Implications of DNA Methylation Classification in Diagnosing Ependymoma

BACKGROUND

Ependymoma is a central nervous system (CNS) tumor that arises from the ependymal cells of the brain's ventricles and spinal cord. The histopathology of ependymomas is indistinguishable regardless of the site of origin, and the prognosis varies. Recent studies have revealed that the development site and prognosis reflect the genetic background. In this study, we used genome-wide DNA methylation array analysis to investigate the epigenetic background of ependymomas from different locations treated at our hospital.

METHODS

Four cases of posterior fossa ependymomas and 11 cases of spinal ependymomas were analyzed.

RESULTS

DNA methylation profiling using the DKFZ methylation classifier showed that the methylation diagnoses of the 2 cases differed from the histopathological diagnoses, and 2 cases could not be classified. Tumor that spread from the brain to the spinal cord was molecularly distinguishable from other primary spinal tumors.

CONCLUSIONS

Although adding DNA methylation classification to conventional diagnostic methods may be helpful, the diagnosis in some cases remains undetermined. This may affect decision-making regarding treatment strategies and follow-up. Further investigations are required to improve the diagnostic accuracy of these tumors.

TERT promoter mutation and chromosome 6 loss define a high-risk subtype of ependymoma evolving from posterior fossa subependymoma

Subependymomas are benign tumors characteristically encountered in the posterior fossa of adults that show distinct epigenetic profiles assigned to the molecular group “subependymoma, posterior fossa” (PFSE) of the recently established DNA methylation-based classification of central nervous system tumors. In contrast, most posterior fossa ependymomas exhibit a more aggressive biological behavior and are allocated to the molecular subgroups PFA or PFB. A subset of ependymomas shows epigenetic similarities with subependymomas, but the precise biology of these tumors and their potential relationships remain unknown. We therefore set out to characterize epigenetic traits, mutational profiles, and clinical outcomes of 50 posterior fossa ependymal tumors of the PFSE group. On histo-morphology, these tumors comprised 12 ependymomas, 14 subependymomas and 24 tumors with mixed ependymoma–subependymoma morphology. Mixed ependymoma–subependymoma tumors varied in their extent of ependymoma differentiation (2–95%) but consistently exhibited global epigenetic profiles of the PFSE group. Selective methylome analysis of microdissected tumor components revealed CpG signatures in mixed tumors that coalesce with their pure counterparts. Loss of chr6 (20/50 cases), as well as TERT mutations (21/50 cases), were frequent events enriched in tumors with pure ependymoma morphology (p < 0.001) and confined to areas with ependymoma differentiation in mixed tumors. Clinically, pure ependymoma phenotype, chr6 loss, and TERT mutations were associated with shorter progression-free survival (each p < 0.001). In conclusion, our results suggest that subependymomas may acquire genetic and epigenetic changes throughout tumor evolution giving rise to subclones with ependymoma morphology (resulting in mixed tumors) that eventually overpopulate the subependymoma component (pure PFSE ependymomas).

Automatic Machine Learning to Differentiate Pediatric Posterior Fossa Tumors on Routine MR Imaging

BACKGROUND AND PURPOSE

Differentiating the types of pediatric posterior fossa tumors on routine imaging may help in preoperative evaluation and guide surgical resection planning. However, qualitative radiologic MR imaging review has limited performance. This study aimed to compare different machine learning approaches to classify pediatric posterior fossa tumors on routine MR imaging.

MATERIALS AND METHODS

This retrospective study included preoperative MR imaging of 288 patients with pediatric posterior fossa tumors, including medulloblastoma (n = 111), ependymoma (n = 70), and pilocytic astrocytoma (n = 107). Radiomics features were extracted from T2-weighted images, contrast-enhanced T1-weighted images, and ADC maps. Models generated by standard manual optimization by a machine learning expert were compared with automatic machine learning via the Tree-Based Pipeline Optimization Tool for performance evaluation.

