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

Clinical characteristics and prognostic factors of primary spinal subependymoma: a single-center cohort study and systematic review

PURPOSE

This study analyzed spinal subependymoma (SP-SE) cases to evaluate treatment outcomes and identify factors influencing patient outcomes.

METHOD

Clinical data from our institution, along with relevant literature, were reviewed and summarized. Univariate and multivariate logistic regression analyses were conducted to assess factors impacting the prognosis of patients with primary spinal ependymomas.

RESULTS

Our cohort included 16 males and 11 females, with a mean age of 46.2 ± 12.1 years. Tumors most commonly involved the thoracic spinal cord (37.0%) and an average of 4.8 segments. Approximately half of the tumors exhibited intramedullary to extramedullary growth (48.1%), and the tumors were predominantly eccentric in growth (85.2%). The median symptom duration was 48.0 months (IQR: 18.0-78.0 months), with limb weakness as the most frequent symptom. The median follow-up period was 61.0 months (IQR: 26.0-96.0 months). At the final follow-up, tumor regrowth occurred in 1 patient (3.7%), and 9 patients (33.3%) achieved good neurological outcomes (modified McCormick Scale [MSS] grades I). Multivariate logistic regression analysis revealed that tumors located at the T3-9 vertebral level were associated with worse postoperative neurological function (OR: 0.070, 95% Confidence Interval [CI]: 0.006-0.826, P = 0.035). Additionally, although the difference was not statistically significant, male gender also showed a trend towards an association with worse postoperative neurological function (OR: 0.126, 95% CI: 0.014-1.119, P = 0.063).

CONCLUSION

SP-SE generally follows a benign clinical course with favorable long-term survival. However, tumors located at T3-T9 and male patients tend to have worse postoperative neurological outcomes, requiring special attention during treatment.

Advances in molecular prognostication and treatments in ependymoma

Ependymoma is the third most common brain tumour of childhood and historically has posed a major challenge to both pediatric and adult neuro-oncologists. Ependymoma can occur anywhere in the central nervous system throughout the entire age spectrum. Treatment options have been limited to surgery and radiation, and outcomes have been widely disparate across studies. Indeed, these disparate outcomes have rendered it extraordinarily difficult to compare studies and to truly understand which patients are low and high-risk. Over the past two decades there have been tremendous advances in our understanding of the biology of ependymoma, which have changed risk stratification dramatically. Indeed, it is now well accepted that ependymoma comprises multiple distinct entities, whereby each compartment (supratentorial, posterior fossa, spinal) are distinct, and within each compartment there exist unique groups. The driver events, demographics and response to treatment vary widely across these groups and allow for a better classification of thee disease. Herein, we review the advances in the molecular stratification of ependymoma including how an improved classification and risk stratification allows for more precise therapies.

Strong nuclear expression of HOXB13 is a reliable surrogate marker for DNA methylome profiling to distinguish myxopapillary ependymoma from spinal ependymoma

Spinal ependymoma and myxopapillary ependymoma are the two most common spinal ependymal tumor types that feature distinct histological characteristics, genetic alterations and DNA methylation profiles. Their histological distinction may be difficult in individual cases and molecular diagnostic assessment, in particular DNA methylome profiling, may then be required to assign the correct diagnosis. Expression of the homeobox gene HOXB13 at the mRNA and protein levels has been reported as a frequent finding in myxopapillary ependymoma that may serve as a diagnostic marker for these tumors. Here, we evaluated the diagnostic role of HOXB13 immunostaining in 143 spinal neoplasms, comprising 54 histologically classified myxopapillary ependymomas, 46 histologically classified spinal ependymomas, and various other tumor types. Immunohistochemical results for HOXB13 protein were compared to molecular findings obtained by bead array-based DNA methylation and DNA copy number profiling, as well as next generation gene panel sequencing-based mutational analysis. Our findings indicate strong nuclear HOXB13 expression as a reliable diagnostic marker for molecularly confirmed myxopapillary ependymoma. Moreover, we provide evidence that differential HOXB13 protein expression is related to differential HOXB13-associated CpG site methylation in myxopapillary vs. spinal ependymomas, which can be assessed by targeted DNA methylation analysis. Taken together, immunohistochemistry for HOXB13 protein expression and targeted DNA methylation analysis of HOXB13 represent useful surrogate approaches that may substitute for DNA methylome profiling in routine diagnostics and facilitate precise classification of spinal ependymal tumors. In particular, strong nuclear HOXB13 immunoreactivity may serve as a novel diagnostic criterion for the classification of myxopapillary ependymoma.

