Infrequency of p53 gene mutations in ependymomas

Mutation profiling of anaplastic ependymoma grade III by Ion Proton next generation DNA sequencing

Background: Ependymomas are glial tumors derived from differentiated ependymal cells. In contrast to other types of brain tumors, histological grading is not a good prognostic marker for these tumors. In order to determine genomic changes in an anaplastic ependymoma, we analyzed its mutation patterns by next generation sequencing (NGS). Methods:  Tumor DNA was sequenced using an Ion PI v3 chip on Ion Proton instrument and the data were analyzed by Ion Reporter 5.6. Results: NGS analysis identified 19 variants, of which four were previously reported missense variants; c.395G>A in IDH1, c.1173A>G in PIK3CA, c.1416A>T in KDR and c.215C>G in TP53. The frequencies of the three missense mutations ( PIK3CA c.1173A>G, KDR c.1416A>T, TP53, c.215C>G) were high, suggesting that these are germline variants, whereas the IDH1 variant frequency was low (4.81%). However, based on its FATHMM score of 0.94, only the IDH1 variant is pathogenic; other variants TP53, PIK3CA and KDR had FATHMM scores of 0.22, 0.56 and 0.07, respectively. Eight synonymous mutations were found in FGFR3, PDGFRA, EGFR, RET, HRAS, FLT3, APC and SMAD4 genes. The mutation in FLT3 p.(Val592Val) was the only novel variant found. Additionally, two known intronic variants in KDR were found and intronic variants were also found in ERBB4 and PIK3CA. A known splice site mutation at an acceptor site in FLT3, a 3'-UTR variant in the CSF1R gene and a 5'_UTR variant in the SMARCB1 gene were also identified. The p-values were below 0.00001 for all variants and the average coverage for all variants was around 2000x. Conclusions: In this grade III ependymoma, one novel synonymous mutation and one deleterious missense mutation is reported. Many of the variants reported here have not been detected in ependymal tumors by NGS analysis previously and we therefore report these variants in brain tissue for the first time.

Mutation profiling of anaplastic ependymoma grade III by Ion Proton next generation DNA sequencing

Background: Ependymomas are glial tumors derived from differentiated ependymal cells. In contrast to other types of brain tumors, histological grading is not a good prognostic marker for these tumors. In order to determine genomic changes in an anaplastic ependymoma, we analyzed its mutation patterns by next generation sequencing (NGS). Methods:  Tumor DNA was sequenced using an Ion PI v3 chip on Ion Proton instrument and the data were analyzed by Ion Reporter 5.6. Results: NGS analysis identified 19 variants, of which four were previously reported missense variants; c.395G>A in IDH1, c.1173A>G in PIK3CA, c.1416A>T in KDR and c.215C>G in TP53. The frequencies of the three missense mutations ( PIK3CA c.1173A>G, KDR c.1416A>T, TP53, c.215C>G) were high, suggesting that these are germline variants, whereas the IDH1 variant frequency was low (4.81%). However, based on its FATHMM score of 0.94, only the IDH1 variant is pathogenic; other variants TP53, PIK3CA and KDR had FATHMM scores of 0.22, 0.56 and 0.07, respectively. Eight synonymous mutations were found in FGFR3, PDGFRA, EGFR, RET, HRAS, FLT3, APC and SMAD4 genes. The mutation in FLT3 p.(Val592Val) was the only novel variant found. Additionally, two known intronic variants in KDR were found and intronic variants were also found in ERBB4 and PIK3CA. A known splice site mutation at an acceptor site in FLT3, a 3'-UTR variant in the CSF1R gene and a 5'_UTR variant in the SMARCB1 gene were also identified. The p-values were below 0.00001 for all variants and the average coverage for all variants was around 2000x. Conclusions: In this grade III ependymoma, one novel synonymous mutation and one deleterious missense mutation is reported. Many of the variants reported here have not been detected in ependymal tumors by NGS analysis previously and we therefore report these variants in brain tissue for the first time.

Low-dose Actinomycin-D treatment re-establishes the tumoursuppressive function of P53 in RELA-positive ependymoma

Ependymomas in children can arise throughout all compartments of the central nervous system (CNS). Highly malignant paediatric ependymoma subtypes are Group A tumours of the posterior fossa (PF-EPN-A) and RELA-fusion positive (ST-EPN-RELA) tumours in the supratentorial compartment. It was repeatedly reported in smaller series that accumulation of p53 is frequently observed in ependymomas and that immunohistochemical staining correlates with poor clinical outcome, while TP53 mutations are rare. Our TP53 mutation analysis of 130 primary ependymomas identified a mutation rate of only 3%. Immunohistochemical analysis of 398 ependymomas confirmed previous results correlating the accumulation of p53 with inferior outcome. Among the p53-positive ependymomas, the vast majority exhibited a RELA fusion leading to the hypothesis that p53 inactivation might be linked to RELA positivity.

In order to assess the potential of p53 reactivation through MDM2 inhibition in ependymoma, we evaluated the effects of Actinomycin-D and Nutlin-3 treatment in two preclinical ependymoma models representing the high-risk subtypes PF-EPN-A and ST-EPN-RELA. The IC-50 of the agent as determined by metabolic activity assays was in the lower nano-molar range (0.2–0.7 nM). Transcriptome analyses of high-dose (100 nM), low-dose (5 nM) and non-treated cells revealed re-expression of p53 dependent genes including p53 upregulated modulator of apoptosis (PUMA) after low-dose treatment. At the protein level, we validated the Actinomycin-D induced upregulation of PUMA, and of p53 interaction partners MDM2 and p21. Proapoptotic effects of low-dose application of the agent were confirmed by flow cytometry. Thus, Actinomycin-D could constitute a promising therapeutic option for ST-EPN-RELA ependymoma patients, whose tumours frequently exhibit p53 inactivation.

