Human ependymomas reveal frequent deletions on chromosomes 6 and 9

Individualized Prediction of Overall Survival for Primary Intramedullary Spinal Cord Grade II/III Ependymoma

BACKGROUND

The purpose of this study was to develop and validate a nomogram to predict overall survival (OS) for adult patients with primary intramedullary spinal cord grade II/III ependymoma (PISCGE). We also elucidated the effectiveness of postoperative radiotherapy for this disease.

METHODS

Clinical data of patients with PISCGE between 1988 and 2015 were collected from the Surveillance, Epidemiology, and End Results (SEER) registry database. The independent prognostic factors were identified using univariate and multivariate Cox analyses. The nomogram was established from the results of the multivariate Cox analysis. We also use some methods to verify the superiority of the prediction model. The effectiveness of postoperative radiotherapy for PISCGE was assessed through coarsened exact matching and survival analyses.

RESULTS

Multivariate Cox analysis revealed that sex, age, surgical treatment, tumor grade, and marital status were independent prognostic factors of OS. The nomogram model was established based on these factors and validated internally. Calibration plots based on bootstrap resampling validation showed good consistency between the nomogram prediction and actual observation. This model also exhibited favorable discrimination characteristics. A risk classification system based on a nomogram was established to promote risk stratification of PISCGE and optimize clinical management. Moreover, we found no association between radiation treatment and the OS for these patients (P > 0.05).

CONCLUSIONS

We built the first nomogram model and risk classification system for PISCGE patients. Our model accurately estimated the individual OS probability of these patients, and proposes different treatment approaches for patients based on the risk classification system. Furthermore, from our findings, radiotherapy confers no survival advantage to these patients.

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.

Simultaneous subependymomas in monozygotic female twins: further evidence for a common genetic or developmental disorder background

In this paper, a rare case of subependymoma of the fourth ventricle in identical female twins is reported. Magnetic resonance imaging and CT showed nearly identical locations of the tumors in the fourth ventricle and similar growth patterns of the tumors in both sisters. Likewise, postoperative histopathological analysis of both tumors revealed the typical histological appearance of subependymomas. Subependymoma is a rare, low-grade glioma of the CNS, slowly growing and usually asymptomatic. If symptomatic, a subependymoma can in some cases lead to sudden death caused by pressure on the brainstem or decompensated secondary hydrocephalus. This case demonstrates the importance of detecting tumors early and thereby preventing symptoms arising from increasing intracranial pressure, and optimizing therapy options.

Genomic characterization of ependymomas reveals 6q loss as the most common aberration

Ependymomas are rare tumors of the central nervous system (CNS). They are classified based on tumor histology and grade, but the prognostic value of the WHO grading system remains controversial. Treatment is mainly surgical and by radiation. An improved knowledge of ependymoma biology is important to elucidate the pathogenesis, to improve classification schemes, and to identify novel potential treatment targets. Only 113 ependymoma karyotypes with chromosome aberrations are registered in the Mitelman database. We present the first study of ependymoma genomes combining karyotyping and high resolution comparative genomic hybridization (HR-CGH). Nineteen tumor samples were collected from three pediatric and 15 adult patients treated at Oslo University Hospital between 2005 and 2012. Histological diagnoses included subependymoma and myxopapillary ependymoma (WHO grade I), ependymoma (WHO grade II) and anaplastic ependymoma (WHO grade III). Four tumors were intraspinal and 15 were intracranial. Seventeen samples were successfully karyotyped, HR-CGH analysis was undertaken on 17 samples, and 15 of 19 tumors were analyzed using both methods. Twelve tumors had karyotypic abnormalities, mostly gains or losses of whole chromosomes. Structural rearrangements were found in four tumors, in two of which 2p23 was identified as a breakpoint region. Twelve tumors displayed genomic imbalances by HR-CGH analysis with loss of material at 6q as the most common. 6q loss, which was detected by one or both methods in seven of 12 (58%) abnormal tumors, and 5p gain (observed in five tumors; 42%) were the most common genomic aberrations in this series.

