Molecular genetic alterations on chromosomes 11 and 22 in ependymomas

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.

Beyond the "3 Ps": A critical appraisal of the non-endocrine manifestations of multiple endocrine neoplasia type 1

Multiple endocrine neoplasia type 1 (MEN1), an autosomal-dominantly inherited tumor syndrome, is classically defined by tumors arising from the "3 Ps": Parathyroids, Pituitary, and the endocrine Pancreas. From its earliest descriptions, MEN1 has been associated with other endocrine and non-endocrine neoplastic manifestations. High quality evidence supports a direct association between pathogenic MEN1 variants and neoplasms of the skin (angiofibromas and collagenomas), adipose tissue (lipomas and hibernomas), and smooth muscle (leiomyomas). Although CNS tumors, melanoma, and, most recently, breast cancer have been reported as MEN1 clinical manifestations, the published evidence to date is not yet sufficient to establish causality. Well-designed, multicenter prospective studies will help us to understand better the relationship of these tumors to MEN1, in addition to verifying the true prevalence and penetrance of the well-documented neoplastic associations. Nevertheless, patients affected by MEN1 should be aware of these non-endocrine manifestations, and providers should be encouraged always to think beyond the "3 Ps" when treating an MEN1 patient.

Spinal Cord Tumor Microenvironment

Intramedullary spinal cord tumors (IMSCT) are rare entities for which there currently exist no standardized treatment paradigms. Consequently, patients usually receive treatment modalities that were established for intracerebral tumors; these approaches, however, typically result in functional impairment, recurrent tumor growth, and short overall survival. There is a distinct lack of promising research efforts in this field, which raises questions about whether spinal cord tumor microenvironment (TME) might promote the development, progression, and treatment resistance of IMSCT. In this review, we aim to examine spinal cord biology, compare spinal cord and brain microenvironments, and discuss mutual interactions between IMSCT and TME. Manipulating these pathways may provide new treatment approaches for future patient groups.

Genomic Landscape of Intramedullary Spinal Cord Gliomas

Intramedullary spinal cord tumors (IMSCTs) are rare neoplasms that have limited treatment options and are associated with high rates of morbidity and mortality. To better understand the genetic basis of these tumors we performed whole exome sequencing on 45 tumors and matched germline DNA, including twenty-nine spinal cord ependymomas and sixteen astrocytomas. Though recurrent somatic mutations in IMSCTs were rare, we identified NF2 mutations in 15.7% of tumors (ependymoma, N = 7; astrocytoma, N = 1), RP1 mutations in 5.9% of tumors (ependymoma, N = 3), and ESX1 mutations in 5.9% of tumors (ependymoma, N = 3). We further identified copy number amplifications in CTU1 in 25% of myxopapillary ependymomas. Given the paucity of somatic driver mutations, we further performed whole-genome sequencing of 12 tumors (ependymoma, N = 9; astrocytoma, N = 3). Overall, we observed that IMSCTs with intracranial histologic counterparts (e.g. glioblastoma) did not harbor the canonical mutations associated with their intracranial counterparts. Our findings suggest that the origin of IMSCTs may be distinct from tumors arising within other compartments of the central nervous system and provides the framework to begin more biologically based therapeutic strategies.

High-Grade Glioma is not a Feature of Neurofibromatosis Type 2 in the Unirradiated Patient

BACKGROUND

The Manchester criteria for neurofibromatosis type 2 (NF2) include a range of tumors, and gliomas were incorporated in the original description. The gliomas are now widely accepted to be predominantly spinal cord ependymomas.

OBJECTIVE

To determine whether these gliomas include any cases of malignant glioma (WHO grade III and IV) through a database review.

METHODS

The prospective database consists of 1253 patients with NF2. 1009 are known to be alive at last follow-up.

RESULTS

There was a single case of glioblastoma multiforme (GBM; World Health Organization grade IV) in the series and no WHO grade III gliomas. The GBM was in a patient who had previously undergone stereotactic radiosurgery for a vestibular schwannoma.

CONCLUSION

High-grade gliomas are not a feature of NF2 in the unirradiated patient and should be excluded from the diagnostic criteria.

Recent advances in intradural spinal tumors

Intradural spinal tumors are rare tumors of the central nervous system. Due to the eloquence of the spinal cord and its tracts, the compact architecture of the cord and nerves, and the infiltrative nature of some of these tumors, surgical resection is difficult to achieve without causing neurological deficits. Likewise, chemotherapy and radiotherapy are utilized more cautiously in the treatment of intradural spinal tumors than their cranial counterparts. Targeted therapies aimed at the genetic alterations and molecular biology tailored to these tumors would be helpful but are lacking.Here, we review the major types of intradural spinal tumors, with an emphasis on genetic alterations, molecular biology, and experimental therapies for these difficult to treat neoplasms.