The Similarities and Differences between Intracranial and Spinal Ependymomas : A Review from a Genetic Research Perspective

Ependymomas occur in both the brain and spine. The prognosis of these tumors sometimes differs for different locations. The genetic landscape of ependymoma is very heterogeneous despite the similarity of histopathologic findings. In this review, we describe the genetic differences between spinal ependymomas and their intracranial counterparts to better understand their prognosis. From the literature review, many studies have reported that spinal cord ependymoma might be associated with NF2 mutation, NEFL overexpression, Merlin loss, and 9q gain. In myxopapillary ependymoma, NEFL and HOXB13 overexpression were reported to be associated. Prior studies have identified HIC-1 methylation, 4.1B deletion, and 4.1R loss as common features in intracranial ependymoma. Supratentorial ependymoma is usually characterized by NOTCH-1 mutation and p75 expression. TNC mutation, no hypermethylation of RASSF1A, and GFAP/NeuN expression may be diagnostic clues of posterior fossa ependymoma. Although MEN1, TP53, and PTEN mutations are rarely reported in ependymoma, they may be related to a poor prognosis, such as recurrence or metastasis. Spinal ependymoma has been found to be quite different from intracranial ependymoma in genetic studies, and the favorable prognosis in spinal ependymoma may be the result of the genetic differences. A more detailed understanding of these various genetic aberrations may enable the identification of more specific prognostic markers as well as the development of customized targeted therapies.

An overview of the management of adult ependymomas with emphasis on relapsed disease

Ependymomas are rare neoplasms of the central nervous system. Disease-free survival after relapse is poor and approaches to treatment in recurrent disease often palliative. This overview summarises the management of primary disease for which broad consensus exists. We also extensively review treatment options in relapsed disease for which approaches to treatment are varied due to the paucity of literature evidence. Incorporated in this overview is a survey of UK neuro-oncology units to form a snapshot of current UK practise with respect to preferred systemic therapy regimens for patients with recurrent ependymoma. The outcome reflects a preference for mainly oral-based regimens. Universal guidance is lacking in the management of non-operable irradiated recurrent ependymoma and there are worthy therapeutic avenues for further investigation, in particular the role of radical re-irradiation and also the potential of bevacizumab in advanced disease. It is hoped that advances can be achieved by multicentre collaboration in future studies to overcome the difficulties posed by achieving meaningful data in such a rare tumour with extensive natural history.

Prognostic value of Ki-67 (MIB-1) and p53 in ependymomas

To determine whether Ki-67 (MIB-1) and p53 have prognostic value in ependymomas, clinicopathologic study was undertaken in 29 patients with this tumor. The clinical course correlated well with the histological grade according to the World Health Organization (WHO) grading system, and it was the worst in patients with anaplastic ependymoma. The percent expression of MIB-1 and p53 correlated with the histological grade of malignancy. With regard to the subtypes of benign ependymoma, the clinical course was the worst in clear-cell ependymoma, which had a significantly higher expression of MIB-1 and p53 than the other subtypes. Tanycytic ependymoma showed the most benign clinical course and the lowest expression of MIB-1 and p53. Although the WHO grading generally tended to correlate with the clinical course of ependymomas, these two subtypes--clear-cell ependymoma and tanycytic ependymoma--exhibited biological properties different from those of other grade II ependymomas.

The genetic and epigenetic basis of ependymoma

INTRODUCTION

Although ependymoma is the third most common pediatric brain tumor, we know little about the genetic/epigenetic basis of its initiation, maintenance, or progression. This is due in part to the heterogeneity of the disease, as well as the small sample size of the cohorts analyzed in most studies.

METHODS

Many of the genetic aberrations identified to date are large genomic regions, making the differentiation between passenger and driver genes difficult. The finding of a balanced karyotype in a significant subset of pediatric posterior fossa ependymomas increases the difficulty of identifying targets for rationale therapy.

CONCLUSION

The paucity of in vitro and in vivo model systems for ependymoma compound the difficulties outlined above. In this review, we discuss the published literature on ependymoma genetics and epigenetics and discuss possible future directions for the field.

Ependymal tumors

Ependymomas represent a heterogeneous group of glial tumors whose biological behavior depends on various histological, molecular, and clinical variables. The scope of this chapter is to review the clinical and histo-logical features as well as the molecular genetics of ependymomas with special emphasis on their influence on tumor recurrence and prognosis. Furthermore, potential molecular targets for therapy are outlined.

Pediatric ependymoma: biological perspectives

Pediatric ependymomas are enigmatic tumors that continue to present a clinical management challenge despite advances in neurosurgery, neuroimaging techniques, and radiation therapy. Difficulty in predicting tumor behavior from clinical and histological factors has shifted the focus to the molecular and cellular biology of ependymoma in order to identify new correlates of disease outcome and novel therapeutic targets. This article reviews our current understanding of pediatric ependymoma biology and includes a meta-analysis of all comparative genomic hybridization (CGH) studies done on primary ependymomas to date, examining more than 300 tumors. From this meta-analysis and a review of the literature, we show that ependymomas in children exhibit a different genomic profile to those in adults and reinforce the evidence that ependymomas from different locations within the central nervous system (CNS) are distinguishable at a genomic level. Potential biological markers of prognosis in pediatric ependymoma are assessed and the ependymoma cancer stem cell hypothesis is highlighted with respect to tumor resistance and recurrence. We also discuss the shifting paradigm for treatment modalities in ependymoma that target molecular alterations in tumor-initiating cell populations.