Molecular genetics of ependymoma

Brain tumors are the leading cause of cancer death in children, with ependymoma being the third most common and posing a significant clinical burden. Its mechanism of pathogenesis, reliable prognostic indicators, and effective treatments other than surgical resection have all remained elusive. Until recently, ependymoma research was hindered by the small number of tumors available for study, low resolution of cytogenetic techniques, and lack of cell lines and animal models. Ependymoma heterogeneity, which manifests as variations in tumor location, patient age, histological grade, and clinical behavior, together with the observation of a balanced genomic profile in up to 50% of cases, presents additional challenges in understanding the development and progression of this disease. Despite these difficulties, we have made significant headway in the past decade in identifying the genetic alterations and pathways involved in ependymoma tumorigenesis through collaborative efforts and the application of microarray-based genetic (copy number) and transcriptome profiling platforms. Genetic characterization of ependymoma unraveled distinct mRNA-defined subclasses and led to the identification of radial glial cells as its cell type of origin. This review summarizes our current knowledge in the molecular genetics of ependymoma and proposes future research directions necessary to further advance this field.

Chromosomal anomalies and prognostic markers for intracranial and spinal ependymomas

Ependymomas are neoplasms that can occur anywhere along the craniospinal axis. They are the third most common brain tumor in children, representing 10% of pediatric intracranial tumors, 4% of adult brain tumors, and 15% of all spinal cord tumors. As the heterogeneity of ependymomas has severely limited the prognostic value of the World Health Organization grading system, numerous studies have focused on genetic alterations as a potential basis for classification and prognosis. However, this endeavor has proven difficult due to variations of findings depending on tumor location, tumor grade, and patient age. While many have evaluated chromosomal abnormalities for ependymomas as a whole group, others have concentrated their efforts on specific subsets of populations. Here, we review modern findings of chromosomal analyses, their relationships with various genes, and their prognostic implications for intracranial and spinal cord ependymomas.

Expression profiling of ependymomas unravels localization and tumor grade-specific tumorigenesis

BACKGROUND

Ependymomas derive from ependymal cells that cover the cerebral ventricles and the central canal of the spinal cord. The molecular alterations leading to ependymomal oncogenesis are not completely understood.

METHODS

The authors performed array-based expression profiling on a series of 34 frozen ependymal tumors with different localizations and histologic grades. Data were analyzed by nonsupervised and supervised clustering methods along with Gene Ontology and Pathway Analyzer tools.

RESULTS

Class discovery experiments indicated a strong correlation between profiles and tumor localization as well as World Health Organization (WHO) tumor grades. On the basis of supervised clustering, intracranial ependymomas were associated with high expression levels of Notch, Hedgehog, and bone morphogenetic protein pathway members. In contrast, most of the homeobox-containing genes manifested high expression in extracranial ependymomas. The results also revealed that WHO grade 2 ependymomas differed from WHO grade 3 ependymomas by genes implicated in Wnt/beta-catenin signaling, cell cycle, E2F transcription factor 1 destruction, angiogenesis, apoptosis, remodeling of adherens junctions, and mitotic spindle formation.

CONCLUSIONS

Taken together, the tumor localization-related gene sets mainly implicated in stem cell maintenance, renewal, and differentiation suggest the dysregulation of localized cancer stem cells during ependymoma development. The WHO grade differentiating pathways suggested that alteration of the Wnt/beta-catenin signaling pathway is a key event in the tumorigenesis of WHO grade 3 ependymomas. On the basis of the current data, the authors suggest a developmental scheme of ependymomas that integrates tumor localization and tumor grades, and that pinpoints new targets for the development of future therapeutic approaches.

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.

EDG3 and SHC3 on chromosome 9q22 are co-amplified in human ependymomas

By qPCR we found that EDG3 and SHC3 were amplified in 60% of ependymomas but none in choroid plexus papillomas. In ependymomas EDG3 and SHC3 amplification increased Shc3 protein levels while EDG3 was less affected. Both proteins were co-immunoprecipitated from ependymoma and Shc3 was tyrosine phosphorylated thus presumably active. We showed by digestion with N-glycosidase-F that EDG3 was glycosylated indicating that EDG3 protein was not retained in the endoplasmic reticulum. The co-immunoprecipitation of Shc3 and EDG3 proteins from ependymomas with amplification of SHC3 and EDG3 genes suggests that the two proteins co-operate and are important for ependymomas in vivo.