RESULTS

For 3-way classification, the radiomics model by automatic machine learning with the Tree-Based Pipeline Optimization Tool achieved a test micro-averaged area under the curve of 0.91 with an accuracy of 0.83, while the most optimized model based on the feature-selection method χ2 score and the Generalized Linear Model classifier achieved a test micro-averaged area under the curve of 0.92 with an accuracy of 0.74. Tree-Based Pipeline Optimization Tool models achieved significantly higher accuracy than average qualitative expert MR imaging review (0.83 versus 0.54, P < .001). For binary classification, Tree-Based Pipeline Optimization Tool models achieved an area under the curve of 0.94 with an accuracy of 0.85 for medulloblastoma versus nonmedulloblastoma, an area under the curve of 0.84 with an accuracy of 0.80 for ependymoma versus nonependymoma, and an area under the curve of 0.94 with an accuracy of 0.88 for pilocytic astrocytoma versus non-pilocytic astrocytoma.

CONCLUSIONS

Automatic machine learning based on routine MR imaging classified pediatric posterior fossa tumors with high accuracy compared with manual expert pipeline optimization and qualitative expert MR imaging review.

Molecular heterogeneity and CXorf67 alterations in posterior fossa group A (PFA) ependymomas

Of nine ependymoma molecular groups detected by DNA methylation profiling, the posterior fossa type A (PFA) is most prevalent. We used DNA methylation profiling to look for further molecular heterogeneity among 675 PFA ependymomas. Two major subgroups, PFA-1 and PFA-2, and nine minor subtypes were discovered. Transcriptome profiling suggested a distinct histogenesis for PFA-1 and PFA-2, but their clinical parameters were similar. In contrast, PFA subtypes differed with respect to age at diagnosis, gender ratio, outcome, and frequencies of genetic alterations. One subtype, PFA-1c, was enriched for 1q gain and had a relatively poor outcome, while patients with PFA-2c ependymomas showed an overall survival at 5 years of > 90%. Unlike other ependymomas, PFA-2c tumors express high levels of OTX2, a potential biomarker for this ependymoma subtype with a good prognosis. We also discovered recurrent mutations among PFA ependymomas. H3 K27M mutations were present in 4.2%, occurring only in PFA-1 tumors, and missense mutations in an uncharacterized gene, CXorf67, were found in 9.4% of PFA ependymomas, but not in other groups. We detected high levels of wildtype or mutant CXorf67 expression in all PFA subtypes except PFA-1f, which is enriched for H3 K27M mutations. PFA ependymomas are characterized by lack of H3 K27 trimethylation (H3 K27-me3), and we tested the hypothesis that CXorf67 binds to PRC2 and can modulate levels of H3 K27-me3. Immunoprecipitation/mass spectrometry detected EZH2, SUZ12, and EED, core components of the PRC2 complex, bound to CXorf67 in the Daoy cell line, which shows high levels of CXorf67 and no expression of H3 K27-me3. Enforced reduction of CXorf67 in Daoy cells restored H3 K27-me3 levels, while enforced expression of CXorf67 in HEK293T and neural stem cells reduced H3 K27-me3 levels. Our data suggest that heterogeneity among PFA ependymomas could have clinicopathologic utility and that CXorf67 may have a functional role in these tumors.

Posterior fossa ependymomas: new radiological classification with surgical correlation

PURPOSE

The key determinant of long-term outcome in infratentorial ependymomas remains the extent of surgical resection. We describe a new radiological classification system which is validated against surgical findings and correlated with risk of post-operative residual tumour.

METHODS

Twenty-five consecutive patients (12 females, mean age 4.9 years, range 0.5-17 years) with infratentorial ependymomas were studied. Lesions were classified on pre-operative MRI according to the pattern of extension, brainstem displacement and involvement of the obex, as lateral-type or midfloor-type tumours. Twenty-one operative records were reviewed with respect to the microanatomical tumour origin by a paediatric neurosurgeon, blinded to MRI findings. Follow-up imaging studies were evaluated for residual tumour.

RESULTS

There were 15 cases of midfloor-type tumour (anterior displacement of brainstem, infiltration of obex) and 10 cases of lateral-type tumour (lateral displacement of brainstem, obex free of tumour). Extension into prepontine or cerebellopontine cisterns was more common in lateral-type tumours. Agreement between the radiological classification and tumour origin, as defined by operative records, was seen in 18 out of 20 cases. Risk of residual tumour in lateral-type tumours was more than twice that of midfloor-type tumours (80% vs. 33%, p=0.04). Risk of tumour residual was also significantly higher when vessel encasement or prepontine extension was observed.