Telomere maintenance and dysfunction predict recurrence in paediatric ependymoma

We have recently described the enzymatic subunit of telomerase (hTERT) as an important prognostic marker for paediatric ependymoma. Because of the lack of good, representative pre-clinical models for ependymoma, we took advantage of our large cohort of ependymoma patients, some with multiple recurrences, to investigate telomere biology in these tumours. Our cohort consisted of 133 ependymomas from 83 paediatric patients and included 31 patients with recurrences. Clinical outcome was measured as overall survival, progression-free survival and response to therapy. In all 133 tumours, hTERT expression correlated with proliferative markers, including MIB-1 index (P<0.0001) and mitotic index (P=0.005), as well as overall tumour grade (P=0.001), but not with other markers of anaplasia. There was no correlation between telomere length and hTERT expression or survival. Surprisingly, prior radiation or chemotherapy neither induced sustained DNA damage nor affected telomere maintenance in recurrent tumours. There was an inverse correlation between hTERT expression and telomere dysfunction as measured by gamma H2AX expression (P=0.016). Combining gamma H2AX and hTERT expressions could segregate tumours into three different survival groups (log rank, P<0.0001) such that those patients whose tumours expressed hTERT and showed no evidence of DNA damage had the worst outcome. This study emphasises the importance of telomere biology as a prognostic tool and telomerase inhibition as a therapeutic target for paediatric ependymoma. Furthermore, we have demonstrated that analysing tumours as they progress in vivo is a viable approach to studying tumour biology in humans.

Biological background of pediatric medulloblastoma and ependymoma: a review from a translational research perspective

Survival rates of pediatric brain tumor patients have significantly improved over the years due to developments in diagnostic techniques, neurosurgery, chemotherapy, radiotherapy, and supportive care. However, brain tumors are still an important cause of cancer-related deaths in children. Prognosis is still highly dependent on clinical characteristics, such as the age of the patient, tumor type, stage, and localization, but increased knowledge about the genetic and biological features of these tumors is being obtained and might be useful to further improve outcome for these patients. It has become clear that the deregulation of signaling pathways essential in brain development, for example, sonic hedgehog (SHH), Wnt, and Notch pathways, plays an important role in pathogenesis and biological behavior, especially for medulloblastomas. More recently, data have become available about the cells of origin of brain tumors and the possible existence of brain tumor stem cells. Newly developed array-based techniques for studying gene expression, protein expression, copy number aberrations, and epigenetic events have led to the identification of other potentially important biological abnormalities in pediatric medulloblastomas and ependymomas.

Giant cell ependymoma: a case report

Ependymomas account for 3-9% of all neuroepithelial tumors. A peculiar variant of ependymoma known as "giant cell ependymoma" ("GCE") is especially rarely reported, it may pose some difficulties for the diagnosing neuropathologist. Here we present a case of a giant cell ependymoma occuring in a 17-year-old patient with the history of 2-year recurrent headaches and a 1-month history of vision impairment. CT scanning demonstrated a mass in the left occipital lobe, arising from the occipital horn of the lateral ventricle. Histological, immunohistochemical and electron microscopic findings were consistent with high-grade ependymoma. Especially striking was the presence of bizzare pleomorphic giant cells which predominated in the tumor tissue. As a result the diagnosis of GCE was established. This type of neoplasm necessitates, at least in theory, differentiation with anaplastic oligodendroglioma, clear cell ependymoma, pleomorphic xanthoastrocytoma, giant cell glioblastoma, and subependymal giant cell astrocytoma. To date giant cell ependymomas (GCEs) were reported in seven cases in the literature. To the best of our knowledge this is the 8th case in the literature. In spite of apparently "worrisome" histology GCE seems to be a neoplasm with a relatively good prognosis.

Current concepts in the molecular genetics of pediatric brain tumors: implications for emerging therapies

BACKGROUND

The revolution in molecular biology that has taken place over the past 2 decades has provided researchers with new and powerful tools for detailed study of the molecular mechanisms giving rise to the spectrum of pediatric brain tumors. Application of these tools has greatly advanced our understanding of the molecular pathogenesis of these lesions.

REVIEW

After familiarizing readers with some promising new techniques in the field of oncogenomics, this review will present the current state of knowledge as it pertains to the molecular biology of pediatric brain neoplasms. Along the way, we hope to highlight specific instances where the detailed mechanistic knowledge acquired thus far may be exploited for therapeutic advantage.

p53 Pathway dysfunction in primary childhood ependymomas

BACKGROUND

Childhood ependymoma remains a major therapeutic challenge despite surgery, chemotherapy, and irradiation. We hypothesized that p53 function might be abrogated in ependymomas and implicated in their resistance to anti-cancer therapy.

PROCEDURE

Primary ependymomas at diagnosis or relapse from 24 children were analyzed for p53 pathway, using a functional assay in yeast, RT-PCR, Western blot analysis, and/or immunohistochemistry for TP53 mutation, p14(ARF) deletion and promoter hypermethylation, MDM2 and PAX5 expression, respectively. p53-mediated response to radiation-induced DNA damage was evaluated using Western blot and flow cytometry analysis in two ependymoma xenograft models, IGREP37 and IGREP83, derived from primary anaplastic childhood ependymomas.

RESULTS

No TP53, MDM2, p14(ARF), PAX5 gene abnormalities were detected in the primary ependymomas tumors and xenografts tested. Interestingly, despite the lack of these abnormalities, p53 induced p21-mediated G(1) growth arrest in response to irradiation was altered in the IGREP37 xenograft tumors. Although irradiation induced necrosis and apoptotic cell death, IGREP37 tumors were moderately sensitive to radiation therapy in vivo. In contrast, irradiation yielded significant tumor growth delays and tumor regressions in the p53 functional IGREP83 xenografts.

CONCLUSION

Alterations in p53-mediated growth arrest in ependymomas might be implicated in the radio-resistance of these tumors and demand further evaluation.

Infratentorial giant cell ependymoma: a rare variant of ependymoma

We describe a giant cell ependymoma occurring in a 50-year-old man. The mass was located in the posterior aspect of the foramen magnum, extending from the cerebellar tonsil to the upper cervical spine. The tumor was a highly cellular neoplasm showing biphasic histology. Diffuse sheets of non-cohesive atypical giant cells, having eccentrically located single or multiple nuclei and plump eosinophilic cytoplasm, partly infiltrated the desmoplastic inflammatory stroma. Parts of perivascular pseudorosette-forming or pseudopapillary areas were composed of atypically elongated cells, which looked like conventional anaplastic ependymoma. There was a transitional area between two patterns. Numerous mitoses and focal necrosis were observed. Immunohistochemically, the tumor cells were immunoreactive for glial fibrillary acidic protein, vimentin, S-100 protein, and CD99. None of the tumor cells showed immunoreactivity for epithelial membrane antigen except for the intracytoplasmic lumen of a few vacuolated cells. Ultrastructurally, tumor cells were ependymal in nature; we noted cytoplasmic intermediate filaments and intercellular microrosettes with microvilli, cilia, and long zonula adherens. The features of this tumor, e.g. its superficial location, mixed giant cells, perivascular pseudorosettes or papillaries, complicated its differentiation from rhabdoid/papillary meningioma. However, immunohistochemistry and electron microscopy confirmed the diagnosis of ependymoma. The giant cell variant should be included in the subclassification of the ependymoma.

