Exon scanning for mutations of the NF2 gene in pediatric ependymomas, rhabdoid tumors and meningiomas

Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation

Ependymomas encompass multiple clinically relevant tumor types based on localization and molecular profiles. Tumors of the methylation class "spinal ependymoma" (SP-EPN) represent the most common intramedullary neoplasms in children and adults. However, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations, but neither types and frequency of these alterations nor their clinical relevance have been described in a large, epigenetically defined series. Transcriptomic (n = 72), epigenetic (n = 225), genetic (n = 134), and clinical data (n = 112) were integrated for a detailed molecular overview on SP-EPN. Additionally, we mapped SP-EPN transcriptomes to developmental atlases of the developing and adult spinal cord to uncover potential developmental origins of these tumors. The integration of transcriptomic ependymoma data with single-cell atlases of the spinal cord revealed that SP-EPN display the highest similarities to mature adult ependymal cells. Unsupervised hierarchical clustering of transcriptomic data together with integrated analysis of methylation profiles identified two molecular SP-EPN subtypes. Subtype A tumors primarily carried previously known germline or sporadic NF2 mutations together with 22q loss (bi-allelic NF2 loss), resulting in decreased NF2 expression. Furthermore, they more often presented as multilocular disease and demonstrated a significantly reduced progression-free survival as compared to SP-EP subtype B. In contrast, subtype B predominantly contained samples without NF2 mutation detected in sequencing together with 22q loss (monoallelic NF2 loss). These tumors showed regular NF2 expression but more extensive global copy number alterations. Based on integrated molecular profiling of a large multi-center cohort, we identified two distinct SP-EPN subtypes with important implications for genetic counseling, patient surveillance, and drug development priorities.

Redefining germline predisposition in children with molecularly characterized ependymoma: a population-based 20-year cohort

Ependymoma is the second most common malignant brain tumor in children. The etiology is largely unknown and germline DNA sequencing studies focusing on childhood ependymoma are limited. We therefore performed germline whole-genome sequencing on a population-based cohort of children diagnosed with ependymoma in Denmark over the past 20 years (n = 43). Single nucleotide and structural germline variants in 457 cancer related genes and 2986 highly evolutionarily constrained genes were assessed in 37 children with normal tissue available for sequencing. Molecular ependymoma classification was performed using DNA methylation profiling for 39 children with available tumor tissue. Pathogenic germline variants in known cancer predisposition genes were detected in 11% (4/37; NF2, LZTR1, NF1 & TP53). However, DNA methylation profiling resulted in revision of the histopathological ependymoma diagnosis to non-ependymoma tumor types in 8% (3/39). This included the two children with pathogenic germline variants in TP53 and NF1 whose tumors were reclassified to a diffuse midline glioma and a rosette-forming glioneuronal tumor, respectively. Consequently, 50% (2/4) of children with pathogenic germline variants in fact had other tumor types. A meta-analysis combining our findings with pediatric pan-cancer germline sequencing studies showed an overall frequency of pathogenic germline variants of 3.4% (7/207) in children with ependymoma. In summary, less than 4% of childhood ependymoma is explained by genetic predisposition, virtually restricted to pathogenic variants in NF2 and NF1. For children with other cancer predisposition syndromes, diagnostic reconsideration is recommended for ependymomas without molecular classification. Additionally, LZTR1 is suggested as a novel putative ependymoma predisposition gene.

Ependymal Tumors

Ependymomas (EPN) are commonly encountered brain tumors in the pediatric population. They may arise in the supratentorial compartment, posterior fossa and spinal cord. Histopathologic grading of EPN has always been challenging with poor interobserver reproducibility and lack of correlation between histologic grade and patient outcomes. Recent studies have highlighted that, despite histopathological similarities among variants of EPN at different anatomical sites, they possess site-specific genetic and epigenetic alterations, transcriptional profiles and DNA copy number variations. This has led to a molecular and location-based classification for EPN which has been adopted by the World Health Organization Classification of Central Nervous System Tumors and more accurately risk-stratifies patients than histopathologic grading alone. Given the complexity of this evolving field, the purpose of this paper is to offer a practical approach to the diagnosis of EPN, including the selection of the most appropriate molecular surrogate immunohistochemical stains, basic molecular studies and more sophisticated techniques if needed. The goal is to reach a rapid, sound diagnosis, providing essential information regarding prognosis and guiding clinical decision-making.

