of a bivalent chromatin signature at CpG island promoters in stem cells predisposes not only to hypermethylation, as widely documented, but more generally to all types of transcriptional alterations in transformed cells. In addition, the gene expression strength in healthy brain cells influences the choice between DNA methylation-and H3K27me3-associated silencing in glioma. Highly expressed genes were more likely to be repressed by H3K27me3 than by DNA methylation. Our findings support a model in which altered H3K27me3 dynamics, more specifically defects in the interplay between polycomb protein complexes and the brain-specific transcriptional machinery, is the main cause of transcriptional alteration in glioma cells. Our study provides the first comprehensive description of epigenetic changes in glioma and their relative contribution to transcriptional changes. It may be useful for the design of drugs targeting cancer-related epigenetic defects.

HOX gene cluster (de)regulation in brain: from neurodevelopment to malignant glial tumours

“…This issue has been less studied at the other HOX clusters. Nonetheless, it was recently shown that overexpression of eight HOX genes distributed over the HOXB, C and D clusters was CNV-independent in IDH-wildtype samples [172]. Altogether, these observations support the hypothesis that CNV, if present, are not the main driving force of HOX gene overexpression in aggressive glioma.…”

“…As the HOXA locus is on chromosome 7, chromosome 7 trisomy might increase HOXA gene expression in these patients. Indeed, a correlation was observed between chromosome 7 gain and HOXA1, HOXA4 [172], and HOXA5 [149] expression in GBM and IDH-wildtype patients. However, this is not true for all HOXA genes because no correlation was observed between CNV and expression of HOXA2 [172], HOXA9 [150], HOXA10 [161], and HOXA13 [172].…”

“…At other genes, extensive methylation of their main CpG islands/promoter was associated with the use of an alternative promoter. For instance, in IDH-wildtype glioma, HOXC11 transcription initiated from an unmethylated alternative promoter located 5 kb upstream the canonical, aberrantly methylated promoter[172]. This picture becomes even more complex in the case of chromosome 7 gain.…”

“…Kurscheid et al[175] suggested that hypermethylation of the HOXA cluster could compensate the CNV at this cluster in GBM cells with low expression level (HOX-low), while key CpG sites located in the HOXA locus could escape this hypermethylation phenotype in HOX-high GBM cells. Specifically, they showed that a CpG island located at the HOXA10 non-canonical promoter escape to hypermethylation in HOX-high GBM cells.Court et al[172] provided evidences that besides the DNA methylation gain, HOX clusters in IDHwildtype glioma samples are characterized also by dramatic reduction of H3K27me3. Given the importance of this mark for HOX gene repression in normal brain[59] (as previously detailed in section 2), its loss might be crucial for their aberrant expression in aggressive glioma.…”

“…Moreover, they demonstrated that this process is reversible, because PI3K pathway pharmacological inhibition abolished HOXA gene overexpression in GBM cells. Court et al[172] also proposed that loss of H3K27me3 at HOX genes is a consequence of genome-wide hypomethylation that characterizes cancer cells. In the mouse, widespread DNA methylation depletion triggers H3K27me3 redistribution[179,180] that in turn leads to dramatic loss of H3K27me3 and ectopic expression at a subset of polycomb target genes,…”