Expression alterations define unique molecular characteristics of spinal ependymomas

Ependymomas are glial tumors that originate in either intracranial or spinal regions. Although tumors from different regions are histologically similar, they are biologically distinct. We therefore sought to identify molecular characteristics of spinal ependymomas (SEPN) in order to better understand the disease biology of these tumors. Using gene expression profiles of 256 tumor samples, we identified increased expression of 1,866 genes in SEPN when compared to intracranial ependymomas. These genes are mainly related to anterior/posterior pattern specification, response to oxidative stress, glial cell differentiation, DNA repair, and PPAR signalling, and also significantly enriched with cellular senescence genes (P = 5.5 × 10-03). In addition, a high number of significantly down-regulated genes in SEPN are localized to chromosome 22 (81 genes from chr22: 43,325,255 - 135,720,974; FDR = 1.77 × 10-23 and 22 genes from chr22: 324,739 - 32,822,302; FDR = 2.07 × 10-09) including BRD1, EP300, HDAC10, HIRA, HIC2, MKL1, and NF2. Evaluation of NF2 co-expressed genes further confirms the enrichment of chromosome 22 regions. Finally, systematic integration of chromosome 22 genes with interactome and NF2 co-expression data identifies key candidate genes. Our results reveal unique molecular characteristics of SEPN such as altered expression of cellular senescence and chromosome 22 genes.

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.

BRMS1 suppresses glioma progression by regulating invasion, migration and adhesion of glioma cells

Breast cancer metastasis suppressor 1 (BRMS1) is a metastasis suppressor gene in several solid tumors. However, the expression and function of BRMS1 in glioma have not been reported. In this study, we investigated whether BRMS1 play a role in glioma pathogenesis. Using the tissue microarray technology, we found that BRMS1 expression is significantly decreased in glioma compared with tumor adjacent normal brain tissue (P<0.01, χ² test) and reduced BRMS1 staining is associated with WHO stages (P<0.05, χ² test). We also found that BRMS1 was significantly downregulated in glioma cell lines compared to normal human astrocytes (P<0.01, χ² test). Furthermore, we demonstrated that BRMS1 overexpression inhibited glioma cell invasion by suppressing uPA, NF-κB, MMP-2 expression and MMP-2 enzyme activity. Moreover, our data showed that overexpression of BRMS1 inhibited glioma cell migration and adhesion capacity compared with the control group through the Src-FAK pathway. Taken together, this study suggested that BRMS1 has a role in glioma development and progression by regulating invasion, migration and adhesion activities of cancer cells.

Acquired resistance of EGFR-mutant lung adenocarcinomas to afatinib plus cetuximab is associated with activation of mTORC1

Patients with EGFR-mutant lung adenocarcinomas (LUADs) who initially respond to first-generation tyrosine kinase inhibitors (TKIs) develop resistance to these drugs. A combination of the irreversible TKI afatinib and the EGFR antibody cetuximab can be used to overcome resistance to first-generation TKIs; however, resistance to this drug combination eventually emerges. We identified activation of the mTORC1 signaling pathway as a mechanism of resistance to dual inhibition of EGFR in mouse models. The addition of rapamycin reversed resistance in vivo. Analysis of afatinib-plus-cetuximab-resistant biopsy specimens revealed the presence of genomic alterations in genes that modulate mTORC1 signaling, including NF2 and TSC1. These findings pinpoint enhanced mTORC1 activation as a mechanism of resistance to afatinib plus cetuximab and identify genomic mechanisms that lead to activation of this pathway, revealing a potential therapeutic strategy for treating patients with resistance to these drugs.

Tanycytic ependymoma of the filum terminale associated with multiple endocrine neoplasia type 1: first reported case

BACKGROUND CONTEXT

Ependymoma associated with multiple endocrine neoplasia type 1 (MEN-1) is an extremely rare clinical entity. To the best of our knowledge, only five cases of ependymoma associated with MEN-1 have been previously described. Furthermore, there has been no case of tanycytic ependymoma of the filum terminale associated with MEN-1.

PURPOSE

The present case report illustrates a 53-year-old man with tanycytic ependymoma of the filum terminale associated with MEN-1. We review the literature on ependymoma with MEN-1 and tanycytic ependymoma of the cauda equina region and also discuss the risk of recurrence.

