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.
Project description:Tumor associated macrophages are contributing to local invasion, angiogensis, and metastasis during the progression of many kinds of tumor including glioma We used microrray to study the difference of expression of glioma associated macrophages and normal brain tissue associated macrophages The macrophgages were isolated based on the markers of GFP and F4/80+ from Gl261 glioma and normal brain, RNA were extracted for microarray analysis
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.
Project description:Mosaic Analysis with Double Markers (MADM) based glioma mouse model, which homozygously lacks Tp53 and Nf1, spontaneously developed gliomas at the post-natal 90-120 days. Tp53 and Nf1 are among the most frequently mutated genes in human glioma patients. Investigating the expression changes of genes induced by inactivation of Tp53, Nf1 and EZH2 can be a clue to clarify the mechanism of gliomagenesis. We examined the expressions of glioma cells in MADM mouse (n=2), EZH2 knocked-out MADM glioma tissues (n=3) and neural stem cell (NSC), astrocyte established with normal mice brains (n=2, respectively) and TP53 knocked-out astrocytes, derived from TP53 knocked-out mice (n=2). We used SurePrint G3 Mouse GE 8×60K array slides (G4858A, Agilent Technologies).
Project description:Tumor associated macrophages are contributing to local invasion, angiogensis, and metastasis during the progression of many kinds of tumor including glioma We used microrray to study the difference of expression of glioma associated macrophages and normal brain tissue associated macrophages
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.