Clinicopathological and molecular characteristics of pediatric meningiomas

Molecular and clinical characteristics of pediatric meningiomas are poorly defined. Therefore, we analyzed clinical, morphological and molecular profiles of pediatric meningiomas. Forty pediatric meningiomas from January 2002 to June 2015 were studied. 1p36, 14q32 and 22q-deletion were assessed by fluorescent in situ hybridization and mutations of most relevant exons of AKT, SMO, KLF4, TRAF and pTERT using sequencing. Expression of GAB1, stathmin, progesterone receptor (PR), p53 along with MIB-1 LI was examined using immunohistochemistry. There were 36 sporadic and four NF2 associated meningiomas. Among sporadic meningiomas, the majority (72.2%) of cases harbored 22q-deletion. Difference in frequency of combined 1p/14q deletion in Grade-I versus Grade-II/III tumors was not significant (13.7% vs 28.5%, P = 0.57). PR immunoreactivity was seen in 65.5% of Grade-I and 14.2% of Grade-II/III tumors (P = 0.03). The majority (97.2%) of meningiomas were immunonegative for p53. Stathmin and GAB co-expression was observed in 58.3% of cases. Notably, AKT, SMO, KLF4, TRAF7 (exon 17) and pTERT mutations were seen in none of the cases analyzed. 1p/14q codeletion was frequent in skull base as compared to non-skull base meningiomas (23% vs 11.1%, P = 0.37). All NF2 meningiomas harbored 22q-deletion and showed GAB and stathmin co-expression while none showed 1p/14q loss. Pediatric meningiomas share certain phenotypic and cytogenetic characteristics with adult counterparts, but GAB and stathmin co-expression in the majority of cases and non-significant difference in frequency of 1p/14q co-deletion between low- and high-grade meningiomas indicate an inherently aggressive nature. Characteristic AKT/SMO, KLF4/TRAF7 and pTERT genetic alterations seen in adults are distinctly absent in pediatric meningiomas.

Evaluation of NF2 Gene Deletion in Pediatric Meningiomas Using Chromogenic In Situ Hybridization

Meningiomas are uncommon childhood tumors. They could be of significant size at presentation, which has been associated with difficult surgical excision, high recurrence rate, and possibly aggressive clinical behavior. Monosomy 22 is a common molecular event in this neoplasm. Additionally, losses on chromosomes 1,7,10, and 14 have been identified in clinically aggressive meningiomas. Using chromogenic in situ hybridization, we studied a group of pediatric meningiomas, including neurofibromatosis type II—associated, sporadic, and radiation-induced cases. We found NF2 gene deletion in about 72% of the cases, with corresponding absent or minimal merlin protein expression by immunohistochemistry. Our findings confirm that the NF2 gene plays a role in the tumorigenesis of pediatric meningiomas and that chromogenic in situ hybridization is an efficient, economic, and reliable method for routinely assessing NF2 gene deletion in formalin-fixed, paraffin-embedded tissues.

Understanding Ependymoma Oncogenesis: an Update on Recent Molecular Advances and Current Perspectives

Remarkable progress has been made in the last decade in understanding the biology and oncogenesis of this relatively rare childhood brain tumor-the ependymoma. Surgery and irradiation are the mainstays of therapeutic options; chemotherapy is yet to predictably affect outcome, and its role is currently being explored in several clinical trials. While WHO scores this tumor into three grades, grading of ependymoma into grade II and grade III is controversial because of its elusive histological criteria where no cut-offs have been defined for mitoses or percentage of tumor depicting increased cellularity. Grading remains unreliable in predicting outcome in several instances. There is a compelling need to integrate the molecular biomarkers highlighted in several studies over the past decade into patient risk stratification to help in better predicting the clinical outcome and to design effective tailored therapy. Genomic and transcriptomic studies lately have defined distinct molecular subgroups within ependymoma arising at three anatomic compartments-supratentorial, posterior fossa, and spinal cord. Review of pertinent literature on several seminal studies that have established a paradigm shift in understanding the oncogenesis of ependymoma has been carried out. The outcome, impact, and clinical relevance of these studies are also discussed. The review provides an update on progress and recent advances in understanding the biology and oncogenesis of ependymoma. The establishment of robust subgroups which are demographically, clinically, and molecularly distinct will provide new avenues for further refinement of therapeutic strategies.

Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups

Ependymal tumors across age groups are currently classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patients' outcome. We aimed at establishing a uniform molecular classification using DNA methylation profiling. Nine molecular subgroups were identified in a large cohort of 500 tumors, 3 in each anatomical compartment of the CNS, spine, posterior fossa, supratentorial. Two supratentorial subgroups are characterized by prototypic fusion genes involving RELA and YAP1, respectively. Regarding clinical associations, the molecular classification proposed herein outperforms the current histopathological classification and thus might serve as a basis for the next World Health Organization classification of CNS tumors.

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.

Loss of chromosome 1 in myxopapillary ependymoma suggests a region out of chromosome 22 as critical for tumour biology: a FISH analysis of four cases on touch imprint smears

OBJECTIVE

Ependymomas are glial tumours. They constitute approximately 5-10% of intracranial tumours and are tumours which can recur. Predictive factors of outcome in ependymomas are not well established. Karyotypic studies are relatively scarce and loss of chromosome 22 has been described to correlate with recurrence. We are unaware of any reports involving chromosome 1 aberrations in the malignant progression of ependymomas.

METHODS

Cytogenetic analysis of four myxopapillary ependymomas was performed using double target fluorescent in situ hybridization (FISH), focusing on chromosomes 1 and 22.

RESULTS

One patient's tumour had recurred. FISH was performed on 500 nuclei/tumours. All four cases showed a loss of chromosome 22q while only one showed an additional loss of chromosome 1p, and this was the one that recurred.

CONCLUSIONS

We support the presence of a tumour suppressor gene on 1p associated with relapse in myxopapillary ependymomas and suggest that status of chromosome 1p by FISH may indicate a high-risk group of patients harbouring this tumour. More studies of this type are needed towards this direction as our results refer to a minimal number of individuals analysed.

Effects of surgical resection and adjuvant therapy on pediatric intracranial ependymomas

The optimal therapy of pediatric ependymomas is controversial. The benefit of surgical resection is widely accepted, but the role of adjuvant therapy is subject to debate. Due to the relatively low survival rates of ependymoma patients, as well as the tumor's high recurrence rates, further research into the efficacy of treatment strategies and adjuvant therapy is necessary. Extent of resection remains the most important determinant of survival in patients with ependymomas. Expectantly, gross total resection yields the best outcome for patients. The optimal roles of chemotherapy and radiation therapy are poorly understood. A closer look at the efficacy of tailored radiation therapy and the possible use of chemotherapy to delay radiation therapy sheds light on potential treatment modalities for ependymomas. The greatest increase in survival on the ependymoma population will likely come from an increase in the rate of complete resections. An improvement in the efficacy of radiation therapy in addition to an understanding of chemotherapy protocols and treatment durations will hopefully provide further means for successfully treating ependymomas.

Meningeal tumors of childhood and infancy. An update and literature review

Meningeal derived tumors of the first 2 decades of life are often diagnostically challenging due to the wide morphologic spectrum encountered and the rarity of most individual entities. The 2 most common patterns include the dural/leptomeningeal-based mass and neoplastic meningitis. Both primary and secondary meningeal presentations may occur, either early or late in the course of various meningothelial, mesenchymal, embryonal, glial, hematopoietic, histiocytic, melanocytic, and inflammatory tumors. As in other areas of pediatric pathology, there are significant differences between this patient cohort and adults, differences which will be emphasized in this review.

Molecular genetics of meningiomas

In this article the authors provide a brief description of the current understanding of meningioma genetics. Chromosome 22 abnormalities, especially in the Neurofibromatosis Type 2 (NF2) gene, have been associated with meningioma development. Loss of heterozygosity of chromosome 22 occurs in approximately 60% of meningiomas; however, loss of NF2 gene function occurs in only one third of these lesions. This discrepancy supports the theory that a second tumor suppressor gene exists on chromosome 22, and the authors introduce several possible gene candidates, including BAM22, LARGE, INI1, and MN1 genes. Deletions of 1p have also been shown to correlate with meningioma progression. The genetic similarities and differences among sporadic, NF2-associated, pediatric, and radiation-induced meningiomas are discussed, with the observation that the nonsporadic meningiomas have a higher incidence of multiple chromosomal abnormalities at presentation. Ultimately, a better understanding of the molecular pathways of meningioma tumorigenesis will lead to new, successful treatments.