STUDY DESIGN

A case report.

METHODS

The patient presented with complaints of nocturnal pain in the lower back, accompanied by numbness around the anus and intermittent claudication for approximately 1 year. Magnetic resonance imaging (MRI) identified an intradural-enhancing, large mass lesion at the level from Th12 to L2 vertebrae, with a cranial cystic lesion.

RESULTS

Open-door laminoplasty of the Th12, L1, and L2 and en bloc tumor resection with thickened filum terminale were performed. Histopathologic examination of the tumor specimens showed tanycytic ependymoma (World Health Organization Classification Grade II). At the time of the 2-year and 8-month follow-up examination, MRI did not show tumor recurrence.

CONCLUSIONS

This is the first reported case of this clinical entity. A careful follow-up of patients with this unusual tumor is strongly recommended.

Ependymoma in children: molecular considerations and therapeutic insights

A multi-modality approach that encompasses maximal surgical resection in combination with adjuvant therapy is critical for achieving optimal disease control in children with ependymoma. In view of its complex biology and variable response to therapy, ependymoma remains a challenge for clinicians involved in the care of these patients. Meanwhile, translation of molecular findings can characterize unique features of childhood ependymoma and their natural history. Furthermore, understanding the biology of pediatric ependymoma serves as a platform for development of future targeted therapies. In line with these goals, we review the molecular basis of pediatric ependymoma and its prognostic implications, as well as novel therapeutic advances in the management of ependymoma in children.

Spinal cord tumours: advances in genetics and their implications for treatment

Tumours of the spinal cord, although rare, are associated with high morbidity. Surgical resection remains the primary treatment for patients with this disease, and offers the best chance for cure. Such surgical procedures, however, carry substantial risks such as worsening of neurological deficit, paralysis and death. New therapeutic avenues for spinal cord tumours are needed, but genetic studies of the molecular mechanisms governing tumourigenesis in the spinal cord are limited by the scarcity of high-quality human tumour samples. Many spinal cord tumours have intracranial counterparts that have been extensively studied, but emerging data show that the tumours are genetically and biologically distinct. The differences between brain and spine tumours make extrapolation of data from one to the other difficult. In this Review, we describe the demographics, genetics and current treatment approaches for the most commonly encountered spinal cord tumours--namely, ependymomas, astrocytomas, haemangioblastomas and meningiomas. We highlight advances in understanding of the biological basis of these lesions, and explain how the latest progress in genetics and beyond are being translated to improve patient care.

Genetic expression profiles of adult and pediatric ependymomas: molecular pathways, prognostic indicators, and therapeutic targets

Ependymomas are tumors that can present within either the intracranial or spinal regions. While 90% of all pediatric ependymomas are intracranial, spinal cord ependymomas are more commonly found in patients 20-40 years old. Treatment for spinal lesions has achieved local control rates up to 100% following gross total resection, while pediatric intracranial tumors have 40-60% mortality. Given the inability to effectively treat ependymomas with current standard practices, researchers have focused their efforts on evaluating chromosomal alterations, genetic expression profiles, epigenetic events, and molecular pathways. While these studies have provided critical insight into the potential mechanisms underlying ependymoma pathogenesis, understanding of the intricate interplay between the various pathways involved in tumor initiation, development, and progression will require deeper investigation. However, several potential prognostic markers and therapeutic targets have been identified, providing key areas of focus for future research. The utilization of unique genetic expression profiles based upon patient age, tumor location, tumor grade, and subtype has revealed a multitude of findings warranting further study. Inspection of various molecular pathways associated with ependymomas may establish the foundation for developing novel therapies capable of achieving significant clinical improvements with individualized regimens specifically designed for personalized treatment strategies.

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.

Malignancies of the spinal cord

The management of intramedullary spinal cord tumors (IMSCT) is primarily concerned with the preservation of existing neurologic function. To this end, clinical scientists are continually seeking tools and techniques to improve the safety and efficacy of tumor resection and control. Further advances in safety and efficacy can be proposed at each phase of management, from pre-operative screening to post-treatment monitoring. Innovations within the areas of molecular biology and genetics, intraoperative imaging and stereotactic radiosurgery offer exciting new options to explore in the management of IMSCT. This section will review the pathophysiology and epidemiology of IMSCT and the state-of-the-art management before delving into the promising new tools and techniques for each phase of management.