Pediatric supratentorial ependymomas show more frequent deletions on chromosome 9 than infratentorial ependymomas: a microsatellite analysis

Numerous human malignancies, including brain tumors, have been reported to show aberrations on chromosome 9. In our previous screening study in ependymomas, we used microsatellite analysis to identify frequent aberrations on this chromosome. To refine our preliminary analysis of candidate regions, here we use 15 polymorphic microsatellite markers spanning the entire chromosome 9. A total of 48 pairs of matched normal and tumor specimens from patients with ependymoma, including 28 children (mean age, 4.4 years) and 20 adults (mean age, 44.9 years), were genotyped. Allelic imbalances were found in 30/48 patients (62.5%). Pediatric tumors, which were predominantly anaplastic, showed fewer aberrations (57.1%) than adult tumors (70%), and two common regions of deletions were identified (9p21.1 approximately p22.3 and 9q31.3 approximately q33.2). We found that 9q31.3 approximately q33.2, an approximately 8.5-megabase segment containing the DCR1 gene, exhibited the highest number of aberrations (n=33). Adults with ependymomas harboring aberrations on chromosome 9 (n=14) showed significantly longer overall survival than patients of the same group without this aberration (n=6; P=0.034), irrespective of the extent of resection in multivariate analysis. Aberrations of chromosome 9, and particularly of DCR1, may play a role in the prognostic evaluation for ependymomas in adults in the future. In pediatric patients, genetic aberrations were found significantly more often in supratentorial tumors than in tumors with infratentorial location (P=0.007). This result may underscore differences in the origin of these tumors.

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.

Stepwise accumulation of distinct genomic aberrations in a patient with progressively metastasizing ependymoma

Nonresectable ependymomas are associated with poor prognosis despite intensive radiochemotherapy and radiation. The molecular pathogenesis of ependymoma initiation and progression is largely unknown. We here present a case of therapy-refractory, progressive ependymoma with cerebrospinal as well as extraneural metastases, which allowed us for the first time to follow the stepwise accumulation of chromosome aberrations during disease progression. Genome-wide DNA copy-number analysis showed sequential deletions on chromosomes 1, 9, and 14 as well as a homozygous deletion of the CDKN2A locus, underscoring its role in tumor progression. Gradual loss at 1p36 was associated with loss of protein expression of the putative tumor suppressor gene AJAP1/SHREW1. In summary, this is the first report on acquired genomic aberrations in ependymoma over time pointing to novel candidate tumor suppressor genes. This analysis provides molecular insights into the chronology of genetic events in this case from initial localized tumor to widespread metastasized disease.

Spinal tumors in neurofibromatosis-2: management considerations - a review

Neurofibromatosis Type 2 (NF-2) is a distinct clinical entity, characterized by multiple intracranial and spinal tumors. While bilateral vestibular schwannomas are the pathological hallmark of the disease, significant morbidity in NF-2 is attributable to the presence of both intramedullary and extramedullary spinal tumors. With the advent of MRI as a screening modality, multiple, extensive spinal tumors in the NF-2 population are often seen, which may be clinically quiescent at the time of initial diagnosis. All NF-2 patients should have routine screening with full spinal MRI at the time of diagnosis, regardless of symptoms. Early surgical intervention is indicated in cases where a neurological deficit is attributable to a focal expanding spinal lesion. In asymptomatic patients, the decision to operate is tailored to the individual patient, with the ultimate goal of preserving function. In these cases, surgery should be considered where there is evidence of progressive tumor growth, with attendant risk to the patient of functional deterioration.