Microarray analysis of pediatric ependymoma identifies a cluster of 112 candidate genes including four transcripts at 22q12.1-q13.3

Ependymomas are glial cell-derived tumors characterized by varying degrees of chromosomal abnormalities and variability in clinical behavior. Cytogenetic analysis of pediatric ependymoma has failed to identify consistent patterns of abnormalities, with the exception of monosomy of 22 or structural abnormalities of 22q. In this study, a total of 19 pediatric ependymoma samples were used in a series of expression profiling, quantitative real-time PCR (Q-PCR), and loss of heterozygosity experiments to identify candidate genes involved in the development of this type of pediatric malignancy. Of the 12,627 genes analyzed, a subset of 112 genes emerged as being abnormally expressed when compared to three normal brain controls. Genes with increased expression included the oncogene WNT5A; the p53 homologue p63; and several cell cycle, cell adhesion, and proliferation genes. Underexpressed genes comprised the NF2 interacting gene SCHIP-1 and the adenomatous polyposis coli (APC)-associated gene EB1 among others. We validated the abnormal expression of six of these genes by Q-PCR. The subset of differentially expressed genes also included four underexpressed transcripts mapping to 22q12.313.3. By Q-PCR we show that one of these genes, 7 CBX7(22q13.1), was deleted in 55% of cases. Other genes mapping to cytogenetic hot spots included two overexpressed and three underexpressed genes mapping to 1q31-41 and 6q21-q24.3, respectively. These genes represent candidate genes involved in ependymoma tumorigenesis. To the authors' knowledge, this is the first time microarray analysis and Q-PCR have been linked to identify heterozygous/homozygous deletions.

Microarray analysis of pediatric ependymoma identifies a cluster of 112 candidate genes including four transcripts at 22q12.1-q13.3

Ependymomas are glial cell-derived tumors characterized by varying degrees of chromosomal abnormalities and variability in clinical behavior. Cytogenetic analysis of pediatric ependymoma has failed to identify consistent patterns of abnormalities, with the exception of monosomy of 22 or structural abnormalities of 22q. In this study, a total of 19 pediatric ependymoma samples were used in a series of expression profiling, quantitative real-time PCR (Q-PCR), and loss of heterozygosity experiments to identify candidate genes involved in the development of this type of pediatric malignancy. Of the 12,627 genes analyzed, a subset of 112 genes emerged as being abnormally expressed when compared to three normal brain controls. Genes with increased expression included the oncogene WNT5A; the p53 homologue p63; and several cell cycle, cell adhesion, and proliferation genes. Underexpressed genes comprised the NF2 interacting gene SCHIP-1 and the adenomatous polyposis coli (APC)-associated gene EB1 among others. We validated the abnormal expression of six of these genes by Q-PCR. The subset of differentially expressed genes also included four underexpressed transcripts mapping to 22q12.313.3. By Q-PCR we show that one of these genes, 7 CBX7(22q13.1), was deleted in 55% of cases. Other genes mapping to cytogenetic hot spots included two overexpressed and three underexpressed genes mapping to 1q31-41 and 6q21-q24.3, respectively. These genes represent candidate genes involved in ependymoma tumorigenesis. To the authors' knowledge, this is the first time microarray analysis and Q-PCR have been linked to identify heterozygous/homozygous deletions.

Molecular pathogenesis of meningiomas

Meningiomas are common central nervous system tumors that originate from the meningeal coverings of the brain and the spinal cord. Most meningiomas are slowly growing benign tumors that histologically correspond to World Health Organization (WHO) grade I. However, certain rare histological variants (clear cell, chordoid, papillary, and rhabdoid), as well as atypical (WHO grade II) and anaplastic (WHO grade III) meningiomas show a more aggressive biological behavior and are clinically associated with a high risk of local recurrence and a less favorable prognosis. This review summarizes the most important features of meningioma pathology and provides an up-to-date overview about the molecular mechanisms involved in meningioma initiation and progression. Current data indicate that meningioma initiation is closely linked to the inactivation of one or more members of the highly conserved protein 4.1 superfamily, including the neurofibromatosis type 2 gene product merlin/schwannomin, protein 4.IB (DAL-1) and protein 4.1R. The genetic alterations in atypical meningiomas are complex and involve losses on 1p, 6q, 10, 14q and 18q, as well as gains on multiple chromosomes. The relevant genes are still unknown. Anaplastic meningiomas show even more complex genetic alterations, including frequent alteration of the CDKN2A, p14ARF, and CDKN2B tumor suppressor genes at 9p21, as well as gene amplification on 17q23. A better understanding of the molecular mechanisms involved in meningioma pathogenesis may not only lead to the identification of novel diagnostic and prognostic marker but will also facilitate the development of new pathogenesis-based therapeutic strategies.