Bilateral Papilledema in a Child with Spinal Myxopapillary Ependymoma: A Case Report

BACKGROUND Myxopapillary ependymomas, a subtype of spinal ependymomas, are relatively rare in children and adolescents, primarily affecting the lower spinal region; however, they can also metastasize along the spinal axis, as well as intracranially. The clinical presentation typically involves signs and symptoms of conus medullaris or cauda equina dysfunction, including paralysis and sensory loss, accompanied by lower back pain. Ocular complications are not commonly seen in myxopapillary ependymomas. This case report emphasizes the need to consider spinal tumors in patients presenting with bilateral papilledema, particularly in the presence of neurological symptoms or increased cerebrospinal fluid protein levels. It also stresses the importance of spinal MRI to prevent misdiagnosis during ophthalmic assessments. CASE REPORT A 12-year-old boy, previously diagnosed with neuromyelitis optica at another hospital and initially responsive to intravenous methylprednisolone, returned with relapsed vision loss and neck and back pain. At Shenzhen Children's Hospital, an ophthalmological examination showed bilateral papilledema with poorly defined margins. Due to his neurological symptoms, a consultation was conducted, revealing several positive signs. A lumbar puncture indicated elevated cerebrospinal fluid pressure and protein levels. A subsequent spinal MRI identified a space-occupying lesion in the spinal column. The patient underwent neurosurgical intervention to remove the intradural lesion, and the pathology confirmed a WHO Grade 2 myxopapillary ependymoma. Postoperatively, his right eye vision improved to 20/40, and his left eye vision to 20/20, resolving his diplopia and restoring normal muscle strength and tone in all limbs. However, a tumor recurrence 3 months later necessitated a second surgery. CONCLUSIONS Ocular complications are rare in pediatric patients with myxopapillary ependymoma. Timely recognition of associated symptoms by ophthalmologists, followed by a comprehensive neurological evaluation to uncover potential neurologic issues, can significantly improve outcomes through early intervention for myxopapillary ependymoma.

SNUH methylation classifier for CNS tumors

BACKGROUND

Methylation profiling of central nervous system (CNS) tumors, pioneered by the German Cancer Research Center, has significantly improved diagnostic accuracy. This study aimed to further enhance the performance of methylation classifiers by leveraging publicly available data and innovative machine-learning techniques.

RESULTS

Seoul National University Hospital Methylation Classifier (SNUH-MC) addressed data imbalance using the Synthetic Minority Over-sampling Technique (SMOTE) algorithm and incorporated OpenMax within a Multi-Layer Perceptron to prevent labeling errors in low-confidence diagnoses. Compared to two published CNS tumor methylation classification models (DKFZ-MC: Deutsches Krebsforschungszentrum Methylation Classifier v11b4: RandomForest, 767-MC: Multi-Layer Perceptron), our SNUH-MC showed improved performance in F1-score. For 'Filtered Test Data Set 1,' the SNUH-MC achieved higher F1-micro (0.932) and F1-macro (0.919) scores compared to DKFZ-MC v11b4 (F1-micro: 0.907, F1-macro: 0.627). We evaluated the performance of three classifiers; SNUH-MC, DKFZ-MC v11b4, and DKFZ-MC v12.5, using specific criteria. We set established 'Decisions' categories based on histopathology, clinical information, and next-generation sequencing to assess the classification results. When applied to 193 unknown SNUH methylation data samples, SNUH-MC notably improved diagnosis compared to DKFZ-MC v11b4. Specifically, 17 cases were reclassified as 'Match' and 34 cases as 'Likely Match' when transitioning from DKFZ-MC v11b4 to SNUH-MC. Additionally, SNUH-MC demonstrated similar results to DKFZ-MC v12.5 for 23 cases that were unclassified by v11b4.

CONCLUSIONS

This study presents SNUH-MC, an innovative methylation-based classification tool that significantly advances the field of neuropathology and bioinformatics. Our classifier incorporates cutting-edge techniques such as the SMOTE and OpenMax resulting in improved diagnostic accuracy and robustness, particularly when dealing with unknown or noisy data.

Molecular Testing for the World Health Organization Classification of Central Nervous System Tumors: A Review

Importance

Molecular techniques, including next-generation sequencing, genomic copy number profiling, fusion transcript detection, and genomic DNA methylation arrays, are now indispensable tools for the workup of central nervous system (CNS) tumors. Yet there remains a great deal of heterogeneity in using such biomarker testing across institutions and hospital systems. This is in large part because there is a persistent reluctance among third-party payers to cover molecular testing. The objective of this Review is to describe why comprehensive molecular biomarker testing is now required for the accurate diagnosis and grading and prognostication of CNS tumors and, in so doing, to justify more widespread use by clinicians and coverage by third-party payers.