Merlin expression in pediatric anaplastic ependymomas real time PCR study

The most common genetic abnormalities of ependymomas involve the chromosome 22 where there is the oncosuppressor gene neurofibromin 2 (NF2). NF2 mutations are primarily encountered in spinal lesions. In contrast, NF2 alterations do not seem related to tumor grade. We studied the NF2 expression through a real-time polymerase chain reaction in 25 pediatric anaplastic ependymomas. We compared the NF2 expression in neoplastic and non-neoplastic tissues, in supratentorial and infratentorial ependymomas and in primitive and non-primitive tumors (recurrences and metastases). Statistical analysis did not prove significant differences. Our results suggest that NF2 alterations are not typical of intracranial anaplastic ependymomas.

Spinal myxopapillary ependymoma with Down syndrome: exploring an unusual association

In patients with Down syndrome, cancers like leukemia and testicular tumors are frequent, but association with central nervous system tumors is rare. Only 1 case of ependymoma has been observed as an incidental autopsy finding in a 19-week-old female fetus. We herein report the second case of ependymoma and the fifth case of spinal tumor occurring in association with Down syndrome. We have also attempted to elucidate the various mechanisms of tumorigenesis implicated in this multiple malformation syndrome. A 13-year-old girl with Down syndrome presented with progressively increasing paraparesis and neurogenic bladder. Magnetic resonance imaging of dorsolumbar spine revealed an intramedullary mass (L1 to L5 level). The patient underwent near total excision of tumor with postoperative histopathology showing myxopapillary ependymoma. Karyotyping showed classic Down syndrome with trisomy 21. Postoperative irradiation (45 Gy in 25 fractions over 5 wk followed by boost up to 55 Gy) was subsequently delivered. One year after the completion of the tumor-directed therapy, the patient is in radiologic complete remission, with improved power in both lower limbs. Association of ependymoma with Down syndrome is a rarity, which at best, can be explained as a chance phenomenon.

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.

Giant cell ependymoma of the thoracic spine: pathology case report

INTRODUCTION AND IMPORTANCE: Spinal ependymomas are slow-growing lesions that comprise the majority of primary spinal cord neoplasms. When surgery is indicated, the extent of tumor removal is most prognostic for long-term survival. Unusual histological subtypes can make intraoperative diagnosis spurious, possibly altering the surgical approach from gross total resection for ependymomas to debulking for high-grade astrocytomas.

CLINICAL PRESENTATION

We describe a 67-year-old woman with a thoracic spine intramedullary giant cell ependymoma. She presented with decreased lower extremity sensation leading to unsteadiness and an eventual fall. A physical examination revealed lower extremity hyperreflexia and ankle clonus, but no clear sensory level. Magnetic resonance imaging demonstrated an intramedullary T1 and T2 hypointense, homogenously enhancing lesion at T8 with extensive cephalad and caudal edema.

INTERVENTION AND TECHNIQUE

A laminectomy at T8 to T9 afforded gross total resection of the lesion that had a clear cleavage plane with normal spinal cord. Intraoperative pathology suggested a high-grade glioblastoma, but final section showed sporadic giant cells with marked pleomorphism, uniform immunofluorescence staining with both glial fibrillary acidic protein and cluster of differentiation 99, and high MIB-1 index. Electron microscopy showed "zipper-like" junctions. There were no detected genomic abnormalities consistent with glioblastoma.

CONCLUSION

We present this first reported case of thoracic spine giant cell ependymoma alongside scant literature yielding 1 case in the cervical spine and 2 cases at the filum terminale. Those cases had benign courses, whereas ours demonstrates a high degree of proliferation, making the malignant potential difficult to assess.

Ependymomas of the adult: molecular biology and treatment

PURPOSE OF REVIEW

To review state of art and relevant advances in the molecular biology and management of ependymomas of the adult.

RECENT FINDINGS

Ependymomas of the adult are uncommon neoplasms of the central nervous system, and may occur either in the brain or the spinal cord. Compared with intracranial ependymomas, spinal ependymomas are less frequent and exhibit a better prognosis. Studies performed on genetic changes in ependymoma provide some insight into the pathogenesis and prognostic markers and yield new therapeutic targets, particularly focused on signal transduction modulators. The majority of studies have shown a major impact of extent of resection; thus, a complete resection must be performed, whenever possible, at first surgery or at reoperation. Involved field radiotherapy is recommended for anaplastic or incompletely resected grade II tumors. Craniospinal irradiation is reserved for metastatic disease. Chemotherapy is not advocated as primary treatment, and is best utilized as salvage treatment for patients failing surgery and radiotherapy.