Epigenetic inactivation of the RASSF1A tumour suppressor gene in ependymoma

To investigate the role of aberrant epigenetic events in ependymoma and identify critical genes in its pathogenesis, the methylation status of nine tumour suppressor genes (TSGs: p14(ARF), p15(INK4B), p16(INK4A), CASP8, MGMT, TIMP3, TP73, RB1 and RASSF1A) was assessed. Extensive hypermethylation across the RASSF1A CpG island was detected frequently in ependymomas of all clinical and pathological disease subtypes (86% of cases, n=35), but not in non-neoplastic brain tissues (n=6). Less frequent methylation was observed for CASP8, MGMT and TP73 (5-20%). The remaining TSGs showed no evidence of methylation. RASSF1A hypermethylation represents the most common gene-specific defect identified in ependymoma highlighting the importance of its further investigation in this disease.

Allele-specific loss of heterozygosity at theDAL-1/4.1B (EPB41L3) tumor-suppressor gene locus in the absence of mutation

DAL-1/4.1B (EPB41L3)is a member of the protein 4.1 superfamily, which encompasses structural proteins that play important roles in membrane processes via interactions with actin, spectrin, and the cytoplasmic domains of integral membrane proteins. DAL-1/4.1B localizes within chromosomal region 18p11.3, which is affected by loss of heterozygosity (LOH) in various adult tumors. Reintroduction of this protein into DAL-1/4.1B-null lung and breast tumor cell lines significantly reduced the number of cells, providing functional evidence that this protein possesses a growth suppressor function not confined to a single cell type. For characterization of the mutational mechanisms responsible for loss of DAL-1/4.1B function in tumors, the exon-intron structure of DAL-1/4.1B was examined for mutations in 15 normal/tumor pairs of non-small cell lung carcinoma by single-strand conformation polymorphism analysis. These studies revealed that small intragenic mutations are uncommon in DAL-1/4.1B. Furthermore, LOH analysis on 129 informative early-stage breast tumors utilizing a new intragenic C/T single-nucleotide polymorphism in exon 14 revealed that LOH resulted in preferential retention of the C-containing allele, suggesting that allele-specific loss is occurring. These studies indicate that mechanisms such as imprinting or monoallelic expression in combination with loss of heterozygosity may be responsible for loss of the DAL-1/4.1B protein in early breast disease.

Comparative analysis of the NF2, TP53, PTEN, KRAS, NRAS and HRAS genes in sporadic and radiation-induced human meningiomas

Irradiation to the head is associated with a significantly increased incidence of meningiomas. Radiation-induced meningiomas morphologically resemble their sporadically arising counterparts; however, they frequently exhibit a more malignant phenotype. Several genes have been shown to carry mutations in meningiomas, with the NF2 gene being most frequently affected. To examine whether the NF2 gene also plays a role in the development of radiation-induced meningiomas, we compiled a series of meningiomas from 25 patients with a history of previous cranial radiation. This series was compared with 21 atypical WHO grade II meningiomas and 15 anaplastic WHO grade III meningiomas, all from patients without a history of prior irradiation. NF2 mutations occurred significantly more often in sporadic atypical and anaplastic than in radiation-induced meningiomas (p < 0.02). In addition, all meningiomas were examined for mutations in the PTEN, TP53, HRAS, KRAS and NRAS genes. Two mutations in the TP53 gene in a sporadic and a radiation-induced tumor were detected. PTEN mutations were observed in 1 anaplastic and 1 radiation-induced meningioma. No structural alterations were seen in the RAS genes. Our data suggest that, while there is a certain overlap in the mutational spectrum, NF2 mutations may not play such a prominent role in the pathogenesis of radiation-induced compared to sporadic meningiomas.

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.