Supratentorial extraventricular ependymal neoplasms

BACKGROUND

Published research on the clinicopathologic features of extraventricular ependymal neoplasms of the cerebral hemispheres has been scant.

METHODS

Thirty-two archival cases were studied to investigate the prognostic impact of clinicopathologic parameters including flow cytometry, the proliferation (Ki-67) labeling index, and p53 expression.

RESULTS

Among these 32 cases were 2 subependymomas, 19 ependymomas, and 11 anaplastic ependymomas. No significant gender predilection was observed, and 45% of patients were in their second or third decade of life. The left cerebral hemisphere was 1.5 times more commonly involved. On available imaging studies, lesions were often cystic, with or without a mural nodule. Tumors expressed glial fibrillary acidic protein (87%), S-100 protein (77%), cytokeratin (43%), and epithelial membrane antigen (17%). Ki-67 proliferation index paralleled tumor grade. Immunoreactivity for p53 protein was observed in the 2 cases of subependymoma, in 10 of 11 anaplastic ependymomas, and in 6 of 17 ependymomas. Flow cytometry performed in 27 tumors revealed diploidy in 20 cases and aneuploidy in 4 cases (3 anaplastic and 1 classic ependymomas), with S-phase fraction ranging from 0.2-9.7. Eleven subjects were additionally treated with radiotherapy, and 3 with chemotherapy. Follow up was available in 25 (78%) patients.

CONCLUSIONS

The results of the current study suggest that there is no significant relation between histopathology, Ki-67 proliferation index, p53 immunolabeling, tumor ploidy, and biologic behavior.

Aberrant promoter methylation of multiple genes in oligodendrogliomas and ependymomas

Promoter hypermethylation represents a primary mechanism in the inactivation of tumor suppressor genes during tumorigenesis. To determine the frequency and timing of hypermethylation during carcinogenesis of nonastrocytic tumors, we analyzed promoter methylation status of 10 tumor-associated genes in a series of 41 oligodendrogliomas (22 World Health Organization [WHO] grade II; 13 WHO grade III; 6 WHO grade II-III oligoastrocytomas) and 7 WHO grade II-III ependymomas, as well as 2 nonneoplastic brain samples, by a methylation-specific polymerase chain reaction. Aberrant CpG island methylation was detected in 9 of 10 genes analyzed, and all but one sample displayed anomalies in at least one gene. The frequencies of hypermethylation for the 10 genes were as follows, in oligodendrogliomas and ependymomas, respectively: 80% and 28% for MGMT; 70% and 28% for GSTP1; 66% and 57% for DAPK; 44% and 28% for TP14(ARF); 39% and 0% for THBS1; 24% and 28% for TIMP3; 24% and 14% for TP73; 22% and 0% for TP16(INK4A); 3% and 14% for RB1; and 0% in both neoplasms for TP53. No methylation of these genes was detected in normal brain tissue samples. We conclude that a high frequency of aberrant methylation of the 5' CpG island of the MGMT, GSTP1, TP14(ARF), THBS1, TIMP3, and TP73 genes is observed in nonastrocytic neoplasms. This aberration seems to occur early in the carcinogenesis process (it is already present in the low-grade forms), although in some instances (DAPK, THBS1, and TP73) it appears also associated with the genesis of anaplastic forms.

The expression of p73, p21 and MDM2 proteins in gliomas

p73 protein, a member of the p53 family protein, induce p21 and MDM2 transcription. In some carcinomas, the expression of p73 was higher in carcinoma than in normal tissue, and the overexpression was correlated to grade, stage or prognosis. However, either the expression of p73 protein or the relationship among p73, p21 and MDM2 proteins was not known well in glioma. In this study, we examined the expression of p73, p21 and MDM2 proteins immunohistochemically and analyzed the relationship among these three proteins in sixty surgical specimens of gliomas including 10 glioblastomas, 10 anaplastic astrocytomas, 6 diffuse astrocytomas, 8 pilocytic astrocytomas, 1 anaplastic ependymoma, 8 ependymomas, 9 anaplastic oligodendroglial tumors and 8 low grade oligodendroglial tumors. The p73 labelling index (LI)s and p21 LIs differed among the tumor types, but there was no difference in the MDM2 LIs among all of the tumor types. The mean p73 LI of ependymomas was significantly higher than in any other tumor type. The mean p2I LIs of ependymomas and pilocytic astrocytomas were significantly higher than in any other tumor type. There were no significant correlations among p73 LIs, p21 LIs, MDM2 LIs and MIB-1 LIs in all p73 immunopositive tumors. The present results suggest that p73 and p21 overexpression of ependymomas and p21 overexpression of pilocytic astrocytomas are one of the features of these tumors, and that p73 overexpression does not influence the expression manners of either p21 or MDM2 in gliomas.

Genetic alterations of human brain tumors as molecular prognostic factors

Despite a number of basic and clinical studies, it is still very difficult to improve the prognosis of patients with high-grade astrocytoma. However, the recent success of procarbazine, N-(2-chloroethyl)-N'-cyclohexyl-N-nitrosourea and vincristine (PCV) chemotherapy for oligodendrogliomas that have lost chromosomes 1p and 19q has encouraged the authors to evaluate the biological behavior of brain tumors by means of genetic analysis. Both the disorders of the p53/MDM2/p14(ARF) and the p16(INK4a)/RB signaling pathways have been found to play an essential role in tumorigenesis of various brain tumors. Herein, the authors summarize the genetic alterations of brain tumors by mainly focusing on two pathways that appear to affect significantly the patient prognosis.