SUMMARY

Owing to the rarity of the disease, the literature regarding ependymomas in adults is scarce and limited to retrospective series. Thus, the level of evidence regarding therapeutic strategies is low and universally accepted guidelines are lacking. Molecular biology studies suggest some potential new therapeutic targets.

Epidemiology of brain tumors

Gliomas account for more than 70% of all brain tumors, and of these, glioblastoma is the most frequent and malignant histologic type (World Health Organization [WHO] grade IV). There is a tendency toward a higher incidence of gliomas in highly developed, industrialized countries. Some reports indicate that Caucasians have a higher incidence than African or Asian populations. With the exception of pilocytic astrocytomas (WHO grade I), the prognosis of glioma patients is still poor. Fewer than 3% of glioblastoma patients are still alive at 5 years after diagnosis, older age being the most significant and consistent prognostic factor of poorer outcome. Gliomas are components of several inherited tumor syndromes, but the prevalence of these syndromes is very low. Many environmental and lifestyle factors including several occupations, environmental carcinogens, and diet have been reported to be associated with an elevated glioma risk, but the only factor unequivocally associated with an increased risk is therapeutic X-irradiation. In particular, children treated with X-irradiation for acute lymphoblastic leukemia show a significantly elevated risk of developing gliomas and primitive neuroectodermal tumors, often within 10 years after therapy. Significant correlation between G:C --> A:T transitions in the TP53 gene and promoter methylation of the O6 -methylguanine-DNA methyltransferase (MGMT) gene in glio-mas have been reported in several studies, suggesting the possible involvement of O6-methylguanine DNA adducts, which may be produced by exogenous or endogenous alkylating agents in the development of gliomas.

Pediatric gliomas

Pediatric gliomas comprise a clinically, histologically, and molecularly very heterogeneous group of CNS tumors. In addition, these tumors are largely different from their counterparts occurring in adults, although they are histologically indistinguishable and uniformly classified by the current WHO classification for CNS tumors. Pilocytic astrocytoma (WHO grade I), mainly arising in the posterior fossa, is the most common representative in children, whereas glioblastoma multiforme (WHO grade IV) predominates in adults. When radical surgical resection is possible in low-grade gliomas, it will likely cure the patient. If complete surgical resection is not possible, however, for example in brainstem gliomas, which are defined by their anatomic localization rather than by their histological or molecular features, therapeutic options are limited and prognosis is usually poor. Recent genome-wide analyses applying different microarray-based methods to investigate DNA copy-number aberrations, mRNA expression signatures, and methylation patterns have shed some light on the pathways involved in the pathogenesis of pediatric glio-mas. Mitogen-activated protein kinase (MAPK) and PI3K/AKT signaling were identified as prominent oncogenic pathways in astrocytic tumors in several studies, whereas NOTCH signaling was implicated in the pathogenesis of a subset of intracranial ependymomas. Future therapeutic strategies targeting these (and other) pathways or conferring epigenetic modifications in the tumor might contribute to a better treatment outcome of patients with unresectable or disseminated tumors at diagnosis. Consideration of reliable molecular markers for outcome prediction will most likely result in a better stratification of patients into different risk groups with adjusted treatment intensity in the future.

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.

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.

Intramedullary ependymoma associated with Lhermitte–Duclos disease and Cowden syndrome

The authors describe the case of a 45-year-old man with progressive gait ataxia and sensorimotor deficits of the upper and lower extremities. The patient had been diagnosed earlier with Lhermitte-Duclos disease (LDD) in the left cerebellar hemisphere and Cowden syndrome (CS). MR imaging studies revealed an intraspinal tumor at C6-C7. Microsurgical gross total resection of the tumor was achieved. Histolopathological examination revealed an intramedullary ependymoma. Postoperatively, neurological deficits gradually improved. This is the first reported case of ependymoma in a patient with LDD and CD. Coexistence of an intraspinal ependymoma with cerebellar LDD and CS appears to be rare, but can lead to treatment failure if missed.

Ependymoma

Ependymomas are rare tumours of neuroectodermal origin classified as myxopapillary ependymoma and subependymoma (grade I), ependymoma (grade II) and anaplastic ependymoma (grade III). The more common location is infratentorial (60%). Age <40 years and extent of surgery appear related to better prognosis, while the role of other prognostic factors, such as tumour grade and tumour site are equivocal. This emphasizes the role of surgery as the standard treatment. Postoperative radiotherapy is indicated in high-grade ependymomas, and is recommended in low-grade ependymomas after subtotal or incomplete resection (confirmed by postoperative MR). Deferral of radiotherapy until recurrence may be considered on an individual basis for patients with MR confirmation of a radical resection. Recommended dose to involved fields is 45-54 Gy for low-grade (grade II) and 54-60 Gy for high-grade ependymomas (grade III). There is no proof that postoperative chemotherapy improves the outcome. At recurrence, platinum-, nitrosourea- or temozolomide-based chemotherapy can be administered, although there is no evidence of efficacy.