Molecular genetic alterations on chromosomes 11 and 22 in ependymomas

Ependymomas arise from the ependymal cells at different locations throughout the brain and spinal cord. These tumors have a broad age distribution with a range from less than 1 year to more than 80 years. In some intramedullary spinal ependymomas, mutations in the neurofibromatosis 2 (NF2) gene and loss of heterozygosity (LOH) on chromosome arm 22q have been described. Cytogenetic studies have also identified alterations involving chromosome arm 11q, including rearrangements at 11q13, in ependymomas. We analyzed 21 intramedullary spinal, 14 ventricular, 11 filum terminale and 6 intracerebral ependymomas for mutations in the MEN1 gene, which is located at 11q13, and mutations in the NF2 gene, which is located at 22q12, as well as for LOH on 11q and 22q. NF2 mutations were found in 6 tumors, all of which were intramedullary spinal and all of which displayed LOH 22q. Allelic loss on 22q was found in 20 cases and was significantly more frequent in intramedullary spinal ependymomas than in tumors in other locations. LOH 11q was found in 7 patients and exhibited a highly significant inverse association with LOH 22q (p<0.001). A hemizygous MEN1 mutation was identified in 3 tumors, all of which were recurrences from the same patient. Interestingly, the initial tumor corresponded to WHO grade II and displayed LOH 11q but not yet a MEN1 mutation. In 2 subsequent recurrences, the tumor had progressed to anaplastic ependymoma (WHO grade III) and exhibited a nonsense mutation in exon 10 of MEN1 (W471X) in conjunction with LOH 11q. This suggests that loss of wild-type MEN1 may be involved in the malignant progression of a subset of ependymomas. To conclude, our findings provide evidence for different genetic pathways involved in ependymoma formation and progression, which may allow to define genetically and clinically distinct tumor entities.

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.

Comparative genomic hybridization detects losses of chromosomes 22 and 16 as the most common recurrent genetic alterations in primary ependymomas

In this study, we used comparative genomic hybridization to provide an overview of chromosomal imbalances in a series of 20 adult and 8 childhood ependymomas. All tumors displayed multiple genomic imbalances. Loss of genetic material was observed in chromosomes 22q (71%), 16 (57%), 17 (46%), 6 (39%), 19q (32%), 20q (32%), and 1p (29%), with the overlapped deletion regions determined at 16p13.1-13.3, 16q22-q24, 19q13.1-13.4, 20q13.1-13.2 and 1p36.1-36.3. Gain of DNA was commonly detected on chromosomes 5q (46%), 12q (39%), 7q (36%), 9q (36%), and 4q (32%), with overlapped regions of gain mapped to 5q21-22, 12q15-24.1, 7q11.2-31.2, 9q12-32, and 4q23-28, respectively. These findings suggest a greater degree of genomic imbalance in ependymomas than has been recognized previously and highlight chromosomal loci likely to contain oncogenes or tumor suppressor genes that may contribute to the molecular pathogenesis of this tumor. Our study also confirmed previous findings on frequent losses of 17 and 22q in ependymomas and further identified chromosome 16 loss as a common recurrent genetic aberration in ependymomas.

Evidence for an ependymoma tumour suppressor gene in chromosome region 22pter-22q11.2

Ependymomas are glial tumours of the brain and spinal cord. The most frequent genetic change in sporadic ependymoma is monosomy 22, suggesting the presence of an ependymoma tumour suppressor gene on that chromosome. Clustering of ependymomas has been reported to occur in some families. From an earlier study in a family in which four cousins developed an ependymoma, we concluded that an ependymoma-susceptibility gene, which is not the NF2 gene in 22q12, might be located on chromosome 22. To localize that gene, we performed a segregation analysis with chromosome 22 markers in this family. This analysis revealed that the susceptibility gene may be located proximal to marker D22S941 in 22pter-22q11.2. Comparative genomic hybridization showed that monosomy 22 was the sole detectable genetic aberration in the tumour of one of the patients. Loss of heterozygosity studies in that tumour revealed that, in accordance to Knudson's two-hit theory of tumorigenesis, the lost chromosome 22 originated from the parent presumed to have contributed the wild-type allele of the susceptibility gene. Thus, our segregation and tumour studies collectively indicate that an ependymoma tumour suppressor gene may be present in region 22pter-22q11.2.