CONCLUSIONS

Infratentorial ependymomas can be pre-operatively classified as lateral-type or midfloor-type tumours. This correlates well with operative findings. Lateral-type tumours have significantly increased risk of residual tumour compared to midfloor- type tumours and this may influence intensity of imaging surveillance.

Central nervous system atypical teratoid rhabdoid tumor: experience at the National Institute of Pediatrics, Mexico City

OBJECTIVE

The purpose of this study is to present our experience with ten cases of Central nervous system atypical teratoid rhabdoid tumor (CNS/ATRT).

PATIENTS AND METHODS

A series of ten patients with CNS/ATRT, were diagnosed and treated between 1990 and 2005, at the National Institute of Pediatrics, in Mexico City. The gender, age of presentation, clinical features, tumor localization, imaging studies, grade of tumor resection, complications, adjuvant therapy, and survival are presented.

RESULTS

The mean age at diagnosis was 37.8 months, seven cases were male, and their average clinical course was 1.3 months. The more common clinical presentation was intracranial hypertension with cranial nerve deficits; location was infratentorial in four patients and supratentorial in six. Hydrocephalus was present as the most common complication (seven cases). In nine patients, the grade of resection was total or subtotal. In one case, it was only possible to perform a biopsy. There were two cases with longer survival (9 and 16 months), and their tumors were resected in total or subtotal manner and received adjuvant therapy (radiotherapy and chemotherapy).

CONCLUSIONS

Preliminary results, show that in older children, we can improve their survival with the subtotal or total resection of the tumor and the addition of chemotherapy and radiotherapy.

Posterior petrous face meningiomas: an algorithm for surgical management

OBJECTIVE

The objective of the present study was to report our surgical strategy in the management of 81 patients with posterior petrous face meningiomas.

STUDY DESIGN

Retrospective study.

SETTING

This study was conducted at a quaternary private otology and cranial base center.

PATIENTS

Of 139 patients with posterior fossa meningioma, 81 occurred on the posterior petrous face of the temporal bone and were the object of this study.

INTERVENTIONS

Thirty-one patients were approached by the enlarged translabyrinthine approach. The enlarged translabyrinthine approach with transapical extension Type II was performedin 29 patients. The combined retrosigmoid-retrolabyrinthine approach was chosen in 8 cases. The modified transcochlear approach Type A with permanent posterior transposition of the facial nerve (FN) was performed in 6 patients. Two patients underwent a retrolabyrinthine subtemporal transapical approach. One patient underwent a transpetrous middle cranial fossa approach. Four patients with intracanalicular meningiomas were operated on through the enlarged middle cranial fossa approach.

RESULTS

Total removal of the tumor (Simpson Grades I and II) was achieved in most patients (92.5%). The FN was anatomically preserved in 79 of the 81 (97.5%) patients. Five patients had less than 1 year follow-up, and 2 patients were lost to follow-up and were excluded in evaluation of the final FN outcome. At 1-year follow-up, 46 patients (63%) had Grade I to II, 19 (26%) had Grade III, 4 (5.4%) had Grade IV, 1 (1.3%) had Grade V, and 3 (4.1%) had Grade VI. Hearing-preserving surgery was attempted in 15 patients (18.5%) with preoperative serviceable hearing. Of these 15 patients, 11 had their hearing preserved at the same preoperative level, and 4 experienced postoperative deafness. Postoperatively, a new deficit of 1 or more of the lower cranial nerves was recorded in 3 patients. One patient experienced subcutaneous cerebrospinal fluid collection that required surgical management.

CONCLUSION

Total tumor removal (Simpson Grades I-II) remains our treatment of choice and takes priority over hearing preservation. Subtotal resection is indicated for older and debilitated patients with giant lesions to relieve the tumor compression on the cerebellum and brainstem. Subtotal removal is also preferred in the face of the absence of a plane of cleavage between the tumor and the brainstem, in the presence of encasement of vital neurovascular structures, in elderly patients with tumors adherent to preoperatively normal facial or lower cranial nerves.