Mutational spectrum of the NF2 gene: a meta-analysis of 12 years of research and diagnostic laboratory findings

The NF2 tumor suppressor gene on chromosome 22 is a member of the protein 4.1 family of cytoskeletal elements. A number of single- and multiple-tumor phenotypes have been linked to alterations of NF2 since its characterization in 1993. We present a meta-analysis of 967 constitutional and somatic NF2 alterations from 93 published reports, along with 59 additional unpublished events identified in our laboratory and 115 alterations identified in clinical samples submitted to the Massachusetts General Hospital (MGH) Neurogenetics DNA Diagnostic Laboratory. In total, these sources defined 1,070 small genetic changes detected primarily by exon scanning, 42 intragenic changes of one whole exon or larger, and 29 whole gene deletions and gross chromosomal rearrangements. Constitutional single-exon events (N=422) were significantly more likely to be nonsense or splice site changes than somatic events (N=533), which favored frameshift changes (chi(2) test; P<0.001). Somatic events also differed markedly between tumors of different pathology, most significantly in the tendency of somatic events in meningiomas to lie within the 5' FERM domain of the transcript (Fisher's exact test; P<0.01 in comparison to schwannomas) with a complete absence of mutations in exons 14 and 15. There was no statistically significant difference in mutation type or exon distribution between published constitutional events and those found by the clinical laboratory. Less than 10% of all published and unpublished small alterations are nontruncating (N=63) and these changes are clustered in exons 2 and 3, suggesting that this region may be especially crucial to tumor suppressor activity in the protein.

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.

Identification of gains on 1q and epidermal growth factor receptor overexpression as independent prognostic markers in intracranial ependymoma

PURPOSE

Pathogenesis of ependymomas is still poorly understood and molecular markers for risk-adapted patient stratification are not available. Our aim was to screen for novel genomic imbalances and prognostic markers in ependymal tumors.

EXPERIMENTAL DESIGN

We analyzed 68 sporadic tumors by matrix-based comparative genomic hybridization using DNA microarrays containing >6,400 genomic DNA fragments. Novel recurrent genomic gains were validated by fluorescence in situ hybridization using a tissue microarray consisting of 170 intracranial ependymomas. Candidate genes were also tested for mRNA expression by quantitative real-time PCR, and protein expression was determined by immunohistochemistry on the tissue microarray.

RESULTS

Chromosomal gain of 1q correlated with pediatric patients (P = 0.004), intracranial ependymomas (P = 0.05), and tumors of grade III (P = 0.002). Gain of 1q21.1-32.1 was associated with tumor recurrence in intracranial ependymomas (P < 0.001). Furthermore, gain of 1q25 as determined by fluorescence in situ hybridization represented an independent prognostic marker for either recurrence-free survival (P < 0.001) or overall survival (P = 0.003). Recurrent gains at 5p15.33 covering hTERT were validated by immunohistochemistry, and elevated protein levels correlated with adverse prognosis (P = 0.01). In addition to frequent gains and high-level amplification of epidermal growth factor receptor (EGFR) at 7p11.2, immunohistochemistry revealed protein overexpression to be correlated with poor prognosis (P = 0.002). EGFR protein status subdivides intracranial grade II ependymomas into two different risk groups (P = 0.03) as shown by multivariate analysis.

CONCLUSIONS

Thus, the states of 1q25 and EGFR represent independent prognostic markers for intracranial ependymomas to identify patient subgroups with different risk profiles in further clinical investigations. Moreover, EGFR might serve as therapeutic target for more specific chemotherapy applications.

Fluorescence in situ hybridization (FISH) in diagnostic and investigative neuropathology

Over the last decade, fluorescence in situ hybridization (FISH) has emerged as a powerful clinical and research tool for the assessment of target DNA dosages within interphase nuclei. Detectable alterations include aneusomies, deletions, gene amplifications, and translocations, with primary advantages to the pathologist including its basis in morphology, its applicability to archival, formalin-fixed paraffin-embedded (FFPE) material, and its similarities to immunohistochemistry. Recent technical advances such as improved hybridization protocols, markedly expanded probe availability resulting from the human genome sequencing initiative, and the advent of high-throughput assays such as gene chip and tissue microarrays have greatly enhanced the applicability of FISH. In our lab, we currently utilize only a limited battery of DNA probes for routine diagnostic purposes, with determination of chromosome 1p and 19q dosage in oligodendroglial neoplasms representing the most common application. However, research applications are numerous and will likely translate into a growing list of clinically useful markers in the near future. In this review, we highlight the advantages and disadvantages of FISH and familiarize the reader with current applications in diagnostic and investigative neuropathology.