Cytogenetic study of 33 ependymomas

Ependymomas are glial tumors. They constitute approximately 5-10% of intracranial tumors. Ependymomas are tumors which can recur. Predictive factors of outcome in ependymomas are not well-established. Karyotypic studies on ependymomas are relatively scarce, and no specific chromosomal change has been described in these neoplasms. We performed a cytogenetic study of 33 ependymomas, of which eight were recurrent tumors, to determine the type and incidence of cytogenetic changes.

Karyotype studies in 18 ependymomas with literature review of 107 cases

Cytogenetic studies from 17 pediatric ependymomas and 1 ependymoblastoma are presented. Eight tumors had abnormal karyotypes. Another 107 published cases of cytogenetic analyses from pediatric and adult ependymomas or ependymoblastomas were reviewed. Of the total 125 tumors, 83 (66%) had abnormal karyotypes, of which 24 had a sole autosomal abnormality. Approximately one third had monosomy 22 (-22) or breakpoint 22q11-13, with a higher incidence in adult (56%) versus pediatric (28%) tumors. Structural abnormalities of chromosomes 1, 6, and 17, and numerical abnormalities of 7, 9, 12, and 20, in particular, are also discussed. Although no primary cytogenetic abnormality is evident, these findings may provide direction for additional investigations regarding the classification of these tumors.

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.

Simultaneous presentation of atypical teratoid/rhabdoid tumor in siblings

Atypical rhabdoid/teratoid tumor (ATT/RHT) is a rare malignant neoplasm which appears in early childhood. The present paper describes clinical and pathological features of ATT/RHT which occurred simultaneously in 2 sisters diagnosed at a 15 day interval. Both children were treated by surgical resection, subtotal in the first case and total in the second. Postoperatively, chemotherapy followed by radiotherapy, 50.4 Gy on the posterior fossa, were administered. Despite this therapy, both sisters died at 14 months and 26 months respectively. The tumors express vimentin and EMA; cells contained intracytoplasmic inclusions. No karyotypic anomaly was detected. This is the first description of familial ATT/RHT.

Chromosome arm 6q loss is the most common recurrent autosomal alteration detected in primary pediatric ependymoma

We analyzed 23 samples of primary pediatric ependymoma for significant gains or losses of genomic DNA, using comparative genomic hybridization (CGH) and a rigorous statistical approach. Nine of the tumors in this series (39%) appeared normal by CGH. The remainder had a limited number of regions of genomic imbalance, most often involving losses of chromosome arms 6q and 22q and the X chromosome, or gains of either 1q or 9. Recurrent and exclusive losses of 6q or 22q suggest that these regions harbor tumor suppressor genes that may contribute independently to the pathogenesis of childhood ependymoma.

"Rhabdoid" meningioma: an aggressive variant

It is has been suggested that rhabdoid morphology is associated with a poor prognosis, regardless of tumor histogenesis. We report a series of 15 meningiomas with rhabdoid features. Nine patients had undergone multiple resections. In six, the rhabdoid component was histologically apparent only in recurrences. Rhabdoid morphology was defined as sheets of loosely cohesive cells with eccentric nuclei and hyaline, paranuclear inclusions. Ultrastructurally, the latter consisted of whorls of intermediate filaments often entrapping lysosomes or other organelles. Meningothelial features included whorl formation and nuclear pseudoinclusions, immunohistochemical coexpression of vimentin and epithelial membrane antigen, and the ultrastructural finding of interdigitating cell membranes and intercellular junctions. At the histologic level, a conventional meningioma component was noted in most tumors; only four lesions were entirely rhabdoid. Histologic malignancy (brain invasion or anaplasia) was observed in nine cases, another two tumors being considered malignant on the basis of extracranial metastasis. In the majority, increased cell proliferation was evidenced by a high mitotic rate or MIB-1 LI. At last follow-up, 13 patients (87%) had experienced at least one recurrence and 8 (53%) were dead of disease. Median time to death was 5.8 years after initial surgery and 3.1 years after the first appearance of rhabdoid morphology. Our findings corroborate those from a smaller series recently reported by Kepes et al. on the same entity (Kepes JJ, Moral LA, Wilkinson SB, Abdullah A, Llena JF. Rhabdoid transformation of tumor cells in meningiomas: A histologic indication of increased proliferative activity. Report of four cases. Am J Surg Pathol 1998;22:231-8). They further suggest that rhabdoid meningiomas are highly aggressive tumors and that the rhabdoid phenotype represents a marker of malignant transformation in meningiomas.