Patterns of brain infiltration and secondary structure formation in supratentorial ependymal tumors

Ependymomas are generally considered to be noninfiltrative tumors that have discrete borders with adjacent brain tissue. Most occur in the posterior fossa or spinal cord. Supratentorial ependymal tumors arise near the ventricular system or, more rarely, within the cerebral white matter or cortex. Presented here are 6 supratentorial ependymal tumors, 3 that primarily involve the cerebral cortex and 3 that extend into the cortex from the underlying white matter. By microscopy, all of these tumors locally infiltrate the cortex and/or white matter along small blood vessels and axonal fiber tracts. They also form other glioma secondary structures including perineuronal tumor cell satellitosis and subpial tumor cell mounds. The 3 cortical ependymal tumors show a spectrum of features ranging from conventional and clear-cell ependymoma-like patterns to more angiocentric glioma-like histology. Because ependymal tumors generally have a significantly better prognosis than other infiltrating gliomas, recognition of their capacity to infiltrate adjacent cortex and white matter is important to prevent the misdiagnosis of oligodendroglioma, astrocytoma, or infiltrating glioma, not otherwise specified. Cortical ependymomas and angiocentric gliomas may comprise a group of locally infiltrative ependymal tumors that are associated with an excellent prognosis after gross total surgical resection.

Correlation between 6q25.3 deletion status and survival in pediatric intracranial ependymomas

Losses and rearrangements of genetic material on chromosome 6q are frequently found in several human malignancies, including primary central nervous system tumors. We previously used microsatellite analysis of ependymomas to identify frequent deletions in regions 6q15 approximately q16, 6q21 approximately q22.1, and 6q24.3 approximately q25.3. To refine our preliminary analysis of potential prognostic regions, we used a panel of 25 microsatellite markers located between 6q15 and 6qter in 49 pairs of matched normal and tumor specimens from 28 children and 21 adults with ependymoma. Allelic deletions were detected in 34 of 49 patients (69%), and two common regions of deletions (6q24.3 and 6q25.2 approximately q25.3) were identified. A short segment of approximately 0.4 Mb between D6S1612 and D6S363 on 6q25.3, containing the SNX9 and SYNJ2 genes, exhibited the highest number of aberrations (n = 38). Pediatric tumors showed slightly fewer aberrations (64%) than adult tumors (76%) and also predominantly exhibited small interstitial deletions, in contrast to the extensive losses of genetic material in adults. Pediatric anaplastic intracranial (supra- and infratentorial) ependymomas harboring the 6q25.3 deletion (n = 9) showed significantly longer overall survival than did patients of the same group without the aberration (n = 6), independent of the extent of resection (P = 0.013). This supports the identified deletion on 6q25.3 as a candidate favorable prognostic parameter and warrants further investigation.

Ependymoma gene expression profiles associated with histological subtype, proliferation, and patient survival

Ependymomas are primary tumors of the central nervous system that typically originate from the walls of the cerebral ventricles or from the spinal canal. The pathogenesis of these tumors is poorly understood, and prognostic assessment based on histologic features and clinical parameters is difficult. The aim of this study was to investigate the molecular heterogeneity of ependymomas. We used cDNA microarrays and RT-PCR to examine gene expression in 47 ependymomas. We present results for five comparisons: (1) tumors from children and adults with poor versus favorable outcome, (2) tumors from children with poor versus favorable outcome, (3) tumors with high versus low proliferation indices, (4) subependymomas versus myxopapillary ependymomas, and (5) spinal versus intracranial ependymomas. For patients with an overall survival >10 years after diagnosis, we identified 27 genes associated with favorable prognosis. In contrast, overexpression of BNIP3, MRC1, EPHB3, GLIS3, CDK4, COL4A2, EBP, NRCAM, and CCNA1 genes in tumors with high proliferation indices was associated with a poor outcome. Thirty genes, including ETV6, YWHAE, TOP2A, TLR2, IRAK1, TIA1, and UFD1L were found to be highly expressed in subependymomas but not myxopapillary ependymomas. Also, 30 genes were differentially expressed in spinal versus intracranial ependymomas. There was no relationship between expression profiles and tumor grade, patient age, and patient gender. Our results provide insight into specific molecular events underlying ependymoma tumorigenesis and may contribute to more accurate diagnosis and prediction of clinical outcome.

