Clear cell ependymoma: a clinicopathologic and radiographic analysis of 10 patients

Neuropathologic features of central nervous system hemangioblastoma

Hemangioblastoma is a benign, highly vascularized neoplasm of the central nervous system (CNS). This tumor is associated with loss of function of the VHL gene and demonstrates frequent occurrence in von Hippel-Lindau (VHL) disease. While this entity is designated CNS World Health Organization grade 1, due to its predilection for the cerebellum, brainstem, and spinal cord, it is still an important cause of morbidity and mortality in affected patients. Recognition and accurate diagnosis of hemangioblastoma is essential for the practice of surgical neuropathology. Other CNS neoplasms, including several tumors associated with VHL disease, may present as histologic mimics, making diagnosis challenging. We outline key clinical and radiologic features, pathophysiology, treatment modalities, and prognostic information for hemangioblastoma, and provide a thorough review of the gross, microscopic, immunophenotypic, and molecular features used to guide diagnosis.

Extra-Neural Metastases From Primary Intracranial Ependymomas: A Systematic Review

Background

Primary intracranial ependymomas (IE) are rare brain tumors rarely metastasizing outside the central nervous system. We systematically reviewed the literature on extra-neural metastases from primary IEs.

Methods

PubMed, Scopus, Web-of-Science, and Cochrane were searched following the PRISMA guidelines to include studies of extra-neural metastases from primary IEs. Clinical features, management strategies, and survival were analyzed.

Results

We collected 48 patients from 43 studies. Median age was 13 years (range, 2-65). Primary IEs were frequently located in the parietal (22.9%) and frontal (16.7%) lobes, and mostly treated with resection (95.8%) and/or radiotherapy (62.5%). Most IEs were of grade-III (79.1%), and few of grade-I (6.3%) or grade-II (14.6%). 45 patients experienced intracranial recurrences, mostly treated with resection (86.7%), radiotherapy (60%), and/or chemotherapy (24.4%). Median time-interval from primary IEs was 28 months (range, 0-140). Most extra-neural metastases were diagnosed at imaging (37.5%) or autopsy (35.4%). Extra-neural metastases were multifocal in 38 patients (79.1%), mostly involving cervical or hilar lymph-nodes (66.7%), lung/pleura (47.9%), and/or scalp (29.1%). Surgical resection (31.3%), chemotherapy (31.3%) and locoregional radiotherapy (18.8%) were the most common treatments for extra-neural metastases, but 28 (58.3%) patients were not treated. At last follow-up, 37 patients died with median overall-survivals from primary IEs of 36 months (range, 1-239), and from extra-neural metastases of 3 months (range, 0.1-36). Overall-survival was significantly longer in patients with grade-I and II IEs (P=0.040).

Conclusion

Extra-neural metastases from primary IEs are rare, but mostly occur at later disease stages. Multidisciplinary management strategies should be intended mostly for palliation.

An Insight into Pathophysiological Features and Therapeutic Advances on Ependymoma

Simple Summary

Although biological information and the molecular classification of ependymoma have been studied, the treatment systems for ependymoma are still insufficient. In addition, because the disease occurs infrequently, it is difficult to obtain sufficient data to conduct large-scale or randomized clinical trials. Therefore, this study is intended to emphasize the importance of understanding its pathological characteristics and prognosis as well as developing treatments for ependymoma through multilateral studies.

Abstract

Glial cells comprise the non-sensory parts of the central nervous system as well as the peripheral nervous system. Glial cells, also known as neuroglia, constitute a significant portion of the mammalian nervous system and can be viewed simply as a matrix of neural cells. Despite being the “Nervenkitt” or “glue of the nerves”, they aptly serve multiple roles, including neuron repair, myelin sheath formation, and cerebrospinal fluid circulation. Ependymal cells are one of four kinds of glial cells that exert distinct functions. Tumorigenesis of a glial cell is termed a glioma, and in the case of an ependymal cell, it is called an ependymoma. Among the various gliomas, an ependymoma in children is one of the more challenging brain tumors to cure. Children are afflicted more severely by ependymal tumors than adults. It has appeared from several surveys that ependymoma comprises approximately six to ten percent of all tumors in children. Presently, the surgical removal of the tumor is considered a standard treatment for ependymomas. It has been conspicuously evident that a combination of irradiation therapy and surgery is much more efficacious in treating ependymomas. The main purpose of this review is to present the importance of both a deep understanding and ongoing research into histopathological features and prognoses of ependymomas to ensure that effective diagnostic methods and treatments can be developed.

Intracytoplasmic dot-like inclusions as cytopathologically useful findings of ependymoma: Case report of adolescent supratentorial anaplastic ependymoma with clear cell morphology

Pediatric supratentorial ependymomas often have a clear cell morphology and reveal a RELA fusion. When a clear cell neoplasm is intraoperatively diagnosed, intracytoplasmic dot-like inclusions by cytology are a useful cytopathological feature of ependymoma.

The Effects of Surgery and Adjuvant Therapy on Survival Outcomes in Clear Cell Ependymomas: A Systematic Review and Meta-Analysis of Individual Patient Data

BACKGROUND

The survival outcomes of clear cell ependymomas are poorly understood. This study clarifies the role of surgery and adjuvant therapy when this morphologically distinct tumor is encountered.

METHODS

A systematic search for studies relating to clear cell ependymomas was conducted. Primary outcomes were progression-free survival and overall survival. Prognostic variables were age, sex, tumor consistency, extent of resection, and postoperative adjuvant therapy. Kaplan-Meier survival curves were generated and compared by the log-rank test. Multivariate Cox regression models were constructed, interrogated with Schoenfeld residuals, and used to identify independent prognostic factors.

