Epigenomic Profiling Reveals Novel and Frequent Targets of Aberrant DNA Methylation-Mediated Silencing in Malignant Glioma

Abstract

Malignant glioma is the most common central nervous system tumor of adults and is associated with a significant degree of morbidity and mortality. Gliomas are highly invasive and respond poorly to conventional treatments. Gliomas, like other tumor types, arise from a complex and poorly understood sequence of genetic and epigenetic alterations. Epigenetic alterations leading to gene silencing, in the form of aberrant CpG island promoter hypermethylation and histone deacetylation, have not been thoroughly investigated in brain tumors, and elucidating such changes is likely to enhance our understanding of their etiology and provide new treatment options. We used a combined approach of pharmacologic inhibition of DNA methylation and histone deacetylation, coupled with expression microarrays, to identify novel targets of epigenetic silencing in glioma cell lines. From this analysis, we identified >160 genes up-regulated by 5-aza-2 ¶-deoxycytidine and trichostatin A treatment. Further characterization of 10 of these genes, including the putative metastasis suppressor CST6, the apoptosis-inducer BIK, and TSPYL5, whose function is unknown, revealed that they are frequent targets of epigenetic silencing in glioma cell lines and primary tumors and suppress glioma cell growth in culture. Furthermore, we show that other members of the TSPYL gene family are epigenetically silenced in gliomas and dissect the contribution of individual DNA methyltransferases to the aberrant promoter hypermethylation events. These studies, therefore, lay the foundation for a comprehensive understanding of the full extent of epigenetic changes in gliomas and how they may be exploited for therapeutic purposes. (Cancer Res 2006; 66(15): 7490-501)

MT1-MMP protects breast carcinoma cells against type I collagen-induced apoptosis

“…The reason why these cells fail to express BIK upon MMP inhibition remains unclear. However, BIK is repressed in a number of malignant cell lines because of hypermethylation (Kim et al, 2006;Sturm et al, 2006).…”

Methylation-dependent silencing of CST6 in primary human breast tumors and metastatic lesions

“…Cystatin M is involved in regulating the activity of cathepsin B and cathepsin L, and imbalances between these proteases and cystatin M may lead to the metastatic phenotype in tumor cells (Frosch et al, 1999;Kos et al, 2000;Lah and Kos, 1998). Cystatin M expression has been reported to be diminished or lost in various forms of cancer including, (i) basal and squamous cell carcinomas of the skin (Zeeuwen, 2004), (ii) squamous cell carcinomas of the head/neck and lung (Zeeuwen et al, 2002), (iii) non-small cell lung cancer (Zhong et al, 2006), (iv) metastatic oral cancer cell lines (Vigneswaran et al, 2006), (v) malignant glioma (Kim et al, 2006), and (vi) breast cancer (Ai et al, 2006;Rivenbark et al, 2006a;Schagdarsurengin et al, 2006;Shridhar et al, 2004;Song et al, 2006;Sotiropoulou et al, 1997;Zhang et al, 2004). Cystatin M contains a large CpG island that flanks the transcription start site and spans the proximal promoter and exon 1 regions.…”

DNA methyltransferase-mediated transcriptional silencing in malignant glioma: a combined whole-genome microarray and promoter array analysis

“…We have recently identified a cohort of genes activated in primary GBM cells following exposure to DNMT and HDAC inhibitors (Foltz et al, 2006). Two other studies have also demonstrated that pharmacological inhibition of DNMT enhances the transcriptional activity of genes exhibiting hypermethylated promoters in GBM (Kim et al, 2006b;Mueller et al, 2007). Unfortunately, pharmacological inhibition of DNMT is limited by cell toxicity and other nonspecific drug side effects with chronic treatment.…”

“…Although overall mortality remains high, recent developments have provided a better understanding of key molecular mechanisms, which hold promise for improved therapeutic approaches Mischel et al, 2003;Singh et al, 2004;Hegi et al, 2005;Mellinghoff et al, 2005;Hambardzumyan et al, 2006;Beier et al, 2007). Recent studies have also more clearly defined the role of epigenetic modifications in the aberrant silencing of genes associated with cell proliferation, tumor progression, apoptosis, angiogenesis and astrocyte motility in GBM (Foltz et al, 2006;Kim et al, 2006b;Mueller et al, 2007). In these studies, global genomic screens were employed to identify genes upregulated in GBM cells following short-term exposure to histone deacetylase (HDAC) and/or DNA methyltransferase (DNMT) inhibitors.…”