Molecular genetics of pediatric central nervous system tumors

Recent advances in molecular biology have enhanced our understanding of the pathogenesis of brain tumors, particularly in children. The use of molecular diagnostic tools is quickly becoming a standard component in the diagnosis and classification of brain tumors in children, in addition to providing insight leading to treatment stratification and improved outcome prediction. All new protocols involving treatments for brain tumors in children include studies of biomarkers and biologic correlates as a means to identify new targets for therapeutics and possible intervention strategies.

Chromosomal imbalances in clear cell ependymomas

Clear cell ependymoma is a rare and diagnostically challenging subtype of ependymoma, whose genetic features are essentially unknown. We studied 13 clear cell ependymomas (five cases WHO grade II, eight cases WHO grade III) by comparative genomic hybridization (CGH). Chromosomal imbalances were found in 12/13 cases. The most common aberrations overall were +1q (38%), -9 (77%), -3 (31%), and -22q (23%). Clear cell ependymomas of WHO grade II were characterized by -9 (40%), whereas WHO grade III cases mainly showed +1q (63%), and +13q (25%), as well as -9 (100%), -3 (38%), and -22q (25%). In contrast to other ependymal tumors, clear cell ependymomas of WHO grade II showed fewer imbalances than WHO grade III samples (1.4 vs 3.5 per case). Although some of the implicated chromosomes have previously been shown to be involved in other ependymoma variants, the striking frequency of +1q, -9, and -3 suggests that aberrations differ between clear cell and other types of ependymomas, in particular, for loss of chromosome 9 which can be regarded as the molecular hallmark of clear cell ependymomas.

Molecular cytogenetic analysis in the study of brain tumors: findings and applications

Classic cytogenetics has evolved from black and white to technicolor images of chromosomes as a result of advances in fluorescence in situ hybridization (FISH) techniques, and is now called molecular cytogenetics. Improvements in the quality and diversity of probes suitable for FISH, coupled with advances in computerized image analysis, now permit the genome or tissue of interest to be analyzed in detail on a glass slide. It is evident that the growing list of options for cytogenetic analysis has improved the understanding of chromosomal changes in disease initiation, progression, and response to treatment. The contributions of classic and molecular cytogenetics to the study of brain tumors have provided scientists and clinicians alike with new avenues for investigation. In this review the authors summarize the contributions of molecular cytogenetics to the study of brain tumors, encompassing the findings of classic cytogenetics, interphase- and metaphase-based FISH studies, spectral karyotyping, and metaphase- and array-based comparative genomic hybridization. In addition, this review also details the role of molecular cytogenetic techniques in other aspects of understanding the pathogenesis of brain tumors, including xenograft, cancer stem cell, and telomere length studies.

Localization of a putative low-penetrance ependymoma susceptibility locus to 22q11 using a chromosome 22 tiling-path genomic microarray

Ependymomas frequently display allelic loss of chromosome 22 in the absence of mutations in the known tumor-suppressor genes on chromosome 22, suggesting the role of an alternative predisposing gene or genes from this chromosome. In an effort to localize these genes, 37 ependymomas derived from 33 patients were analyzed for the presence of copy number changes by use of a high-resolution chromosome 22 genomic microarray. Eighteen ependymomas (49%) displayed an array-CGH profile consistent with monosomy of chromosome 22. However, in 10 of these tumors, the fluorescence ratios for 22q clones scored as deleted were different from those at the single gene copy level. This suggests either analysis of mixed populations of tumor and normal stromal cells or analysis of mixed tumor cell populations with different genetic profiles. Four ependymomas derived from two patients showed overlapping interstitial deletions of 2.2 Mb and approximately 510 kb. Further analyses revealed that these deletions were present in the constitutional DNA of these two patients as well as in some of their unaffected relatives. Detailed microsatellite analysis of these families refined the commonly deleted segment to a region of 320 kb between markers RH13801 and D22S419. Our results provide additional evidence for the involvement of genes on chromosome 22 in the development of ependymoma and suggest the presence of a low-penetrance ependymoma susceptibility locus at 22q11.