RESULTS

Of the 384 articles retrieved, 8 articles comprising 77 cases of clear cell ependymoma were included. Five-year overall survival and progression-free survival were 58.1% (95% confidence interval [CI], 46.3%-72.9%) and 46.3% (95% CI, 34.2%-62.8%), respectively. Kaplan-Meier analysis with the log-rank test showed that gross total resection was superior to subtotal resection in prolonging survival (P = 0.047) and delayed time to recurrence (P < 0.01). Multivariate analysis confirmed gross total resection as an independent protective factor against relapse (odds ratio, 0.39; 95% CI, 0.17-0.89; P = 0.03). Age <50 years predicted longer overall survival (odds ratio, 0.16; 95% CI, 0.05-0.49; P < 0.01). Postoperative adjuvant therapy after gross total resection did not affect overall survival (P = 0.98) or progression-free survival (P = 0.93). Adjuvant therapy after subtotal resection favored improved overall survival (P = 0.052).

CONCLUSIONS

Clear cell ependymomas are particularly aggressive in those aged >50 years. Gross total resection remains the cornerstone of management. Postoperative adjuvant therapy is likely to be of survival benefit only after subtotal resection.

Review of ependymomas: assessment of consensus in pathological diagnosis and correlations with genetic profiles and outcome

We focused on histological and immunohistochemical characteristics of ependymoma (EPN) with molecular profiles to develop more reproducible criteria of the diagnosis. Three expert neuropathologists reviewed the pathology of 130 samples from the Japan Pediatric Molecular Neuro-Oncology Group study. Confirmed cases were assessed for histology, surrogate markers, molecular subgrouping, and survival data. We reached a consensus regarding the diagnosis of EPNs in 100% of spinal cord tumors and 93% of posterior fossa (PF) tumors that had been diagnosed as EPNs by local pathologists, whereas we reached a consensus regarding only 77% of the local diagnosis of supratentorial (ST) EPNs. Among the PF-EPNs, most of anaplastic ependymomas (AEPNs) were defined as EPN-A by methylation profiling, which was significantly correlated with the subgroup assignment. Regarding prognosis, the overall survival of patients with PF-EPN was significantly better than that of patients with PF AEPN (p = 0.01). Histologically, all ependymoma, RELA fusion-positive (EPN-RELA) qualified as Grade III. Both L1 cell adhesion molecule and nuclear factor kappaB p65 antibodies showed good sensitivity for detecting EPN-RELA. This study indicated that the expert consensus pathological diagnosis could correlate well with the molecular classifications in EPNs. ST EPNs should be diagnosed more carefully by histological and molecular analyses.

TARBP2-Enhanced Resistance during Tamoxifen Treatment in Breast Cancer

Tamoxifen is the most widely used hormone therapy in estrogen receptor-positive (ER+) breast cancer, which accounts for approximately 70% of all breast cancers. Although patients who receive tamoxifen therapy benefit with respect to an improved overall prognosis, resistance and cancer recurrence still occur and remain important clinical challenges. A recent study identified TAR (HIV-1) RNA binding protein 2 (TARBP2) as an oncogene that promotes breast cancer metastasis. In this study, we showed that TARBP2 is overexpressed in hormone therapy-resistant cells and breast cancer tissues, where it enhances tamoxifen resistance. Tamoxifen-induced TARBP2 expression results in the desensitization of ER+ breast cancer cells. Mechanistically, tamoxifen post-transcriptionally stabilizes TARBP2 protein through the downregulation of Merlin, a TARBP2-interacting protein known to enhance its proteasomal degradation. Tamoxifen-induced TARBP2 further stabilizes SOX2 protein to enhance desensitization of breast cancer cells to tamoxifen, while similar to TARBP2, its induction in cancer cells was also observed in metastatic tumor cells. Our results indicate that the TARBP2-SOX2 pathway is upregulated by tamoxifen-mediated Merlin downregulation, which subsequently induces tamoxifen resistance in ER+ breast cancer.

Prognostic Implications of Histological Clear Cells in High-Grade Intracranial Ependymal Tumors: A Retrospective Analysis from a Tertiary Care Hospital in Pakistan

Background:

Clear cell variant in ependymal tumors is rare. We aimed to compare the features and outcome of the World Health Organization (WHO) Grade 3 ependymal tumors with clear cells to the WHO Grade 3 classic anaplastic ependymoma (AE).

Materials and Methods:

A retrospective cohort study conducted at the Department of Neurosurgery, Aga Khan University, Pakistan, from 2003 to 2013. The medical records and radiology of patients with proven histopathology were reviewed. The analysis was done on SPSS 20.

Results:

Nine cases of clear cell variant and 23 cases of classic AE were found, both of which combined equated to 4% of the total tumor burden in 11 years. The median age of clear cell ependymoma (CCE) and AE were 49 and 37 years, respectively. Presenting symptoms included headache in 66% of CCE and 63% in AE, raised intracranial pressure accounting for 33% of CCE and 54% of AE, dizziness in 22% CCE and 39% AE, while seizures presented equally in both. Supratentorial location was observed in 77% CCE and 48% AE. Both showed hypointense signals on T1-weighted images of magnetic resonance imaging (MRI) while T2-weighted images showed hyperintensity in all cases of CCE but only 80% of AE. MRI characteristics such as the presence of cystic component were found in 89% of CCE and 68% of AE, necrosis in 33% CCE, and 22% AE, hemorrhagic in 22% CCE and 9% AE, and equivalent contrast enhancement. Gross total resection was achieved in 5 (55%) patients of CCE, compared to 6 (26%) patients in AE. Subtotal resection was done in 4 (44%) patients of CCE and 15 (65%) patients of AE. Radiotherapy was given to 5 (55%) patients of CCE and 12 (52%) patients of AE. Recurrence was observed in 77% cases of CCE and 70% of AE, with metastasis in 29% of AE and in only one patient of CCE. Repeat surgery was done in 3 (33%) cases of CCE and 8 (35%) cases of AE. Median progression-free survival and overall survival were 9 and 13 months, respectively, in CCE while 14 and 18 months, respectively, for AE.