The genetic and molecular pathogenesis of NF1 and NF2

Neurofibromatosis types 1 and 2 (NF1 and NF2) are autosomal dominant phakomatoses. The NF1 and NF2 genes encode for neurofibromin and merlin, respectively. These 2 functionally unrelated proteins both act as tumor suppressor genes, possibly through modulation of the RAS/RAC oncogenic pathways. Improved understanding of the mechanisms by which these tumor suppressors act may allow for medical therapies for neurofibromatosis and may offer insights for cancer therapeutics.

No evidence of INI1hSNF5 (SMARCB1) and PARVG point mutations in oligodendroglial neoplasms

Allelic losses of chromosome 22 found in oligodendrogliomas suggest that at least one tumor suppressor gene on chromosome 22 is inactivated during the multistep process of tumorigenesis in this glial tumor. INI1hSNF5 (HUGO symbol: SMARCB1), located at 22q11, encodes a component of the ATP-dependent chromatin remodeling hSWI-SNF complex; it is a tumor suppressor gene that is mutated in several malignant tumors. The PARVG gene, located at 22q13, has been found to exhibit reduced expression in some cancer lines. Both genes are thus candidate tumor suppressors, potentially involved in the pathogenesis of gliomas. We performed mutation analyses of INI1hSNF5 and PARVG in a series of 40 oligodendrogliomas, but only sequence polymorphic variations were identified. Accordingly, INI1hSNF5 and PARVG do not seem to be the tumor suppressor genes involved in oligodendroglioma development and progression.

Alterations of protein 4.1 family members in ependymomas: a study of 84 cases

Ependymomas are common pediatric and adult CNS malignancies with a wide biologic spectrum that is often hard to predict using classic prognostic variables. The molecular pathogenesis is also poorly understood and few reproducible genetic alterations have been identified. The most common genetic alteration has been the loss of the Protein 4.1 family member, NF2, predominantly in spinal ependymomas. In contrast, a pilot study suggested that 4.1B deletions might be more common in intracranial ependymomas. These findings prompted us to study Protein 4.1 family members (NF2, 4.1B, 4.1R, 4.1G) in a larger cohort of 84 ependymomas (51 intracranial and 33 spinal; 11 WHO grade I, 43 grade II, 30 grade III). Fluorescence in situ hybridization was performed using NF2, 4.1B, 4.1R and 4.1G probes and immunohistochemical staining was performed in a subset using merlin, Protein 4.1B and Protein 4.1R antibodies. Additionally, frozen tissue from nine ependymomas (four intracranial and five spinal) was obtained for Western blot analysis for merlin, 4.1B and 4.1R expression. The majority of cases harbored one or more detectable genetic alterations, but we found that 4.1B gene deletions and 4.1R loss of expression were statistically more common in the pediatric vs adult, intracranial vs spinal, and grade III vs grade I/II subsets (P-values of 0.038 to <0.001). Also, 4.1G deletions were seen in 11/27 (41%) patients who either died of disease or had residual/recurrent tumor vs 5/41 patients with no evidence of disease at last follow-up (P=0.009). We conclude that alterations of Protein 4.1 family members are common in ependymal tumors and that specific alterations are associated with distinct clinicopathologic subsets.

Molecular diagnostics in central nervous system tumors

Central nervous system (CNS) neoplasms can be diagnostically challenging, due to remarkably wide ranges in histologic appearance, biologic behavior, and therapeutic approach. Nevertheless, accurate diagnosis is the critical first step in providing optimal patient care. As with other oncology-based specialties, there is a rapidly expanding interest and enthusiasm for identifying and utilizing new biomarkers to enhance the day-to-day practice of surgical neuropathology. In this regard, the field is primed by recent advances in basic research, elucidating the molecular mechanisms of tumorigenesis and progression in the most common adult and pediatric brain tumors. Thus far, few have made the transition into routine clinical practice, the most notable example being 1p and 19q testing in oligodendroglial tumors. However, the field is rapidly evolving and many other biomarkers are likely to emerge as useful ancillary diagnostic, prognostic, or therapeutic aids. The goal of this article is to highlight the most common genetic alterations currently implicated in CNS tumors, focusing most on those that are either already in common use in ancillary molecular diagnostics testing or are likely to become so in the near future.

