Chromosomal and genetic abnormalities in benign and malignant meningiomas using DNA microarray

Lessons from senescence: Chromatin maintenance in non-proliferating cells

Cellular senescence is an irreversible proliferation arrest, thought to contribute to tumor suppression, proper wound healing and, perhaps, tissue and organismal aging. Two classical tumor suppressors, p53 and pRB, control cell cycle arrest associated with senescence. Profound molecular changes occur in cells undergoing senescence. At the level of chromatin, for example, senescence associated heterochromatic foci (SAHF) form in some cell types. Chromatin is inherently dynamic and likely needs to be actively maintained to achieve a stable cell phenotype. In proliferating cells chromatin is maintained in conjunction with DNA replication, but how non-proliferating cells maintain chromatin structure is poorly understood. Some histone variants, such as H3.3 and macroH2A increase as cells undergo senescence, suggesting histone variants and their associated chaperones could be important in chromatin structure maintenance in senescent cells. Here, we discuss options available for senescent cells to maintain chromatin structure and the relative contribution of histone variants and chaperones in this process. This article is part of a Special Issue entitled: Histone chaperones and chromatin assembly.

Detection of genetic and chromosomal aberrations in medulloblastomas and primitive neuroectodermal tumors with DNA microarrays

Medulloblastoma (MB) is the most frequent infratentorial malignant brain tumor in children. In contrast, primitive neuroectodermal tumor (PNET) is defined as a supratentorial malignant tumor generated from the cerebral hemisphere. These tumors have considerable histological overlap but have different clinical outcomes including overall survival period, recurrence rate, and chemosensitivity. We investigated the amplification and/or deletion of genes and the chromosomal gain and/or loss in 10 MBs and 3 PNETs with a genomic DNA microarray system. Genes that are frequently amplified in these both these tumors include MSH2, N-myc, AKT3, and EGFR. Amplifications of SNRPN, MYB, and PTEN are observed only in MB. The genes associated with Wnt/APC and Shh/PTCH pathways also have some aberrations. Common chromosomal aberrations include gains at 17q and 7q and losses at 17p. Minor chromosomal losses were also detected at 1p, 8p + q, 11p, 10p + q, 13q, 16q, and Xp + q in MB. SPNETs tend to contain fewer chromosomal and genetic abnormalities than MBs. In conclusion, there are gene expression and chromosomal differences between MBs and SPNETs. These differences may correlate with the prognosis.

Gene expression profiles of meningiomas are associated with tumor cytogenetics and patient outcome

Cytogenetic analysis is a powerful tool for predicting recurrence in meningiomas, even among histologically benign/grade I tumors. Despite this, no study has been reported in which the impact of tumor cytogenetics on the gene expression profiles (GEP) has been analyzed in meningiomas. Here, we analyzed the GEP of 47 tumors and correlated them with the most clinical relevant cytogenetic subgroups of meningiomas, as confirmed through the analysis of 172 patients. Additionally three normal meningeal samples were also studied. Overall, our results show a clear association between the clinically relevant cytogenetic subgroups of meningiomas including diploid tumors (n = 18), isolated -22/22q- (n = 12), del(1p36) alone (n = 4) and complex karyotypes associated with del(1p36) and/or -14q (n = 13) and their GEP. Accordingly, based on the expression of 85 genes (40 of which were coded in the altered chromosomes used for patient stratification) the cytogenetic class of the tumor could be predicted with an error of <1%, a clear association being found between the GEP and patient outcome (P = 0.03) but not tumor histopathology. In summary, we show a clear association between GEP of neoplastic cells and clinically relevant cytogenetic subgroups of meningiomas.

Meningioma

Meningiomas are mostly benign tumours originating from the arachnoid cap cells, represent 13-26% of all intracranial tumours. They are more common in older age and in females. Deletion in NF2 gene and exposure to ionizing radiation are established risk factors, while the role of sex hormones is yet not clarified. Five-year survival for typical meningiomas exceeds 80%, but is poorer (5-year survival <60%) in malignant and atypical meningiomas. Papillary and haemangiopericytic morphology, large tumour size, high mitotic index, absence of progesterone receptors, deletions and loss of heterozygosity are poor prognostic factors. Complete surgical excision is the standard treatment. Radiotherapy is currently used in the clinical practice in atypical, malignant or recurrent meningioma at a total dose of 45-60Gy. However, the role of adjuvant irradiation is still controversial and has to be compared in a randomised prospective setting with a policy of watchful waiting. Radiosurgery has gained more and more importance in the management of meningiomas, especially in meningiomas that cannot be completely resected as for many skull base meningiomas. Medical therapy for patients with recurrent, progressive and symptomatic disease after repeated surgery, radiosurgery and radiotherapy is investigational. Hormonal therapy with progesterone antagonists has shown modest results, while chemotherapy with hydroxyurea appears moderately active.