Conclusion:

Clear cells in the WHO Grade 3 ependymal tumors are found mainly in a comparatively older adult population with a predilection for supratentorial location and are more aggressive in behavior with poorer outcome than AE.

Extra-Axial and Clear Cell Type Ependymoma, Mimicking a Convexity Meningioma

A 33-year-old woman presented with tingling and paresthesia on left extremity for 2 months. Magnetic resonance imaging revealed that the tumor was iso- and hypo-intensity on T1-weighted image, mixed iso- and high-signal intensity on T2-weighted images and heterogeneously enhanced with rim enhancement. Neither arachnoid cleft nor dural tail was certain but mass was located extra-axially so meningioma was suspected. During operation, tumor wasn't attached to dura at all but arachnoid attachment was seen. Pathologically, clear cell type ependymoma was confirmed. Details of diagnosis and treatment of this tumor is described.

Supratentorial clear cell ependymomas with branching capillaries demonstrate characteristic clinicopathological features and pathological activation of nuclear factor-kappaB signaling

BACKGROUND

Clear cell ependymoma is one of the 4 main histological subtypes of ependymomas defined by the World Health Organization (WHO) classification of tumors of the CNS. DNA methylation profiling can distinguish 4 subgroups of intracranial ependymomas, including supratentorial (ST) ependymomas with Yes-associated protein 1 fusion (YAP1), ST ependymomas with fusion of v-rel avian reticuloendotheliosis viral oncogene homolog A (RELA), posterior fossa ependymomas with balanced genome, and posterior fossa ependymomas with chromosomal instability. In addition, trisomy 19 is a genomic hallmark of ependymomas with rich branching capillaries. However, the relation of histological and molecular subtypes is unclear.

METHODS

Here, we report a series of 20 ependymomas histologically defined by clear cells and branching capillaries.

RESULTS

We observed a strong male predominance. Median age at surgery was 10.4 years (range, 0.8-68.4). All cases were ST, cortical, contrast enhancing, and most often frontal, cystic, and calcified. All tumors qualified as WHO grade III. Some of them exhibited neuronal differentiation. Trisomy 19 was recorded in 13 cases. All samples strongly accumulated p65RelA protein within nuclei, indicating pathological activation of the nuclear factor-kappaB pathway. We identified causative C11ORF95-RELA fusion in almost all cases. Median progression-free survival and overall survival were 11.4 years (95% CI: 5.1-17.8) and not reached, respectively.

CONCLUSION

ST clear cell ependymomas with branching capillaries display characteristic clinicopathological features and are associated with pathological activation of nuclear factor-kappaB signaling, which may indicate a potential novel target for therapy in these patients.

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.

Ependymal tumors with oligodendroglioma like clear cells: Experience from a tertiary care hospital in Pakistan

Background:

Ependymal tumors with oligodendroglioma like clear cells have never been reported from Pakistan. We aimed to see the features and outcomes of this rare entity.

Methods:

It was retrospective cohort conducted at the Department of Neurosurgery, Aga Khan University from 2003 to 2013. The medical records and radiology of patients with proven histopathology were reviewed. Analysis was done on SPSS 20.

Results:

Eleven cases of ependymal tumors with clear cells were found, which equated to 1.5% of the total tumor burden in 11 years. The median age was 49 years. Most common presenting symptom was headache 54.5%. Out of 11 patients, 9 patients had a supratentorial tumor. Magnetic resonance imaging showed hypointense signals on T1 and hyperintense signals on T2-weighted images in all cases. Contrast enhancement was found in 9 patients (77.8%), necrosis and hemorrhage was found in 4 (36%) and 3 (27%) patients, respectively. Immunohistochemistry showed glial fibrillary acidic protein and epithelial membrane antigen positivity in all cases. Ki-67 showed high proliferative index in 6 patients. According to the World Health Organization grading of ependymal tumors, 2 patients had Grade II tumors, and 9 patients had Grade III tumors with clear cells. Gross total resection was achieved in 6 (54.5%) and subtotal resection in 5 patients (45.4%). Recurrence was observed in 9 patients. Six patients died of the disease. Median progression-free survival and overall survival was 8 months and 10 months, respectively.

Conclusion:

Ependymal tumors with clear cells presented more commonly in Grade III lesions and were more aggressive in behavior with poorer outcome compared to similar studies.

Low-grade ependymoma with late metastasis: autopsy case study and literature review

INTRODUCTION

Ependymoma metastasis occurs usually along with local recurrence within 7 years after the initial diagnosis. Later spinal metastasis without local recurrence after the surgical resection has been rarely reported in patients with low-grade ependymomas but not with high-grade ependymomas. Here, we present a case with autopsy revealing late extensive supratentorial metastasis of a fourth ventricle classic WHO grade II ependymoma with no local recurrence or spinal metastasis.

METHODS

A 4-year-old boy underwent a gross total resection (GTR) of the fourth ventricle ependymoma and postoperative radiation therapy. Follow-up MRI showed no recurrence for the next 7 years, but a half year later, extra-axial tumors in the left cerebellopontine angle and right frontal lobe were observed. GTR of the left cerebellopontine angle ependymoma was performed, followed by additional radiation therapy.

RESULTS

He was stable for the following 2 years before MRI revealed growth of the right frontal tumor and new lesions. GTR of the right frontal tumor demonstrated similar pathologic features of ependymoma. Despite chemotherapy, follow-up MRIs exhibited increasing numbers and sizes of supratentorial tumors but no infratentorial or spinal tumors. He died 15 years after the initial diagnosis. Postmortem brain examination confirmed the supratentorial subarachnoid dissemination with multifocal metastases of classic ependymomas but no recurrence at the infratentorial sites.

CONCLUSION

Our case study and literature review suggest that low-grade ependymomas under the current WHO classification have the risk of late metastasis. Therefore, long-term follow-up of the whole neuroaxis is more important for the patients with low-grade ependymomas even in the absence of local recurrence.

