Molecular subclassification of pediatric medullablastomas

Medulloblastoma is one of the most common embryonal tumors of the central nervous system, which can be seen at any age, especially in children. It is considered Grade IV according to the World Health Organization classification and generally has a very poor prognosis. Medulloblastomas are divided into four basic subgroups: WNT-activated, SHH-activated, Group 3 and Group 4. The importance of epigenetic changes between subgroups has been emphasized in recent years, and the relationship between abnormal promoter hypermethylations and the clinic of the disease has become a significant research topic. The aim of this study is to investigate the significance of molecular subclassification in pediatric medulloblastoma cases and to analyze the methylation status of the selected genes for their prognostic significance. For this purpose, formalin fixed paraffin embedded tissues of 47 pediatric medulloblastoma cases were obtained from the archives of Dokuz Eylül University Hospital Patology Department, alongside demographic and clinical data of the patients. A revision of past histological diagnoses was performed for all tissues. Using immunohistochemistry, tumors showing nuclear beta-catenin localization were classified as WNT-activated; tumors showing cytoplasmic beta-catenin positivity, GAB1 and YAP1 expression were classified as SHH-activated medulloblastomas. In SHH-activated medulloblastomas, TP53 wildtype and TP53 mutant subgroups were identified according to p53 immunopositivity. Tumors without beta-catenin expression were defined as non-WNT/SHH-activated (Groups 3 and 4) medulloblastomas. The methylation status of CDKN2A, RASSF1A, HIC1, ZIC2, SPINT2, SFRP1, KLF4, PTCH1 and EZH2 genes were examined by pyrosequencing method after bisulfite conversion using DNA isolated from tissues. As a result of DNA methylation analysis, hypermethylations in KLF4, PTCH1 and ZIC2 genes were associated with SHH-activated medulloblastomas. Hypermethylation of the SPINT2 gene and high-grade hypermethylation of the RASSF1A gene were found to have a statistically significant relationship with the presence of metastasis. Methylation studies in CDKN2A, HIC1 and SFRP1 genes could not be associated with the disease since they did not provide optimal results. Hypermethylation of the EZH2 gene was not detected in any of the samples. We conclude that detection of methylation status in medulloblastomas may be an important tool in predicting the clinical course and the potential importance of methylation changs of KLF4, PTCH1, ZIC2, SPINT2 and RASSF1A genes in this disease.