Long-term neuromotor speech deficits in survivors of childhood posterior fossa tumors: effects of tumor type, radiation, age at diagnosis, and survival years

The cerebellum is important for the coordination of fluent speech. The authors studied how childhood cerebellar tumors affect long-term neuromotor speech outcomes, including the relation between outcome and tumor type, radiation, age at diagnosis, and survival years. Videotaped speech samples of child and adult long-term survivors of childhood cerebellar astrocytoma (nonradiated) and medulloblastoma (radiated) tumors and healthy controls were analyzed by 2 speech pathologists for ataxic dysarthria, dysfluency, and speech rate. Ataxia varied with tumor type/radiation. Medulloblastoma survivors had significantly more ataxic dysarthric features than either survivors of astrocytomas or controls, who did not differ from each other. Dysfluency varied with a history of a posterior fossa tumor. Medulloblastoma and astrocytoma survivors were each significantly more dysfluent than controls but did not differ from each other. Speech rate varied with age and tumor type. Adult controls were significantly faster than child controls, although adult tumor survivors were comparable to their child counterparts. Adult controls had significantly faster speech rates than adult survivors of medulloblastoma tumors. Ataxic dysarthric speech characteristics are more frequent in radiated survivors of medulloblastoma tumors than nonradiated survivors of astrocytoma tumors. Dysfluent and slow speech occur in cerebellar tumor survivors, regardless of tumor type and radiation history. Cerebellar tumors in childhood limit speech rate in adulthood.

Analysis of chromosome 7 in adult and pediatric ependymomas using chromogenic in situ hybridization

Few studies have yielded reliable data that distinguish between ependymal neoplasms based on molecular genetic attributes. The present study utilizes chromogenic in situ hybridization (CISH), a relatively recent hybridization technique, to retrospectively examine chromosome 7-copy number in pediatric and adult ependymomas. Of the 27 hybridizations, polysomy of chromosome 7 was detected in 10 out of 15 (66%) adult ependymomas, and in only three out of 12 (25%) pediatric lesions. All myxopapillary ependymomas showed polysomy. The remaining tumors were diploid. The authors conclude that (1) there are distinct genetic subsets of ependymoma, in particular, increases in copy number of chromosome 7 are almost exclusively found in myxopapillary ependymoma, and that (2) CISH is a rapid and sensitive method of stratifying morphological variants of ependymoma and potentially other central nervous system (CNS) tumors. These results encourage further investigations with CISH on a larger scale to determine its merit as an ancillary diagnostic and prognostic tool.

Prognostic limitations of the Daumas-Duport grading scheme in infratentorial neuroglial tumors in children

The Daumas-Duport grading scheme (DDGS) utilizes four histologic features in an additive method (grade 1 if none present, grade 2 if only one is present, etc.). Its efficacy in achieving prognostically homogeneous groups of childhood infratentorial neuroglial tumors and its concordance with World Health Organization (WHO) diagnoses has not been evaluated. We investigated these questions using the Childhood Brain Tumor Consortium (CBTC) database of 1241 neuroglial tumors limited to the infratentorial compartment. We calculated survival function estimates for various DDGS grades as well as the histologic features within each grade. The feature of endothelial prominence improved survival expectation, whereas the remaining three features of nuclear atypia, mitoses, and necrosis were associated with worsened survival. Survival estimates for tumors with DDGS grades 2 and 3 did not differ. Some grades contained feature subsets with significantly different survival distributions. The survival distributions of DDGS grade 1, DDGS grade 2 with only endothelial prominence, and DDGS grade 3 with nuclear atypia and endothelial prominence were not significantly different. DDGS grade within WHO diagnoses had no significant effect on survival expectation. We conclude that grading by summation of only four histologic features, as in the DDGS, is inappropriate for assessment of childhood neuroglial tumors. A classification scheme considering the complete histologic content is more likely to provide clinically useful diagnoses. Such a scheme, based on the CBTC database is available. This scheme uses 26 histologic features identified as reliable in read-reread studies.