Practical molecular pathologic diagnosis of infiltrating gliomas

Recent advances in molecular diagnostics have led to better understanding of glioma tumorigenesis and biology. Numerous glioma biomarkers with diagnostic, prognostic, and predictive value have been identified. Although some of these markers are already part of the routine clinical management of glioma patients, data regarding others are limited and difficult to apply routinely. In addition, multiple methods for molecular subclassification have been proposed either together with or as an alternative to the current morphologic classification and grading scheme. This article reviews the literature regarding glioma biomarkers and offers a few practical suggestions.

1p/19q testing has no significance in the workup of glioblastomas

AIMS

To determine whether testing for isolated 1p or 19q losses, or as a codeletion, has any significance in the workup of glioblastomas (GBMs).

METHODS

Upfront 1p/19q testing by fluorescence in situ hybridization (FISH) and/or polymerase chain reaction (PCR)-based loss of heterozygosity (LOH) was done in 491 gliomas that were histologically diagnosed as GBMs. Outcomes were determined and measured against 1p/19q results.

RESULTS

Twenty-eight showed apparent 1p/19q codeletion by either FISH and/or PCR-based LOH, but only 1/26 showed codeletion by both tests. Over 90% of tumours with apparent codeletion by either FISH or LOH also had 10q LOH and/or EGFR amplification, features inversely related to true whole-arm 1p/19q codeletion. Furthermore, only 1/28 tumours demonstrated an R132H IDH1 mutation. Neither 1p/19q codeletion by FISH nor LOH had an impact on GBM survival. Isolated losses of 1p or 19q also had no impact on survival.

CONCLUSIONS

These data suggest that (i) 1p/19q testing is not useful on gliomas that are histologically GBMs; (ii) codeletion testing should be reserved only for cases with compatible morphology; and (iii) EGFR, 10q, and IDH1 testing can help act as safeguards against a false-positive 1p/19q result.

A systematic review of treatment outcomes in pediatric patients with intracranial ependymomas

OBJECT

Ependymoma is the third most common primary brain tumor in children. Tumors are classified according to the WHO pathological grading system. Prior studies have shown high levels of variability in patient outcomes within and across pathological grades. The authors reviewed the results from the published literature on intracranial ependymomas in children to describe clinical outcomes as they relate to treatment modality, associated mortality, and associated progression-free survival (PFS).

METHODS

A search of English language peer-reviewed articles describing patients 18 years of age or younger with intracranial ependymomas yielded data on 182 patients. These patients had undergone treatment for ependymoma with 1 of 5 modalities: 1) gross-total resection (GTR), 2) GTR as well as external beam radiation therapy (EBRT), 3) subtotal resection (STR), 4) STR as well as EBRT, or 5) radiosurgery. Mortality and outcome data were analyzed for time to tumor progression in patients treated with 1 of these 5 treatment modalities.

RESULTS

Of these 182 patients, 69% had supratentorial ependymomas and 31% presented with infratentorial lesions. Regardless of tumor location or pathological grade, STR was associated with the highest rates of mortality. In contrast, GTR was associated with the lowest rates of mortality, the best overall survival, and the longest PFS. Children with WHO Grade II ependymomas had lower mortality rates when treated more aggressively with GTR. However, patients with WHO Grade III tumors had slightly better survival outcomes after a less aggressive surgical debulking (STR+EBRT) when compared with GTR.

CONCLUSIONS

Mortality, PFS, and overall survival vary in pediatric patients with intracranial ependymomas. Pathological classification, tumor location, and method of treatment play a role in outcomes. In this study, GTR was associated with the best overall and PFS rates. Patients with WHO Grade II tumors had better overall survival after GTR+EBRT and better PFS after GTR alone. Patients with WHO Grade III tumors had better overall survival after STR+EBRT. Patients with infratentorial tumors had improved overall survival compared with those with supratentorial tumors. Progression-free survival was best in those patients with infratentorial tumors following STR+EBRT. Consideration of all of these factors is important when counseling families on treatment options.

Anaplastic oligodendroglioma arising from the brain stem and featuring 1p/19q co-deletion

With respect to localization, oligodendrogliomas are characterized by a marked preponderance of the cerebral hemispheres. Outside these typical sites, any tumor histopathologically reminiscent of oligodendroglioma a priori is likely to represent one of its morphological mimics, including clear cell ependymoma, neurocytoma, pilocytic astrocytoma or glioneuronal tumors. This is particularly relevant as several of the latter are in principle curable by surgery. Among extrahemispherical sites, bona fide oligodendroglioma - as characterized by loss of heterozygosity (LOH) of chromosome arms 1p and 19q - so far has not been documented to occur in the brain stem. Here, we report the case of a 55-year-old female patient with an anaplastic oligodendroglioma (WHO grade III) of the brain stem and cerebellum diagnosed by stereotactic biopsy and featuring combined LOH of 1p and 19q. A morphological peculiarity was a population of interspersed tumor giant cells, a phenomenon that has been referred to as polymorphous oligodendroglioma. Our findings confirm the notion that - although very infrequently - true oligodendrogliomas do occur in the infratentorial compartment.

Central nervous system tumors

Central nervous system tumors are the most frequent malignant tumor in children and the main cause of death in this age group after traffic accidents. The current estimates are that one adult in 2500 is a survivor of a brain tumor that occurred during childhood. These tumors are particularly heterogeneous in terms of histology/biology, treatment, and outcome. They share, however, a high risk of neurological and cognitive morbidity due to the disease itself and the treatment modalities (radiotherapy, surgery, and chemotherapy). Diagnosis is frequently delayed because symptoms are usually nonspecific at the beginning of the evolution. Posterior fossa is the most frequent site and the tumors present most frequently with signs of intracranial hypertension. Supratentorial tumors are more frequent in infants and in adolescents; seizures are not uncommon, especially for benign tumors. When adjuvant treatment is needed, radiotherapy is usually the mainstay apart from some histologies where chemotherapy may be sufficient: low-grade gliomas, desmoplastic medulloblastomas, malignant glial tumors in infants. Multidisciplinary care is best performed in tertiary care centers and should include early rehabilitation programs soon after surgery.