Complex cytogenetic abnormalities including telomeric associations and MEN1 mutation in a pediatric ependymoma

Ependymomas are neuroectodermal tumors of the brain and spinal cord. Some recurrent cytogenetic aberrations have been reported in these tumors, including alterations involving chromosomes 22, 6, and 11. However, consistent molecular alterations have not been identified in ependymal tumors. We studied a recurrent ependymoma in a 3-year-old patient by standard cytogenetic and molecular analysis of TP53 and MEN1 genes. In the present case, we found many of the cytogenetic features previously described as being recurrent in ependymomas, including unstable telomeric alterations. Furthermore, we detected a novel acquired heterozygous mutation in the MEN1 gene. The chromosomal instability produced by the telomeric alterations and the mutation in the MEN1 gene could be important events in the tumorigenesis of ependymomas.

Immunohistochemical markers for prognosis of ependymal neoplasms

Intracranial ependymomas are the third most common primary brain tumor in children. Although clinical and histological criteria for ependymoma prognosis are recognized, studies have reported contradictory results. Prognostic significance based on immunohistochemistry of ependymomas has been reported in a few studies. One-hundred and twelve patients with intracranial ependymomas were examined retrospectively for immunoexpression of various tumor-associated antigens and apoptosis. The results demonstrated significant preponderance of expression of the tenascin, vascular endothelial growth factor protein (VEGF), epidermal growth factor (EGFR) and p53 protein in high-grade tumors. Also high-grade ependymomas revealed more prominent labeling indices (LI) for proliferative marker Ki-S1 and apoptotic index (AI), and lower LI for cyclin-dependent kinase inhibitors p27/Kipl and pl4ARF. For low-grade ependymomas the progression-free survival time (PFS) was found to be significantly shorter for Ki-S1 LI > 5%, and for tenascin, VEGF and EGFR positivity. For high-grade ependymomas PFS was found to be significantly reduced for p27 LI < 20%, p14ARF LI < 10%, for p53 positivity, and for AI < 1%. The CART modeling process exhibited five final groups of ependymoma patients (1) low-grade and tenascin-negative; (2) low-grade and tenascin-positive; (3) high-grade and p53-negative with p14 LI > 0%; (4) high-grade with combination of either p53 positivity and p14 LI > 10% or p53 negativity and p14 LI < 10%; (5) high-grade and p53-positive with pl4 LI < 10%. In summary, some immunohistochemical variables were found to be the strong predictors of ependymoma recurrence and they seem to be useful for assessing individual tumor prognosis in routinely processed biopsy specimens together with tumor grade. For histologically benign ependymomas immunohistochemical study should be focused on Ki-S1, tenascin, EGFR and VEGF evaluation, whereas p53 expression and number of p27, p14 and ISEL-positive nuclei will be of value in determining PFS from high-grade ependymomas.

Proliferation- and apoptosis-related proteins in intracranial ependymomas: an immunohistochemical analysis

As the value of grading of ependymomas is currently debated we studied the expression of proliferation- and apoptosis-related proteins in these tumors as these mechanisms both are suggested to be important in tumor growth. We characterized the immunohistochemical expression of p53, Mdm2, Bcl-2, and Bax in 51 intracranial ependymomas. We also assessed the apoptosis- and proliferation-index, measured by MIB-1, PCNA-immunohistochemistry, and analyzed the clinical parameters. Of all used antibodies, the correlation with survival and the correlation among ordered categories was assessed. None of the analyzed immunohistochemical variables were significantly correlated with tumor grade. On the other hand, PCNA, MIB-1, and p53 were significantly related to the survival of the patient. In multivariate analysis, p53 was the only independent predictive variable (p = 0.0132).

CONCLUSION

The strongest predictors of survival in univariate analysis were the expression of PCNA, MIB-1 and p53. In multivariate analysis a p53 expression > 1% showed to be significantly related with a worse survival. The predicting value of p53 expression has to be confirmed by others before solid conclusions can be made. Apoptosis seems not to be an important mechanism in tumor growth in ependymomas. The expression of Mdm2, Bcl-2, and Bax were not related to survival.

Isochromosome 1q as an early genetic event in a child with intracranial ependymoma characterized by molecular cytogenetics

Data concerning cytogenetic features of childhood ependymoma are rare. In this article, a gain of 1q was identified as the sole alteration in a primary childhood infratentorial ependymoma by comparative genomic hybridization (CGH). A recurrence of this brain tumor was studied using multiplex-fluorescence in situ hybridization (M-FISH) in addition to CGH and G-banding analysis. In accordance with the primary tumor, a gain of 1q corresponding to an isochromosome 1q was observed indicating an early event in the tumor development. Furthermore, M-FISH classified several other rearranged chromosomes including 6q and 17p that have previously been found to be involved in the development and progression of childhood ependymoma.

Gain of 1q and loss of 22 are the most common changes detected by comparative genomic hybridisation in paediatric ependymoma

Ependymomas are the third most common brain tumour in the paediatric population. Although cytogenetic and molecular analyses have pinpointed deletions of chromosomes 6q, 17, and 22 in a subset of tumours, definitive patterns of genetic aberrations have not been determined. In the present study, we analysed 40 ependymomas from paediatric patients for genomic loss or gain using comparative genomic hybridisation (CGH). Eighteen of the tumours (45%) had no detectable regions of imbalance. In the remaining cases, the most common copy number aberrations were loss of 22 (25% of tumours) and gain of 1q (20%). Three regions of high copy number amplification were noted at 1q24-31 (three cases), 8q21-23 (two cases), and 9p (one case). Although there was no association with the loss or gain of any chromosome arm or with benign versus anaplastic histologic characteristics, the incidence of gain of 7q and 9p and loss of 17 and 22 was significantly higher in recurrent versus primary tumours. This study has identified a number of chromosomal regions that may contain candidate genes involved in the development of different subgroups of ependymoma.

