CDKN2A, CDKN2B and p14 ^ARF are frequently and differentially methylated in ependymal tumours

Abstract

Ependymal tumours are histologically and clinically varied lesions. Numerical abnormalities of chromosome 9 are frequently associated with these tumours. Nevertheless, the three important tumour suppressor genes located in this chromosome, CDKN2A, CDKN2B and p14 ARF, have not been reported to be commonly altered in them. We studied promoter methylation of these genes, an important mechanism associated with gene silencing in a series of 152 ependymal tumours of WHO grades I to III. Methylation status of the CDKN2A, CDKN2B and p14 ARF promoters was assessed by methylation-specific polymerase chain reaction and the genetic results were correlated to clinicopathological features. We observed promoter methylation for CDKN2A in 21% (26/123) of tumours, for CDKN2B in 32% (23/71) and p14 ARF in 21% (23/108). For all three genes, posterior fossa ependymomas were less frequently methylated in paediatric patients than in adults. For CDKN2B, extracranial tumours were more frequently methylated than intracranial ones. For CDKN2B and p14 ARF, methylation was more frequent in low-grade tumours; the reverse was observed for CDKN2A. CDKN2A, CDKN2B and p14 ARF promoters were methylated in 21-32% of the tumours. Frequencies of methylation varied according to clinicopathological features. This suggests a role for these genes in ependymoma tumorigenesis.

Gene Expression Patterns in Ependymomas Correlate with Tumor Location, Grade, and Patient Age

“…Recently, inactivation of both copies of the CDKN2A gene (p16 INK4A and p14 ARF ) because of deletions, point mutations, or methylation has been demonstrated in ependymoma. 37,38 In a recent comparative genomic hybridization study by Hirose and colleagues, 7 intracranial ependymomas showed frequent losses of 9p (9 of 23 patients), whereas spinal ependymomas displayed gains of this chromosomal region (11 of 20 patients). This finding suggests that differential expression levels of CDKN2A in spinal and intracranial ependymomas found in our study might be because of chromosomal aberrations, which lead to deletions or additional copy numbers of CDKN2A.…”

Pediatric Ependymoma: Biological Perspectives

“…Whereas gene expression analysis has revealed that CDKN2A is upregulated in spinal tumors (77,86), it is downregulated by a much stronger magnitude in intracranial tumors (86). Furthermore, while epigenetic analysis has shown a significant difference in the methylation status of neighboring CDKN2B between spinal and intracranial tumors (79), fluorescent in situ hybridization (FISH) has shown that CDKN2A deletion is virtually exclusive to supratentorial ependymomas (34). Other genes on 9p that seem to be downregulated exclusively in supratentorial ependymal tumors include FREM1, C9orf24, and KIAA116 (76).…”

“…These include the overexpression of genes LDHB and STAM (77), the downregulation and deletion of members of the Protein 4.1 superfamily (78), and the reduced methylation of CDKN2A, CDKN2B, and p14ARF in posterior fossa ependymomas (79).…”

Epigenetic mechanisms regulating neural development and pediatric brain tumor formation

“…94 One of the first studies to address the epigenetic silencing of genes in ependymoma found CDKN2A, CDKN2B, and p14/ARF to be frequently methylated in 21%-32% of the tumors, with frequencies varying according to clinicopathological features. 123 Other work detected an abnormal CpG island methylation greater than 20% in MGMT, TIMP3, THBS1, and TP73. 2 The putative tumor repressor gene HIC1, also epigenetically silenced in medulloblastomas, was hypermethylated in 83% of ependymomas that primarily had a nonspinal localization.…”