Something old and something new about molecular diagnostics in gliomas

Progress in our understanding of the molecular biology of neoplasms has been driven by remarkable improvements in molecular biology techniques. This has created a rapidly moving field in which even subspecialists struggle to keep abreast of the current literature. Nowhere is this more clearly demonstrated than in neuro-oncology, wherein molecular diagnostics can now wring more clinically useful information out of very small biopsies than ever before. Herein the biologic and practical aspects of four key molecular biomarkers in gliomas are discussed, including two that have been known for some time (1p/19q codeletion and EGFR amplification) as well as two whose relevance was discovered via advanced whole-genome assays (IDH1/2 mutations and BRAF alterations).

Clear cell tumors of the central nervous system: a case-based review

Clear cell tumors of the central nervous system (CNS) encompass a variety of tumor subtypes that are challenging to diagnose given their similar morphologic features. Here, I use a case-based approach to review the clinicopathologic and radiologic features to help guide the general pathologist in the diagnosis of clear cell tumors of the CNS. First, the reader is invited to study 6 images of different CNS tumors with clear cell morphology. Then, each case is expanded in light of clinical and radiologic data and includes a histopathologic description of the tumor. A brief discussion follows with up-to-date diagnostic tools. Finally, I propose an immunohistochemical algorithm to navigate through the complex features that characterize clear cell tumors of the CNS. This review aims to provide a comprehensive approach to diagnosing clear cell neoplasms of the CNS based on improved assessment of the clinicopathologic and radiologic features of each entity.

Ventricular and Extraventricular Ependymal Tumors in 18 Cats

Ependymal tumors are reported rarely in domestic animals. The aims of this study were to examine the clinical and pathologic features of ventricular and extraventricular ependymomas and subependymomas in 18 domestic cats examined between 1978 and 2011. Parameters examined included age, sex, breed, clinical signs, and macroscopic and histopathologic features. The mean age of affected cats was 9 years, 4 months; median age, 8.5 years. There were 8 female and 4 male cats, and 6 cats for which sex was not recorded. Breeds included 10 domestic shorthaired, 2 domestic longhaired, 1 Persian, and 1 Siamese. Clinical signs included altered mentation or behavior, seizures, circling, propulsive gait, generalized discomfort, and loss of condition. The tumors often formed intraventricular masses and usually arose from the lining of the lateral or third ventricles, followed by the fourth ventricle, mesencephalic aqueduct, and spinal cord central canal. Three tumors were extraventricular, forming masses within the cerebrum and adjacent subarachnoid space. Histologically, 15 tumors were classified as variants of ependymomas (classic, papillary, tanycytic, or clear cell) and 3 as subependymomas. Tumors were generally well demarcated; however, 6 ependymomas focally or extensively infiltrated the adjacent neural parenchyma. Characteristic perivascular pseudorosettes were observed in all ependymomas; true rosettes were less common. Some tumors had areas of necrosis, mineralization, cholesterol clefts, and/or hemorrhage. This cohort study of feline ependymal tumors includes subependymoma and primary extraventricular ependymoma, variants not previously described in the veterinary literature but well recognized in humans.

Loss of tumor suppressor Merlin in advanced breast cancer is due to post-translational regulation

Unlike malignancies of the nervous system, there have been no mutations identified in Merlin in breast cancer. As such, the role of the tumor suppressor, Merlin, has not been investigated in breast cancer. We assessed Merlin expression in breast cancer tissues by immunohistochemistry and by real-time PCR. The expression of Merlin protein (assessed immunohistochemically) was significantly decreased in breast cancer tissues (although the transcript levels were comparable) simultaneous with increased expression of the tumor-promoting protein, osteopontin (OPN). We further demonstrate that the loss of Merlin in breast cancer is brought about, in part, due to OPN-initiated Akt-mediated phosphorylation of Merlin leading to its proteasomal degradation. Restoring expression of Merlin resulted in reduced malignant attributes of breast cancer, characterized by reduced invasion, migration, motility, and impeded tumor (xenograft) growth in immunocompromised mice. The possibility of developing a model using the relationship between OPN and Merlin was tested with a logistic regression model applied to immunohistochemistry data. This identified consistent loss of immunohistochemical expression of Merlin in breast tumor tissues. Thus, we demonstrate for the first time a role for Merlin in impeding breast malignancy, identify a novel mechanism for the loss of Merlin protein in breast cancer, and have developed a discriminatory model using Merlin and OPN expression in breast tumor tissues.

Supratentorial clear cell ependymoma mimicking oligodendroglioma : case report and review of the literature

Clear cell ependymomas (CCEs) are rare variants of ependymomas. Tumors show anaplastic histological features and behave as an aggressive manner. CCEs have a predilection for extraneural metastases and early recurrence, and they demonstrate characteristic radiographic features. These tumors should be radiologically and pathologically differentiated from oligodendrogliomas. On microscopic examination, CCEs are composed of sheets of cells and resemble oligodendroglioma. However, upon closer examination, the nature of CCEs can be detected earlier, resulting in prompt treatment of the tumor. Although we report only one case, we emphasize the importance of early diagnosis and treatment. Future description of more cases of these rare cancers is necessary to aid in their diagnosis and treatment.