CDKN2A/p16 in ependymomas

Sixteen cases of ependymoma were studied for CDKN2A/p16 inactivation by immunohistochemistry using a p16 monoclonal antibody, by homozygous deletion (HD) assay and 5'CpG promoter methylation assay (methylation-specific PCR). Three out of 16 cases were p16 immuno-negative: two corresponded to grade II ependymomas and one to grade III. The latter ependymoma, characterized by a high Ki-67/MIB-1 LI, was the only one of the whole series to show CDKN2A HD. No promoter methylation was found in the two immuno-negative cases without CDKN2A HD. Alternative mechanisms, such as point mutations or alterations in p16 post-translational regulation, may be responsible for p16 inactivation. Since in our series just one out of eight anaplastic cases showed negative immunostaining and CDKN2A HD, p16/CDKN2A inactivation may not play an important role in the malignant transformation of ependymomas. Amplification of CCNDI and CDK4, p27/Kipl degradation and TP53 mutations were previously studied by other authors and were demonstrated not to correlate with anaplasia. Up to date, molecular genetic studies have not been useful in recognizing the anaplastic variant in ependymomas.

Identification of novel regions of allelic loss in ependymomas by high-resolution allelotyping with 384 microsatellite markers

OBJECT

Ependymomas are rare glial neoplasms; little is known about the molecular pathogenesis of this tumor entity. In a previous study the authors found multiple genomic imbalances in ependymomas resected in 20 adults and eight children, including loss of chromosomes 1p, 6, 16, 17, 19q, 20q, and 22q, as well as gain of chromosomes 4q, 5q, 7q, 9q, and 12q on comparative genomic hybridization. The aim of this study was to map in more detail the commonly affected regions in ependymomas.

METHODS

A comprehensive allelotype analysis of 16 ependymomas was conducted using 384 microsatellite markers that span the 22 autosomes. Based on this high-resolution loss of heterozygosity analysis, multiple overlapping deletion regions were identified as follows: 6q25.2-27, 16p12-13.1, 16q22.3-24.1, 17q22-24, 19q12-13.2, 20q13.2-13.3, and 22q13.1-13.3.

CONCLUSIONS

These data confirmed previous reports that loss of chromosomes 17 and 22 were common in ependymomas. Moreover, the authors were able to identify loss of chromosomes 13, 16, 19, and 20 as novel findings in ependymomas. It is believed that potential tumor suppressor genes that reside in these commonly deleted regions may contribute to the molecular tumorigenesis of ependymomas.

Chromosomal abnormalities subdivide ependymal tumors into clinically relevant groups

Ependymoma occurs most frequently within the central nervous system of children and young adults. We determined relative chromosomal copy-number aberrations in 44 ependymomas using comparative genomic hybridization. The study included 24 intracranial and 20 spinal cord tumors from pediatric and adult patients. Frequent chromosomal aberrations in intracranial tumors were gain of 1q and losses on 6q, 9, and 13. Gain of 1q and loss on 9 were preferentially associated with histological grade 3 tumors. On the other hand, gain on chromosome 7 was recognized almost exclusively in spinal cord tumors, and was associated with various other chromosomal aberrations including frequent loss of 22q. We conclude that cytogenetic analysis of ependymomas may help to classify these tumors and provide leads concerning their initiation and progression. The relationship of these aberrations to patient outcome needs to be addressed.

Recurrence of Infantile Supratentorial Ependymoma after 23-Year Remission following Surgical Removal and Radiation Therapy

We report on a patient with ependymoma who had a recurrence after long-term remission. The patient developed frontoparietal ependymoma at the age of one year and ten months. The tumor was radically removed and postoperative radiation therapy was performed. A calcified area adjacent to the area of surgical removal remained unchanged until the patient was 18 years old. The patient was healthy except for mild hemiparesis until an MRI scan performed when he was 25 years old showed regrowth of the tumor. The patient underwent surgery with additional radiation therapy and was discharged. The 23-year interval until tumor recurrence in this case is far beyond the so-called risk period of “Collins’ law”. Immunohistochemical study with MIB-1 and anti-p53 antibody showed a high proliferative potential of the primary and recurrent tumors and possible p53 mutation in the primary tumor. This is the first report to describe the detailed clinical course and histological features of a recurrent infantile ependymoma that progressed after Collins’ risk period. It seems that follow-up of ependymoma patients after initial treatment should be performed regularly for a longer period in cases showing radiological evidence of a residual lesion.

Immunohistochemical markers for intracranial ependymoma recurrence. An analysis of 88 cases

Intracranial ependymomas are the third most common primary brain tumor in children. Although clinical and histological criteria for ependymoma prognosis are recognized, studies have reported contradictory results. Prognostic significance based on immunohistochemistry of ependymomas has been reported in a few studies. Eighty-eight patients with intracranial ependymomas were examined retrospectively for immunoexpression of various tumor-associated antigens and apoptosis. The results demonstrated significant preponderance of expression of the tenascin, vascular endothelial growth factor protein (VEGF), epidermal growth factor (EGFR), and p53 protein in high-grade tumors. Also high-grade ependymomas revealed more prominent labeling indices (LI) for proliferative marker Ki-S1 and lower LI for cyclin-dependent kinase inhibitor p27/Kip1. For low-grade ependymomas the progression free survival time (PFS) was found to be significantly shorter for Ki-S1 LI>/=5%, and for tenascin, VEGF, and EGFR positivity. For high-grade ependymomas PFS was found to be significantly reduced for age <16 years, subtotal tumor removal, p27 LI <20%, p53 positivity, and for apoptotic index (AI) <1%. The classification regression tree analysis exhibited four groups of ependymomas; (1) low-grade tenascin negative (32 cases, recurrence rate=0), (2) high-grade with AI >/=1% (21 cases, recurrence rate=57%), (3) low-grade tenascin-positive (10 cases, recurrence rate=89%), and (4) high-grade with AI <1% (25 cases, recurrence rate=100%). So, the immunohistochemical variables were found to be strongest predictors of ependymoma recurrence and they seem to be useful for assessing individual tumor prognosis in routinely processed biopsy specimen.