De novo versus transformed atypical and anaplastic meningiomas: comparisons of clinical course, cytogenetics, cytokinetics, and outcome

OBJECTIVE

The clinical course of atypical and anaplastic meningiomas is heterogeneous. As malignant gliomas, aggressive meningiomas may arise de novo or transform from a benign tumor. This study aims to compare differences in clinical behavior, cytogenetics, cytokinetics, receptor status, and outcome between de novo malignant meningiomas and meningiomas that progressed to malignancy.

METHODS

Data from 36 patients with atypical or anaplastic meningiomas were selected for retrospective analysis and divided into two subgroups: 1) de novo atypical or anaplastic tumors and 2) tumors that progressed from a lower grade. We analyzed data concerning patients' sex, age, tumor location, number of operations, status of hormone receptors, proliferative indices, cytogenetic findings, additional therapy, and survival. For meningiomas with progression, we calculated the interval between initial diagnosis and tumor progression.

RESULTS

For atypical meningiomas, the subgroups had significant differences in status of progesterone receptors, proliferative indices, cytogenetics, and patients' outcome. The anaplastic group had similar differences, but they did not reach statistical significance because of the small numbers. There was a loss of part or monosomy of chromosome 10 and an increased monosomy or derivative chromosome 1 combined with monosomy of chromosome 14. These phenomena occurred mainly in patients with malignant transformation who had a worse outcome.

CONCLUSION

De novo malignant meningiomas and meningiomas with malignant transformation may represent distinct subgroups of atypical and anaplastic meningiomas.

Evaluation of NF2 gene deletion in sporadic schwannomas, meningiomas, and ependymomas by chromogenic in situ hybridization

Fluorescence in situ hybridization, loss of heterozygosity testing, and comparative genomic hybridization have been used to detect NF2 gene alterations in both sporadic and neurofibromatosis type 2 (NF2)-associated central nervous system tumors. In this study, we performed chromogenic in situ hybridization (CISH) and immunohistochemistry to evaluate for NF2 gene deletion in a group of sporadic meningiomas, schwannomas, and ependymomas. Twenty-two sporadic tumors, including 9 ependymomas, 10 meningiomas, and 3 schwannomas, were studied. CISH and immunohistochemistry were performed using the NF2 gene deletion probe and NF2 polyclonal antibody. Deletion of the NF2 gene was identified in 11 (50%) tumors, including 60% (6/10) of meningiomas, 33% (3/9) of ependymomas, and 67% (2/3) of schwannomas. The remaining 11 (50%) cases were diploid. Overall, immunoexpression of NF2 protein was observed in 50% (11/22) tumors, and concordance between CISH and immunohistochemistry was observed in 73% of cases. Our results support previous observations that schwannomas and meningiomas, and to a lesser degree, ependymomas, express a high incidence of NF2 gene deletion, which supports the hypothesis that NF2 gene plays an important role in their tumorigenesis. In addition, we have validated CISH as an efficient, economic, and reliable method for routinely assessing NF2 gene deletion in these tumors.

From array to array: Confirmation of genomic gains and losses discovered by array-based comparative genomic hybridization utilizing fluorescence in situ hybridization on tissue microarrays

The combination of array-based comparative genomic hybridization (CGH) with fluorescence in situ hybridization utilizing custom-designed bacterial artificial chromosome (BAC) probes applied to tissue microarrays represents a powerful compendium of techniques-greatly enhancing the throughput of genomic analysis and subsequent target validation. Such approach can be automated at various levels and allows managing large volume of targets and samples in a few experiments. As such, this approach facilitates discovery, validation and implementation of findings in the process of identification of new diagnostic, prognostic and potentially therapeutic molecular markers.

Recurrent cytogenetic aberrations in histologically benign, invasive meningiomas of the sphenoid region

Meningiomas that arise in the sphenoid region (MSR) often display growth patterns leading to widespread invasion and destruction of the surrounding structures. Consequently, there is still estimated recurrence rate up to 30% with MSR. Conventional cytogenetic studies have failed to reveal aberrations characteristic of invasive meningiomas. Here we investigated 10 invasive and 5 non-invasive MSR using the array-based comparative genomic hybridization (array-CGH) with the GenoSensor Array 300. Mean number of aberrations detected per tumor was significantly greater for invasive meningiomas-67.4 compared with 40.5 for non-invasive MSR. Additionally, invasive MSR disclosed frequent losses on 1p, 6q, 14q and gains on 15q and 20, which were identified previously as molecular hallmarks of stepwise meningioma progression. Thus, the presence of a complex cytogenetic profile and progression-associated chromosomal aberrations in benign MSR is associated with their increased invasive potential. Inasmuch as no reliable adjuvant therapy for recurrent meningiomas is available thus far, revealed genomic aberrations can provide a potential targets for drug discovery and therapeutic intervention in a future.