Combined genome-wide allelotyping and copy number analysis identify frequent genetic losses without copy number reduction in medulloblastoma.

Detailed analysis of mechanisms of genetic loss for specific tumor suppressor genes (TSGs; e.g., RB1, APC and NF1) indicates that TSG inactivation can occur by allelic loss of heterozygosity (LOH), without any alteration in DNA copy number. However, the role and prevalence of such events in the pathogenesis of specific malignancies remains to be established on a genome-wide basis. We undertook a detailed molecular assessment of chromosomal defects in a panel of nine cell lines derived from primary medulloblastomas, the most common malignant brain tumors of childhood, by parallel genome-wide assessment of LOH (allelotyping) and copy number aberrations (comparative genomic hybridization and fluorescence in situ hybridization). The majority of genetic losses observed were detected by both copy number and LOH methods, indicating they arise through the physical deletion of chromosomal material. However, a significant proportion of losses (17/42, 40%) represented regions of allelic LOH without any associated copy number reduction; these events involved both whole chromosomes (10/17) and sub-chromosomal regions (7/17). Using this approach, we identified medulloblastoma-characteristic alterations, e.g., isochromosome for 17q, MYC amplification and losses on chromosomes 10, 11, and 16, alongside novel regions of genetic loss (e.g., 10q21.1-26.3, 11q24.1-qter). This detailed genetic characterization of the majority of medulloblastoma cell lines provides important precedent for the widespread involvement of copy number-neutral genetic losses in medulloblastoma and demonstrates that combined assessment of copy number aberrations and LOH will be necessary to accurately determine the contribution of chromosomal defects to tumor development.

A 7-year-old boy with midline cerebellar mass.

January 2005. A boy aged 7 years was found to have a tumor arising from the roof of the fourth ventricle. Histopathologically, part of the tumor appeared as a PNET, while neuroglial tissue, striated and smooth muscle, cartilage and small glandular structures were present in other regions. Tumor cells in both primitive and mature elements showed a loss of chromosome 17p accompanied by a gain of 17q, a pattern consistent with the presence of an isochromosome 17q. This abnormality is not characteristic of intracranial germ cell tumors, but is present in over 30% of medulloblastomas. On the basis of the histologic and genetic abnormalities, we propose a diagnosis of PNET with multilineal differentiation.

Combined histopathological and molecular cytogenetic stratification of medulloblastoma patients.

This study examined the utility of stratifying children with medulloblastomas by a combination of refined histopathological classification and molecular cytogenetic evaluation. Detailed histopathological classification of tumors from a cohort of patients (n = 87) composed mainly of children entered into the International Society of Pediatric Oncology (SIOP)/United Kingdom Children's Cancer Study Group PNET3 trial (n = 65), included identification of the large cell/anaplastic phenotype. Fluorescence in situ hybridization was used to detect chromosome 17 abnormalities, losses of 9q22 and 10q24, and amplification of the MYCC and MYCN oncogenes. The large cell/anaplastic phenotype, which was present in 20% of medulloblastomas, emerged as an independent prognostic indicator. Loss of 17p13.3 (38% of medulloblastomas) was found across all of the histopathological variants, whereas MYCC/MYCN amplification (6%/8% of medulloblastomas) was significantly associated with the large cell/anaplastic phenotype. Both of these genetic abnormalities emerged as prognostic indicators. Loss of 9q22 was associated with the nodular/desmoplastic medulloblastoma variant, whereas loss of 10q24 was found in all of the variants. Together with metastatic tumor at presentation, the large cell/anaplastic phenotype, 17p13.3 loss, or high-frequency MYC amplification defined a high-risk group of children whose outcome was significantly (P = 0.0002) poorer than a low-risk group without these tumor characteristics. Combined evaluation of novel histopathological features and molecular cytogenetic abnormalities promises to allow stratification of patients with medulloblastoma, such that those likely to be cured will be spared the side effects of maximal therapy, which can be targeted at those with aggressive disease.

Morphophenotypic variation predicts clinical behavior in childhood non-desmoplastic medulloblastomas.

Histopathologic assessment of 273 non-desmoplastic medulloblastomas (MBs) from children aged 3 to 16 years and entered into the SIOP/UKCCSG (International Society of Pediatric Oncology/United Kingdom Children's Cancer Study Group) PNET3 trial revealed that 47 (17%) fulfilled criteria for the recently proposed anaplastic variant. In addition, an anaplastic phenotype was focally present in all 5 (2%) large cell MBs from this series. Children with large cell MBs had the worst outcome, but there was also a significant difference between the event-free and overall survivals of children with classic MBs and those with anaplastic MBs. While objective morphometric analysis confirmed that subjective evaluation of nuclear size and variability contributed to the separation of MBs into classic, anaplastic, and large cell variants, these cytologic measures were not themselves prognostic indicators. However, anaplastic and classic MBs also possessed significantly different mitotic counts/indices, and these measures of proliferation were related to survival. Significant prognostic indicators in a multivariate survival analysis were histologic variant, metastases at presentation, and subtotal surgical excision of tumor. Our study supports the concept of an anaplastic variant among MBs, demonstrating that it has clinical utility.