Extrarenal rhabdoid tumors of soft tissue: a clinicopathologic and immunohistochemical study of 18 cases

Rhabdoid tumor is a well-accepted clincopathologic entity among childhood renal neoplasms; similar tumors have been described in extrarenal locations. We present the clinicopathologic profile and the immunohistochemical features of a series of soft tissue rhabdoid tumors. Twenty-eight cases coded as extrarenal rhabdoid tumor (ERRT), RT, possible ERRT, and "large cell sarcoma" were retrieved from the Armed Forces Institute of Pathology soft tissue registry. The tumors were reclassified according to strict criteria by light microscopy, clinical information, immunohistochemistry, and, in some cases, electron microscopy. Soft tissue rhabdoid tumor (STRT) was defined as (1) a tumor composed of noncohesive single cells, clusters, or sheets of large tumor cells with abundant glassy eosinophilic cytoplasm, an eccentric vesicular nucleus, and an extremely large nucleolus; (2) positivity for vimentin and/or cytokeratin or other epithelial markers by immunostaining; and (3) exclusion of other tumor types with rhabdoid inclusions (melanoma, other sarcomas, carcinoma). Eighteen cases met our criteria for soft tissue rhabdoid tumors. The median patient age was 13 years (range, 6 months to 56 years). Ninety-four percent of STRT cases were positive for vimentin and 59% for pan-cytokeratin. Sixty-three percent and 60% were positive for CAM 5.2 and EMA, respectively. Seventy-nine percent stained for at least one epithelial marker; 76% stained for both vimentin and epithelial markers simultaneously. Forty-two percent stained for MSA, and 14% for CEA and SMA. CD99, synaptophysin, CD57 (Leu-7), NSE, and focal S100 protein were identified in 75%, 66%, 56%, 54%, and 31% of the STRT cases, respectively. All STRT cases examined were negative for HMB-45, chromogranin, BER-EP4, desmin, myoglobin, CD34, and GFAP. Follow-up examination in 61% of the STRT patients revealed that 64% of patients died of disease within a median follow-up interval of 19 months (range, 4 months to 5 years); 82% had metastases to lung, lymph nodes, or liver; 22% had local recurrences before metastasis; and 18% were alive without known disease status (median, 5.5 years). Soft tissue rhabdoid tumor is a highly aggressive sarcoma, predominantly of childhood. Besides having nearly consistent coexpression of vimentin and epithelial markers, STRTs show positivity for multiple neural/neuroectodermal markers that overlap with those of primitive neuroectodermal tumor.

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.

Molecular genetic analysis of chromosome arm 17p and chromosome arm 22q DNA sequences in sporadic pediatric ependymomas

Ependymomas are glial tumors of the brain and spinal cord occurring both sporadically and in a familial syndrome, neurofibromatosis type 2 (NF2). Previous analyses performed on specimens obtained predominantly from adult patients have shown loss of DNA sequences from chromosome arm 22q, which is the location of the NF2 gene. Previously, we documented the consistent loss of chromosome arm 17p DNA in medulloblastoma and astrocytoma, which are the most common brain tumors in children. Although mutation of the TP53 gene located on 17p is the most frequent genetic mutation in all adult tumor types, such mutations are rare in most childhood brain tumors investigated to date. We studied a series of pediatric ependymoma specimens (16 intracranial and 2 spinal) for loss of 17p and 22q DNA sequences and for mutation of the TP53 and NF2 genes. None of the children had the clinical stigmata of NF2. We detected loss of 17p DNA sequences in 9 of the 18 specimens (50%); in 7 of 9 of these specimens (78%), the 144-D6 marker was deleted. In contrast, only 2 of these same 18 specimens (11%) showed loss of 22q DNA. One TP53 gene mutation was detected in a child from a cancer kindred. No mutations were detected in the NF2 gene. Our results suggest that loss of chromosome arm 17p DNA sequences is common in sporadic pediatric ependymomas and that, in contrast to ependymomas in adults, deletion of chromosome arm 22q sequences is rare. Furthermore, TP53 and NF2 gene mutations do not play an important role in the etiology of sporadic pediatric ependymomas.