Vascular patterns of brain tumors

Multiple vascular patterns are presented in tumors of the central nervous system (CNS), including microvascular hyperplasia, branching capillaries, numerous capillaries without definite pattern, hyalinized vessels, and angiomatous area. These vascular patterns play important roles in pathological diagnosis of brain tumors. Because of insufficient recognition of the significance of the various vascular patterns, only a few of them have been applied in pathological diagnosis, leading to missed diagnosis and diagnostic errors. Microvascular hyperplasia can present in multiple brain tumors but display different diagnostic values. Otherwise, varied brain tumors characterized by branching capillaries or vascular pattern mimicking branching capillaries should be given careful consideration. Therefore, a familiarity of these tumors and their vascular pattern is essential for general pathologists. This study reviews the value of various kinds of vascular patterns for pathological diagnosis of brain tumors, constructs a framework for better understanding, and provides a novel perspective for general pathologists.

Intraparenchymal clear cell ependymoma

Clear cell ependymoma (CCE) is an uncommon variant of ependymoma having a predilection for the supratentorial region. Histologically, it bears an uncanny resemblance to oligodendroglioma, central neurocytoma, hemangioblastoma and metastasis from clear cell carcinoma. Here, we report a rare case of clear cell ependymoma in a 45-year-old male, which histomorphologically resembled anaplastic oligodendroglioma on intraoperative smears, frozen section and routine light microscopy. Immunohistochemistry, however, helped to arrive at the correct diagnosis. Unlike other clear cell tumors of the brain parenchyma, CCE is known to follow an aggressive course and, hence, obtaining a correct diagnosis is imperative since it has a direct therapeutic and prognostic connotation.

Glycogen-rich pleomorphic xanthoastrocytoma with clear-cell features: confirmatory report of a rare variant with implications for differential diagnosis

Central nervous system space-occupying lesions with clear-cell features encompass a nosologically heterogeneous array, ranging from reactive histiocytic proliferations to neuroepithelial or meningothelial neoplasms of various grades and to metastases. In the face of such differential diagnostic breadth, recognizing cytoplasmic lucency as part of the morphological spectrum of some low grade gliomas will directly have an impact on patient care. We describe a prevailing clear-cell change in an epileptogenic left temporal pleomorphic xanthoastrocytoma surgically resected from a 36-year-old man. Mostly subarachnoid and focally calcified, the tumor was composed of fascicles of moderately atypical spindle cells with optically lucent cytoplasm that tended to intermingle with a desmoplastic mesh of reticulin fibers. Immunohistochemically, coexpression of S100 protein, vimentin, GFAP, and CD34 was noted. Conversely, neither punctate staining for EMA nor positivity for CD68 was seen. Mitotic activity was absent, and the MIB1 labeling index was 2-3% on average. Diastase-sensitive PAS-positive granula indicated clear-cell change to proceed from glycogen storage. Electron microscopy showed tumor cell cytoplasm to be largely obliterated by non-lysosomal-bound pools of glycogen, while hardly any fat vacuole was encountered. Neither ependymal-derived organelles nor annular lamellae suggesting oligodendroglial differentiation were detected. The latter differential diagnosis was further invalidated by lack of codeletion of chromosomal regions 1p36 and 19q13 on molecular genetic testing. By significantly interfering with pattern recognition as an implicit approach in histopathology, clear-cell change in pleomorphic xanthoastrocytoma is likely to suspend its status as a "classic", and to prompt more deductive differential diagnostic strategies to exclude look-alikes, especially clear-cell ependymoma and oligodendroglioma.

Gone FISHing: clinical lessons learned in brain tumor molecular diagnostics over the last decade

Fluorescence in situ hybridization (FISH) is a powerful, morphology-based technique to assess targeted copy number alterations or gene rearrangements in formalin-fixed, paraffin-embedded tissues. It has a wide range of applications in routine clinical contexts to identify cytogenetic biomarkers for more accurate diagnosis and prognostic stratification. This review and update addresses practical uses of FISH as a molecular diagnostic tool in the setting of brain tumors, including gliomas, embryonal neoplasms, ependymomas and meningiomas, focusing on key genetic biomarkers, such as 1p19q codeletion, epidermal growth factor receptor (EGFR) gene amplification, BRAF rearrangement and many others. Also discussed are lessons learned over the past decade, including common technical issues to consider when implementing and interpreting FISH results in a clinical setting.

The use of immunohistochemistry in the diagnosis of metastatic clear cell renal cell carcinoma: a review of PAX-8, PAX-2, hKIM-1, RCCma, and CD10

The diagnosis of metastatic clear cell renal cell carcinoma may be difficult in some cases, particularly in the small image-guided biopsies that are becoming more common. As targeted therapies for renal cell carcinoma are now standard treatment, the recognition and diagnosis of renal cell carcinoma has become even more critical. Many adjunctive immunohistochemical markers of renal epithelial lineage such as CD10 and RCCma have been proposed as aids in the diagnosis of metastatic renal cell carcinoma, but low specificities often limit their utility. More recently described markers (PAX-2, PAX-8, human kidney injury molecule-1, hepatocyte nuclear factor-1-β, and carbonic anhydrase-IX) offer the potential for greater sensitivity and specificity in this diagnostic setting; however, knowledge of their expected staining in other neoplasms and tissues is critical for appropriate use. In this review, we discuss the most widely used immunohistochemical markers of renal lineage with an emphasis on their sensitivity and specificity for metastatic clear cell renal cell carcinoma. Subsequently, we present a variety of organ-specific differential diagnostic scenarios in which metastatic clear cell renal cell carcinoma might be considered and we propose immunopanels for use in each situation.