Overexpression of p53 in squamous cell carcinoma of the tongue in young patients with no known risk factors is not associated with mutations in exons 5-9

BACKGROUND

This study investigated the status of the p53 tumor suppressor gene in patients less than 40 years of age who had squamous cell carcinoma of the tongue develop with no known risk factors.

METHODS

Histologic sections from 21 patients were prepared from formalin-fixed, paraffin-embedded tissue and were processed for standard immunohistochemistry for detection of the p53 protein. In addition, tumors were evaluated by single-strand conformation polymorphism and by DNA sequencing to identify potential mutations in the conserved exons (5-9) of the p53 gene.

RESULTS

Eighty-one percent (17 of 21) of the patients overexpressed p53 by immunohistochemical analysis. However, none of these patients demonstrated mutations in exons 5-9 of the gene.

CONCLUSIONS

These data suggest that the molecular mechanisms by which the young individuals with no risk factors had altered p53 function in oral squamous cell carcinoma may differ from those of the more typical population of individuals who have this malignancy develop.

Amplification and overexpression of mdm2 gene in ependymomas

Ependymomas rarely show p53 gene alteration, and the tumorigenic mechanism of ependymomas still remains to be elucidated. We investigated the amplification and overexpression of mdm2 gene, whose product (MDM2) is considered to be one of the major cellular regulators of p53-mediated growth control, in 26 specimens of ependymomas obtained from 20 patients. The majority of the ependymomatous samples (96%) showed at least focal immunopositivity for MDM2; however, only 8% of the samples were immunopositive for p53. mdm2 gene amplification was detected in 35% of the samples by differential polymerase chain reaction, all of which overexpressed MDM2. These results suggest that the amplification and/or overexpression of mdm2 may be one of the major molecular events occurring in the tumorigenesis of ependymomas.

Molecular genetic analysis of ependymal tumors. NF2 mutations and chromosome 22q loss occur preferentially in intramedullary spinal ependymomas

Ependymal tumors are heterogeneous with regard to morphology, localization, age at first clinical manifestation, and prognosis. Several molecular alterations have been reported in these tumors, including allelic losses on chromosomes 10, 17, and 22 and mutations in the NF2 gene. However, in contrast to astrocytic gliomas, no consistent molecular alterations have been associated with distinct types of ependymal tumors. To evaluate whether morphological subsets of ependymomas are characterized by specific genetic lesions, we analyzed a series of 62 ependymal tumors, including myxopapillary ependymomas, subependymomas, ependymomas, and anaplastic ependymomas, for allelic losses on chromosome arms 10q and 22q and mutations in the PTEN and NF2 genes. Allelic losses on 10q and 22q were detected in 5 of 56 and 12 of 54 tumors, respectively. Six ependymomas carried somatic NF2 mutations, whereas no mutations were detected in the PTEN gene. All six of the NF2 mutations occurred in ependymomas of WHO grade II and were exclusively observed in tumors with a spinal localization (P = 0.0063). These findings suggest that a considerable fraction of spinal ependymomas are associated with molecular events involving chromosome 22 and that mutations in the NF2 gene may be of primary importance for their genesis. Furthermore, our data suggest that the more favorable clinical course of spinal ependymomas may relate to a distinct pattern of genetic alterations different from that of intracerebral ependymomas.

Molecular genetic analysis of non-astrocytic gliomas

AIMS

Oligodendroglial tumours follow genetic pathways different from but overlapping with those of astrocytic tumours. The aim of this study was to examine whether major genetic events such as loss of chromosome 10 and p53 mutation found in astrocytic gliomas are also involved in the development and anaplastic transformation of non-astrocytic gliomas and to correlate the findings with histopathological subtypes of these tumours.

METHODS AND RESULTS

Sixty-one formalin-fixed, paraffin-embedded oligodendroglial and ependymal tumours (16 oligodendrogliomas, 12 anaplastic oligodendrogliomas, seven oligoastrocytomas, 24 ependymomas and two anaplastic ependymomas) were examined for allelic deletions on chromosome 10q23 and 10q25-26 regions, mutations of PTEN/MMAC1 and p53, MDM2 gene amplification and apoptosis. The frequencies of allelic deletions at marker D10S2491 (which mapped within PTEN/MMAC1) and between markers D10S209 and D10S587 (where DMBT1 was located) were found to be < 30% in both types of non-astrocytic gliomas. High frequency of allelic deletions was detected at marker D10S215 (80%) at the proximal 10q23 region in both oligodendroglial and ependymal tumours and between markers D10S216 (42%) and D10S169 (67%) at distal 10q25-26 region in oligodendroglial tumours. No mutations of PTEN/MMAC1 were found. p53 mutations were detected in three oligoastrocytomas and one ependymoma; three out of five mutations were found in exon 4. MDM2 gene amplification was found in one ependymoma harbouring wild-type p53. The apoptotic index was lower in p53-mutated tumours than in tumours with wild-type p53.

CONCLUSION

The telomeric end of chromosome 10q could be involved in the development and anaplastic transformation of oligodendroglial tumours. Mutations of PTEN/MMAC1 and p53, amplification of the MDM2 gene and allelic loss on chromosome 10q do not play a major part in the pathogenesis or anaplastic transformation of oligodendrogliomas and ependymal tumours.

p73 gene transcripts in human brain tumors: overexpression and altered splicing in ependymomas

The p73 gene encodes a protein that shares structural and functional homologies with the p53 tumor suppressor protein. The p73 gene is monoallelically expressed in normal tissue, maps to chromosome 1p36 and is deleted in human neuroblastoma cell lines. Alternative splicing of exon 13 in p73 transcripts generates two isoforms, p73alpha and p73beta, that differ in their carboxy-terminus and in their ability to form homotypic interactions. In this study, we investigated, in 129 human central nervous system tumors of various histological types, the levels of p73 transcripts and the splicing characteristics of p73 mRNA. Whereas p73 mRNA content was consistently low in most tumoral types, especially in meningiomas, some glioblastomas, medulloblastomas and metastases exhibited elevated p73 mRNA content. However, ependymomas expressed consistently high amounts of p73 mRNA, significantly different from the other tumoral types. Whereas the short (p73beta) isoform accounted for 20-25% of the total p73 mRNA in most of the tumors, these splicing characteristics were altered in ependymomas (only 9% of p73beta) and in neurinomas (up to 53% of p73beta). These observations suggest tissular or tumoral differences in the control of p73 gene transcription and alternative splicing, and raise the problem of the role of p73 isoforms in the control of tumor growth, particularly in ependymomas.