Differenzialdiagnose infratentorieller Hirntumoren bei Kindern

With the exception of the first year of life, infratentorial brain tumors are more frequent in the first decade than tumors in the supratentorial compartment. In particular these are cerebellar low-grade astrocytomas, medulloblastomas, brainstem gliomas and ependymomas of the fourth ventricle. The morphology on MRI and CT and the mode of dissemination permit differential diagnosis in many cases. To allow correct stratification into different treatments in possibly disseminating malignant brain tumors, knowledge of the status of dissemination is essential, and therefore not only cranial but also spinal MRI is indispensable for staging. If the spinal MRI is performed in the immediate postoperative period, knowledge of the normal non-specific purely postoperative changes, often seen as enhancement in the subdural spinal spaces, is necessary in order to avoid misinterpretation as meningial seeding. The differential diagnosis of pediatric infratentorial brain tumors and the morphology of subdural enhancement are illustrated with typical images. The natural history of the most frequent tumors and its importance for treatment decisions is discussed in light of the literature.

Quantitative histologic factors for grouping childhood supratentorial neuroglial tumors

The histologic heterogeneity of childhood supratentorial neuroglial tumors, when quantified, identifies relatively homogeneous subgroups for prognostic purposes and for assignment in clinical trials. Our sample consisted of supratentorial tumors in the Childhood Brain Tumor Consortium. The data consist of reliably identified histologic features and demographic, clinical, operative, and survival information. Factor analysis was used to identify uncorrelated "factors," each represented by a different combination of histologic features in 703 tumors. The defining histologic features were used to label each factor. The heterogeneity of each tumor was summarized using the factor scores for each factor. We compared the survival estimates of subgroups of tumors within common diagnostic classes. We identified five uncorrelated quantitative factors that accounted for much of the histologic variation. Our factor labels were Jumbo, Fibrillary, Proliferative, Spongy, an Oligodendroglial. Two thirds of tumors had high scores on two or more factors, indicating a high degree of heterogeneity among these tumors. Eighty-four percent of supratentorial tumors were accounted for by 19 nonoverlapping relatively homogeneous histologic groups. The five quantitative factors complement standard qualitative taxonomies by summarizing more completely the histologic feature aspects of a tumor than by diagnosis alone and quantify the histologic heterogeneity of individual tumors. Histologically homogeneous groups of tumors are essential for clinical trials, biologic research, and prognostic models.

Quantitative histologic factors for grouping childhood infratentorial neuroglial tumors

We employed factors analysis to quantify the degree of histologic heterogeneity of childhood infratentorial neuroglial tumors. Our data were 26 reliably ascertained histologic features in 1068 children in the Childhood Brain Tumor Consortium database. The factor analysis identified five uncorrelated quantitative "factors," each derived from a different linear combination of the 26 histologic features, that accounted for much of the histologic variation. Histologic features differed in their importance in each factor. The most important features in each factor were used for naming using simple, histologic, familiar descriptive terms: Spongy, Proliferative, Ring, Fibrillary, and Nuclear. Each tumor has a score on each factor. Two-thirds of tumors had high scores for at least two factors, indicating frequent histologic heterogeneity among these tumors. Ninety-five percent of tumors were allocated to 1 of 11 nonoverlapping histologically homogeneous groups. The five quantitative factors complement standard qualitative taxonomies by making explicit the histologic heterogeneity or homogeneity of individual tumors and provide the pathologist with a method that takes advantage of more of the histology of each tumor than conventional nomenclatures. Histologically homogeneous groups of tumors are likely to be of value in clinical trials and biologic research. Prognostic models based on these factors have been published.

[Brain tumors: classification and clinical aspects]

Brain tumors represent 40% to 50% of all solid tumors in children under 18 years of age, with an average incidence of 2 to 5 cases per 100,000/annum. These tumors are gliomas in 60% to 70% of cases. The most common location is infratentorial (60% of cases), with cerebellar astrocytomas, medulloblastomas and brain stem gliomas occurring in equal measure (20%). Astrocytomas are the predominant form (25%) in the supratentorial compartment. This review analyses clinical symptoms and instrumental procedures for the diagnosis of various types of brain tumor, together with recommendations for their management based on controlled clinical trials.