Intraoperative imprint cytology of central neurocytoma: The great oligodendroglioma mimicker

Intraoperative cytologic evaluation of brain tumors has been used either to render a preliminary interpretation or more often as a complement to frozen section examination. Central neurocytoma is a intraventricular neoplasm, typically located in the region of the foramen of Monro, affecting mostly young to middle age adults. Histologically, central neurocytomas are characterized by monotonous cells with round nuclei and neuronal differentiation within a rich capillary network. Their distinction during intraoperative consultations from oligodendroglioma, ependymoma (mainly clear cell ependymoma), and non-Hodgkin lymphoma can be a diagnostic challenge. We report a case of a 19-year-old female with an intraventricular tumor where imprint cytology preparations were crucial for the intraoperative diagnosis of central neurocytoma. Imprint cytology preparations show a round cell neoplasm associated with neuropil clumps and short straight capillaries admixed with tumor cell clusters. To the best of our knowledge, only a few cases describing the cytologic findings of central neurocytomas have been reported in the medical literature. The differential diagnosis, tissue correlation, clinical-radiologic features, and ancillary studies are discussed.

Differentiation of clear cell ependymoma of the cerebellum from hemangioblastoma by thallium-201 single photon emission computed tomography-case report-

A 57-year-old man suffered from dizziness for about one year and truncal ataxia for about one month. Magnetic resonance imaging demonstrated a cystic tumor with a homogeneously enhanced mural nodule located in the cerebellar vermis. Computed tomography angiography revealed a hypervascular nodule. These findings were compatible with hemangioblastoma. Thallium-201 single photon emission computed tomography ((201)Tl-SPECT) showed moderately high uptake in the early phase and moderately high retention in the delayed phase, whereas hemangioblastoma shows almost no retention in the delayed phase. The patient underwent total removal of the tumor. The histological diagnosis was clear cell ependymoma (CCE). CCE is a rare subtype of ependymoma, which resembles hemangioblastoma in histological and neuroimaging findings, but is considerably more aggressive. (201)Tl-SPECT can provide useful information for the preoperative differential diagnosis of infratentorial CCE and hemangioblastoma.

Clear-cell Ependymoma of the Cerebellum: A Case Report

A case of clear-cell ependymoma occurring in the cerebellum of a 3-year-old girl is reported. Light-microscopically, the tumor consisted mainly of clear cells with a perinuclear halo and showed some vague perivascular pseudorosettes, not true rosettes. In addition, the histological features of anaplasia, characterized by increased mitosis and focal pseudopalisading necrosis, were also observed. Immunohistochemically, the tumor cells were focally positive for glial fibrillary acidic protein and weakly positive for epithelial membrane antigen. Ultrastructurally, the intermediate junctions and rudimentary cilia confirmed the ependymal differentiation. Fifteen cases of infratentorial clear-cell ependymoma have been reported to date, and this case is the second childhood tumor among them, to the best of the authors' knowledge.

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.

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.

Clear cell ependymoma of the temporal lobe in a child: a case report

A 12-year-old boy with a left temporal tumor diagnosed as clear cell ependymoma (CCE) was reported. CCE is an uncommon central variant of ependymomas with a predilection for the supratentorial region in children. Brain tumors with a honeycomb pattern with clear cells having round nuclei and perinuclear halos could pose a problem in the differential diagnosis with the other tumors with clear cells. There were 41 reported cases of CCE in the literature. In 61% of these cases, tumors were located in the supratentorial region, and in the others in the posterior fossa and spinal cord. However, there was none located in the temporal lobe except in the case presented here.

Intramedullary clear cell ependymoma in the thoracic spinal cord: a case with its crush smear and ultrastructural findings

Clear cell ependymoma was included in the World Health Organization classification of the nervous system in 1993, and all the reported cases, except for two in the spinal cord, were located in the brain, mainly in the supratentorial compartment. Astrocytomas outnumber ependymomas in the spinal cord, and the two entities partly share cytologic findings such as long, bipolar glial processes and oval to round nuclei resembling those seen in pilocytic astrocytoma. Here, we report the first Korean case of intramedullary clear cell ependymoma of the spinal cord, which is the third case situated in the spinal cord in the literature. The crush smear revealed round-to-oval nuclei with occasional nuclear eosinophilic inclusion and rare nuclear grooves. Cytoplasm had fluffy eosinophilic glial processes, and acellular fibrillary zone. On hematoxylin-eosin stain, oval to round tumor cells had large central nuclei with indistinct nucleoli and a moderate amount of clear cytoplasm, i.e. perinuclear halo, mimicking oligodendroglioma. Perivascular pseudorosettes and ependymal clefts were rarely found. In retrospect, perinuclear halo was absent on crush smears. Ultrastructurally, they had extensive surface microvilli and edematous cytoplasm filled with abundant glial filaments and microlumens with or without microvilli. Intercellular long cell junctions of the zipper-like zonula adherens type were found.

Trisomy 19 ependymoma, a newly recognized genetico-histological association, including clear cell ependymoma

Ependymal tumors constitute a clinicopathologically heterogeneous group of brain tumors. They vary in regard to their age at first symptom, localization, morphology and prognosis. Genetic data also suggests heterogeneity. We define a newly recognized subset of ependymal tumors, the trisomy 19 ependymoma. Histologically, they are compact lesions characterized by a rich branched capillary network amongst which tumoral cells are regularly distributed. When containing clear cells they are called clear cell ependymoma. Most trisomy 19 ependymomas are supratentorial WHO grade III tumors of the young. Genetically, they are associated with trisomy 19, and frequently with a deletion of 13q21.31-31.2, three copies of 11q13.3-13.4, and/or deletions on chromosome 9. These altered chromosomal regions are indicative of genes and pathways involved in trisomy 19 ependymoma tumorigenesis. Recognition of this genetico-histological entity allows better understanding and dissection of ependymal tumors.