The molecular genetics of central nervous system tumors

Over the past few years, although much has been learned about the molecular genetics of central nervous system (CNS) tumors, researchers and pathologists are only beginning to understand the scientific basis of the development of these tumors. Data accumulated so far support the division of glioblastoma into two clinical and molecular subsets. Primary or de novo glioblastomas occur in older patients, are clinically aggressive and exhibit epidermal growth factor receptor amplification or overexpression. Secondary glioblastomas develop from pre-existing low-grade astrocytomas, have a more protracted clinical course, and frequently contain p53 mutations. Both types of tumors show deletions of chromosome 10 and possibly mutations of the PTEN/MMAC1 gene as an endstage event. Oligodendrogliomas have been shown to have genetic abnormalities distinct from those of the astrocytic tumors, commonly involving chromosomes 1p and 19q. As regards meningiomas, loss of chromosome 22q and mutations of the neurofibromatosis type 2 gene are frequent events and loss of chromosome 14q and 10q may be seen in atypical or malignant transformation. Such genetic findings, apart from providing a better understanding of neoplastic transformation in brain tumors, are beginning to form the basis of a new approach to neuro-oncology.

Molecular cytogenetic studies of pediatric ependymomas

Cytogenetic and molecular studies of ependymomas have previously demonstrated deletions of chromosomes 17 and 22 as frequent abnormalities, implicating inactivation of tumor suppressor genes in the pathogenesis of these tumors. In the present study, we analyzed 22 childhood ependymomas by standard cytogenetic analysis, fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR)-based microsatellite analysis of chromosomes 17 and 22. Microsatellite analysis of chromosome 6 was performed to identify submicroscopic deletions implicated by the cytogenetic studies. Among the 22 cases, we demonstrated loss of chromosome 22 in 2 patients, deletion of chromosome 17 in 2 patients, and rearrangements or deletions of chromosome 6 in 5 patients. These data do not suggest that loss of a gene on chromosome 17p plays a primary role in the initiation of pediatric ependymomas. This is in contrast to what has been reported for pediatric CNS primitive neuroectodermal tumors and malignant astrocytomas, in which deletion of 17p is regarded as a primary event. Furthermore, loss of chromosome 22 may define a subset of ependymomas more commonly seen in adults. Cytogenetic studies in this series, however, suggest that a region on the long arm of chromosome may be involved in the development and/or progression of ependymomas in children.

Genetics of pediatric central nervous system tumors

PURPOSE

Pediatric central nervous system (CNS) tumors comprise a wide variety of histologic subtypes ranging from the benign juvenile pilocytic astrocytoma to the highly aggressive atypical teratoid/rhabdoid tumor. Although some brain tumors are seen in association with inherited genetic disorders which predispose to malignancies, most are sporadic. Current knowledge regarding the cytogenetic and molecular genetic events which have been implicated in the development or progression of common brain tumors in children in the subject of this review.

METHODS

Combined cytogenetic and molecular genetic approaches, including fluorescence in situ hybridization, have been used to identify genomic alterations in different histologic types of pediatric brain tumors.

RESULTS

The most frequent abnormality in primitive neuroectodermal tumor/medulloblastoma is an i(17q), present in approximately 50% of cases. This finding implicates the presence of a tumor suppressor gene on 17p, which is important in tumor development. A number of genes on 17p have been eliminated as candidates for this locus, including TP53. A tumor suppressor gene in chromosome band 22q11.2 has been hypothesized to play a role in atypical teratoid/rhabdoid tumors, and positional cloning strategies are in progress to identify a rhabdoid tumor gene. Chromosome 22 deletions are also seen in meningiomas and a small percentage of ependymomas, but it is not yet known whether the same gene is responsible for more than one malignancy. With regard to childhood astrocytomas, tumor-associated genetic changes have not yet been identified for the common juvenile pilocytic or low grade diffuse astrocytoma. In contrast, malignant anaplastic astrocytomas and glioblastoma multiforme have abnormalities similar to those seen in adults, including loss of alleles on 17p13 and TP53 mutations, trisomy 7, EGFR rearrangements, and loss of chromosomes 10 and 22.

CONCLUSIONS

The presence of tumor-associated genetic abnormalities has clinical utility in a differential diagnostic setting, and has lead to the identification of genes which contribute to tumorigenesis.

The molecular biology of ependymomas

Intracranial ependymomas are the third most common primary brain tumor in the pediatric population. Although an anaplastic variant is recognized, numerous studies examining the prognostic implications of histological features, such as necrosis, endothelial proliferation and mitoses, have yielded contradictory results. In order to improve outcome prediction in affected patients and to refine therapeutic decision-making, there is a strong need for identifying relevant biological correlates of tumor behavior. The molecular biology of tumors is a rapidly expanding field and includes investigations into cytogenetics, oncogenes, growth factors, growth factor receptors, hormonal receptors, proliferation markers, apoptosis, cell cycle genes and cell adhesion molecules, as well as factors potentially related to therapeutic resistance, such as the multidrug resistance gene. The molecular biology of astrocytic tumors in adults has been the subject of many studies; however, relatively few studies have been focused on ependymomas. Herein we review potential oncological markers in ependymomas that have been identified to date and highlight the limitations of our current knowledge as a basis for defining areas for future investigation.