Clustering of hypermethylated genes in neuroblastoma

Abstract

CpG-island hypermethylation of gene promoters is a frequent mechanism for gene inactivation in tumors. Many neuroblastomas have hypermethylation and down-regulation of CASP8, leading to resistance to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). We recently found hypermethylation of the four TRAIL receptors in 9 neuroblastoma cell lines. Here, we analyzed methylation of 34 genes in 22 neuroblastoma cell lines. Of the 29 newly analyzed genes, only FLIP at chromosome band 2q33 was methylated in 8/22 cell lines. The FLIP protein is a negative regulator of Caspase 8. FLIP maps adjacent to CASP8, and their methylation patterns showed a moderate correlation. Furthermore, co-methylation patterns were observed for the TRAIL receptor pairs DCR1 and DCR2 and between DR4 and DR5. All four receptors co-localize in chromosome band 8p21. The 6 genes methylated in neuroblastomas appeared to occur in pairs. The genes within each pair have a strong sequence homology and originated from gene duplication. We found no evidence for regional spreading of methylation, given that we did not observe de novo methylation in additional local CpG islands. However, the gene pairs showed a striking co-regulation at the mRNA expression level. Down-regulation of FLIP strongly corresponds with down-regulation of CASP8, and this was also found for DCR1 and DCR2. Only a subset of the down-regulated genes was methylated. This suggests a mechanism of co-regulated transcriptional silencing of the gene pairs, followed by a methylation event that is less penetrating. The methylation pattern therefore supports a model in which CpG islands are not randomly targeted by methylation in cancer. Specific transcriptional silencing probably marks genes that can become methylated.

RIP1 Protein-dependent Assembly of a Cytosolic Cell Death Complex Is Required for Inhibitor of Apoptosis (IAP) Inhibitor-mediated Sensitization to Lexatumumab-induced Apoptosis

“…A recent study similarly reported that TRAIL-R1 is present at low levels in RMS cell lines, although the underlying molecular mechanisms were not identified (17). As epigenetic events have been described to regulate the expression of apoptosis regulatory proteins, including TRAIL receptors and caspase-8 (21,22), it will be interesting to explore whether epigenetic silencing of TRAIL-R1 may contribute to its low expression in RMS.…”

Analysis of methylation-sensitive transcriptome identifies GADD45a as a frequently methylated gene in breast cancer

“…The presence of CpG-rich regions does not immediately implicate them as regulated by methylation in general or specifically in breast epithelial cells since more than 50% of all human genes may have associated CpG clusters (Murphy and Jirtle, 2001). Only three of these genes have been shown to be hypermethylated in human cancer, CAV1, THBS1, and TNFRSF10B (Li et al, 1999;Cui et al, 2001;Wiechen et al, 2001;Oue et al, 2003;van Noesel et al, 2003). Of these, THBS1 and CAV1 methylation have been linked specifically to breast cancer (Engelman et al, 1999;Li et al, 1999).…”

Transcription initiation sites and promoter structure of the human TRAIL‐R3 gene1

“…and TRAIL-R4, is involved in the down-regulation of the expression of these genes in neuroblastoma and other tumor types, such as brain, colon and skin cancers [18]. Moreover, it has been shown that TRAIL-R3 is a p53-regulated gene highly expressed in primary tumors of gastrointestinal tract [21].…”

“…The involvement of p53 in the regulation of the TRAIL-R2 promoter has been described [17], and hypermethylation of the human TRAIL-R3 and TRAIL-R4 promoters has been suggested to be important for the down-regulation of these receptors in neuroblastoma and other tumor types [18]. It has been recently reported that activator protein 1 (AP-1) regulates TRAIL-R1 expression via the AP-1 binding site located at 3350/3344 within the gene promoter region [19].…”