Frontotemporal clear cell meningioma. Report of 3 cases

Clear cell meningioma (CCM) is an uncommon meningioma. Some cases have been reported, and the localization of most of them is the spinal region. We present 3 cases of CCMs in the frontotemporal lobes. All cases were postmenopausal women with a history of arterial hypertension and uterine leiomyomatosis. The radiologic appearance in 2 cases was similar to that of dural hematomas, and in 1 case, the imaging study was consistent with the diagnosis of meningioma. On histologic examination, there were sheets of glycogenated polygonal cells with abundant clear cytoplasm and round, uniform, bland appearing nuclei. Numerous hyalinized blood vessels and collagenous stroma with fibrillary appearance were present in 2 cases. They were immunoreactive to epithelial membrane antigen, epithelial cell adhesion molecule, and progesterone receptors. However, 2 cases showed weak and focal reaction to Her-2/neu. In our knowledge, some cases of CCMs have been reported and no immunoexpression has been noted with those markers used. These cases illustrate a rare variant of meningioma in the frontotemporal lobes and their immunohistochemical profiles. Differential diagnosis is discussed.

Imaging features of clear-cell ependymoma of the spinal cord

A 10-year-old girl presented with increasing lower back pain without gait or sphincter disturbances. MRI demonstrated a large, intramedullary tumor at the level of the conus. The imaging findings were unlike those of a classic ependymoma or astrocytoma. Histopathologic examination demonstrated clear-cell ependymoma, which is a distinct entity. We found three cases of clear-cell ependymoma of the spinal cord reported in the literature. Clear-cell ependymoma of the spinal cord can be resected completely and needs to be recognized for its imaging features, benign course and favorable prognosis.

The role of electron microscopy in the diagnosis of surgical pathology in the central nervous system

Electron microscopy has played an important role in the diagnosis of surgical pathology and the establishment of new tumor entities and variants in the central nervous system. However, the use of ultrastructural analysis of brain tumors has decreased with the advent of immunohistochemistry. I present here my personal experiences and perspective on the role of electron microscopy in surgical neuropathology.

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.

Shh pathway activity is down-regulated in cultured medulloblastoma cells: implications for preclinical studies

Gene expression profiling indicates that the Sonic Hedgehog (Shh) pathway is active in approximately 30% of human medulloblastomas, suggesting that it could provide a useful therapeutic target. Previously, we showed that spontaneous medulloblastomas in Ptc1(+/-)p53-/- mice could be eradicated by treatment with a small-molecule inhibitor (HhAntag) of Smoothened (Smo). Here, we compared the responses of mouse medulloblastoma cells propagated in flank allografts, either directly or after culture in vitro, to HhAntag. We found that Shh pathway activity was suppressed in medulloblastoma cells cultured in vitro and it was not restored when these cells were transplanted into the flank of nude mice. The growth of these transplanted tumor cells was not inhibited by treatment of mice with doses of HhAntag that completely suppressed Smo activity. Interestingly, tumor cells transplanted directly into the flank maintained Smo activity and were sensitive to treatment with HhAntag. These findings indicate that propagation of tumor cells in culture inhibits Smo activity in a way that cannot be reversed by transplantation in vivo, and they raise concerns about the use of cultured tumor cells to test the efficacy of Shh pathway inhibitors as anticancer therapies.

Extraneural metastasis in intracranial tumors in children: the experience of a single center

Our aim is to evaluate the clinical features and outcomes of children with primary central nervous system (CNS) tumors who develop extraneural metastasis (ENM). We retrospectively evaluated children diagnosed with primary CNS tumors treated at our institution between 1972 and 2004. Of 1,011 patients these tumors, 10 (0.98%) developed ENM. The histopathologic diagnosis was medulloblastoma in six patients, germ cell tumors in two patients, and ependymoma and atypical teratoid rhabdoid tumor (ATRT) in one patient each. In six patients, the primary tumor was located in the posterior fossa; it had a supratentorial location in the patient with ATRT, was located in the sellar and suprasellar region in the two patients with germ cell tumors, and was found in the distal spinal cord in the patient with an ependymoma. In two patients ENM was detected at the time of diagnosis. In other patients ENM developed between 9 and 25 months after diagnosis. Metastatic sites included bone, bone marrow, lung, cervical lymph nodes, liver, and paranasal sinuses. Of the 10 patients who developed ENM, 8 died of their disease 0.27-16.2 months (median, 2.60 months) after it was detected. One patient with dysgerminoma is alive, without disease, 117.80 months after diagnosis of the ENM. One patient with germ cell tumor is alive with disease 11.3 months after diagnosis of the ENM. Systemic metastasis to other extraneural sites is extremely rare in children with intracranial tumors. In our series the rate of ENM is 0.98%. The liver and lung are the most common site for metastasis, followed by the bone and bone marrow. The outcome is poor in patients with CNS tumors with ENM.

STAT3 is activated in a subset of the Ewing sarcoma family of tumours

STAT3 is an oncogene that regulates critical cellular processes and whose constitutive activation has been demonstrated to correlate with biological and clinical features in many types of human malignancy. In this study, STAT3 activation was assessed in the Ewing sarcoma family of tumours (ESFT), which is characterized by fusion of the EWS gene with one of several Ets transcription factors, most commonly EWS-FLI1. STAT3 activation was assessed by immunohistochemistry using a monoclonal antibody specific for tyrosine(705)-phosphorylated STAT3 (pSTAT3(tyr705)) and a tissue microarray containing 49 paraffin-embedded ESFT tumours with known EWS translocations. Twenty-five (51%) tumours were pSTAT3(tyr705)-positive, as defined by more than 10% tumour cell immunostaining. STAT3 activation correlated with tumour site at presentation, with pSTAT3(tyr705)-negative ESFT involving axial sites predominantly (p = 0.008). Notably, among 31 patients who presented with localized disease, high-level STAT3 activation correlated with better overall survival (p = 0.02). STAT3 activation was not directly related to EWS-FLI1 expression, since EWS-FLI1 transfection did not result in STAT3 activation. Furthermore, detailed molecular analysis indicated that STAT3 activation may be seen with EWS-FLI1 or EWS-ERG and appears to be independent of EWS-FLI1 fusion type. In conclusion, STAT3 activation is present in approximately half of ESFT and correlates with clinical features. The role of STAT3 activation in ESFT pathogenesis seems to be independent of the type of EWS/Ets translocation.

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.