Hypermethylation as a potential prognostic factor and a clue to a better understanding of the molecular pathogenesis of medulloblastoma - Results of a genomewide methylation scan

Background: The molecular mechanisms controlling initiation and progression of medulloblastomas are largely unclear. Changes in DNA methylation of pro moter regions have been shown to disturb the expression of growth regulator y genes. Patients and Methods: We evaluated DNA methylation patterns in 17 medulloblastomas, 5 stPNETs and 5 medulloblastoma cell lines using Restrict ion Landmark Genomic Scanning (RLGS), a method displaying up to 2.000 poten tial gene loci in a single gene. To test whether previously characterized t umor suppressor genes are affected by hypermethylation we performed MS-PCR for p15(INK4B), p16(INK4A), VHL, TP53 and E-cadherin. Results: The analysis of RLGS profiles from tumors revealed an abundance of hypermethylation in primary tumors and cell lines. Extrapolated to the human genome with its si milar to 36,000 genes a total of 420 loci become hypermethylated in the tum or genomes. The previously characterized medulloblastoma breakpoint cluster in 17p11.2 appears to be a hotspot for aberrant methylation. Cox regressio n analysis of survival data identified seven CpG islands for which hypermet hylation is suggestive of a poor prognosis. MS-PCR analysis of known genes demonstrated hypermethylation of p16(INK4A) in a limited number of tumors. The pattern of DNA hypermethylation was similar in medulloblastomas and stP NETs. However, some CpG islands were shown to be specific for a tumor type, while others were shared targets. Conclusions: Hypermethylation is a commo n abnormality in primary medulloblastomas and supratentorial PNETs. Several hundreds of CpG islands are potential targets for methylation in medullobl astomas including the breakpoint cluster in 17p11.2. The methylation status of certain gene sequences appears to be associated with the clinical outco me. Promoter hypermethylation has an outstanding potential as a marker for the identification of novel tumor suppressors as well as diagnostic and the rapeutic targets in medulloblastomas.