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.

Epidemiology and etiology of gliomas

Gliomas of astrocytic, oligodendroglial and ependymal origin account for more than 70% of all brain tumors. The most frequent (65%) and most malignant histological type is the glioblastoma. Since the introduction of computerized tomography and magnetic resonance imaging, the incidence rates of brain tumors have been rather stable, with a tendency of higher rates in highly developed, industrialized countries. Some reports indicate that Caucasians have higher incidence than black or Asian populations, but to some extent, this may reflect socio-economic differences and under-ascertainment in some regions, rather than a significant difference in genetic susceptibility. With the exception of pilocytic astrocytomas, the prognosis of glioma patients is still poor. Less than 3% of glioblastoma patients are still alive at 5 years after diagnosis, higher age being the most significant predictor of poor outcome. Brain tumors are a component of several inherited tumor syndromes, but the prevalence of these syndromes is very low. Several occupations, environmental carcinogens, and diet (N-nitroso compounds) have been reported to be associated with an elevated glioma risk, but the only environmental factor unequivocally associated with an increased risk of brain tumors, including gliomas, is therapeutic X-irradiation. In particular, children treated with X-irradiation for acute lymphoblastic leukemia show a significantly elevated risk of developing gliomas and primitive neuroectodermal tumor (PNET), often within 10 years after therapy. TP53 mutations are frequent in low-grade gliomas and secondary glioblastomas derived therefrom. Approximately 60% of mutations are located in the hot spot codons 248 and 273, and the majority of these are G:C-->A:T transitions at CpG sites. TP53 mutations are significantly more frequent in low-grade astrocytomas with promoter methylation of the O(6)-methylguanine-DNA methyltransferase repair gene, suggesting that, in addition to deamination of 5-methylcytosine, exogenous or endogenous alkylation in the O(6) position of guanine may contribute to the formation of these mutations.

9p21 and 13q14 dosages in ependymomas. A clinicopathologic study of 101 cases

Ependymomas are glial neoplasms whose clinical behavior is difficult to predict based on histology alone. Recently, a comparative genomic hybridization study identified frequent chromosome 9p and 13q losses in anaplastic ependymomas, suggesting that p16 and RB alterations may be involved in tumor progression. In order to test this hypothesis further, 101 myxopapillary, conventional, and anaplastic ependymomas (51 spinal and 50 intracranial tumors) were tested for RB and p16 deletions using fluorescence in situ hybridization. Clinical follow-up, ranging from 2 to 198 months (median 46 months), was obtained in 90 cases (91%). RB and p16 deletions were seen in 22 of 92 (24%) and 22 of 89 (25%) informative cases, respectively. Polysomies were more frequent in the grade I and II spinal tumors, consistent with prior reports of increased aneuploidy in such cases. No significant genetic associations were seen with tumor grade, recurrence, or death, suggesting that 9p and 13q deletions do not play a prominent role in the malignant progression of ependymomas, as has been implicated in other glioma subtypes.

Gene expression patterns in ependymomas correlate with tumor location, grade, and patient age

To elucidate the molecular events responsible for tumorigenesis and progression of ependymomas, we analyzed molecular alterations on the gene expression level in a series of newly diagnosed ependymal neoplasms (n = 39). To this aim, tumor RNA was hybridized to microarrays comprising 2600 different genes with relevance to mitosis, cell-cycle control, oncogenesis, or apoptosis. For CLU, IGF-2, and RAF-1, which are apparent candidate genes because they had been previously described to be involved in tumorigenesis of other human malignancies, we found a high expression on the mRNA as well as the protein level. We identified gene expression signatures for the differentiation of tumors with respect to location, grade, and patient age. Spinal ependymomas were characterized by high-expression levels of HOXB5, PLA2G, and CDKN2A and tumors in young patients (< or =16 years of age) by high-expression levels of LDHB and STAM. Notably, we were able to classify supratentorial grade II and III tumors with 100% accuracy, whereas this did not apply for infratentorial ependymomas. The similar gene expression patterns of grade II and III infratentorial malignancies suggest that grade III tumors may develop through a secondary multistep transformation process involving genes that are related to cell proliferation (LDHA, cyclin B, MAT2A) or tumor suppression (PTEN). In summary, our results provide new insight in the biochemical pathways particularly intriguing in the pathomechanism of ependymomas and suggest that this entity comprises molecularly distinct diseases.