Observations

The 5th edition of the World Health Organization (WHO) classification system for CNS tumors incorporates specific molecular signatures into the essential diagnostic criteria for most tumor entities. Many CNS tumor types cannot be reliably diagnosed according to current WHO guidelines without molecular testing. The National Comprehensive Cancer Network also incorporates molecular testing into their guidelines for CNS tumors. Both sets of guidelines are maximally effective if they are implemented routinely for all patients with CNS tumors. Moreover, the cost of these tests is less than 5% of the overall average cost of caring for patients with CNS tumors and consistently improves management. This includes more accurate diagnosis and prognostication, clinical trial eligibility, and prediction of response to specific treatments. Each major group of CNS tumors in the WHO classification is evaluated and how molecular diagnostics enhances patient care is described.

Conclusions and Relevance

Routine advanced multidimensional molecular profiling is now required to provide optimal standard of care for patients with CNS tumors.

Detection of Gene Fusions and Rearrangements in Formalin-Fixed, Paraffin-Embedded Solid Tumor Specimens Using High-Throughput Chromosome Conformation Capture

Chromosomal structural variants (SVs) are major contributors to cancer development. Although multiple methods exist for detecting SVs, they are limited in throughput, such as fluorescent in situ hybridization and targeted panels, and use RNA, which degrades in formalin-fixed, paraffin-embedded (FFPE) blocks and is unable to detect SVs that do not produce a fusion transcript. High-throughput chromosome conformation capture (Hi-C) is a DNA-based next-generation sequencing (NGS) method that preserves the spatial conformation of the genome, capturing long-range genetic interactions and SVs. Herein, a retrospective study analyzing 71 FFPE specimens from 10 different solid tumors was performed. Results showed high concordance (98%) with clinical fluorescent in situ hybridization and RNA NGS in detecting known SVs. Furthermore, Hi-C provided insight into the mechanism of SV formation, including chromothripsis and extrachromosomal DNA, and detected rearrangements between genes and regulatory regions, all of which are undetectable by RNA NGS. Lastly, SVs were detected in 71% of cases in which previous clinical methods failed to identify a driver. Of these, 14% were clinically actionable based on current medical guidelines, and an additional 14% were not in medical guidelines but involve targetable biomarkers. Current data suggest that Hi-C is a robust and accurate method for genome-wide SV analyses from FFPE tissue and can be incorporated into current clinical NGS workflows.

The association between postoperative photon radiotherapy dose and disease control and salvage treatment in pediatric and adolescent ependymoma: a multi-institutional investigation

PURPOSE

We characterized the association between photon radiation dose (< 59.4 versus ≥ 59.4 Gy) and outcomes in intracranial ependymoma. We also examined factors associated with survival after relapse.

METHODS

This multi-institutional retrospective study included patients age ≤ 21 years who received postoperative definitive-intent photon radiotherapy for posterior fossa ependymoma between 1997 and 2021. Clinical characteristics were obtained from medical records. Five-year overall (OS) and progression-free (PFS) survival were estimated using the Kaplan-Meier method. Factors associated with progression after radiotherapy, including dose < 59.4 versus ≥ 59.4 Gy, were analyzed using Fine and Gray's proportional subhazards model. Factors associated with post-relapse survival were explored using the Cox proportional-hazards model.

RESULTS

We identified 45 patients meeting inclusion criteria; 48.9% received ≥ 59.4 Gy. There was no difference in 5-year OS or PFS between those who received < 59.4 Gy versus ≥ 59.4 (OS 49.0% vs. 82.9%, p = 0.11; PFS 36.4% vs. 63.9%, p = 0.08); however, there was a trend towards worse 5-year OS and PFS among patients with grade 2 ependymoma who received < 59.4 Gy (OS 48.8% vs. 88.9%, p = 0.06, PFS 40.0% vs. 83.1%, p = 0.08). Only age > 4 years at diagnosis (subdistribution hazard ratio [SHR]: 0.40, p = 0.03) was associated lower risk of progression. Following radiotherapy, 24 patients relapsed. Receipt of salvage systemic therapy was associated with worse post-relapse OS on multivariable analysis (HR = 2.84, p = 0.04).

CONCLUSION

Underlying biological factors such as age and molecular subtype may hold greater prognostic significance than radiation dose in pediatric ependymoma. Regardless, recurrences are common and outcomes remain poor. Further research into optimal management of relapsed disease is critical.

Mapping naturally presented T cell antigens in medulloblastoma based on integrative multi-omics

Medulloblastoma is the most frequent malignant primary brain tumor in children. Despite recent advances in integrated genomics, the prognosis in children with high-risk medulloblastoma remains devastating, and new tumor-specific therapeutic approaches are needed. Here, we present an atlas of naturally presented T cell antigens in medulloblastoma. We map the human leukocyte antigen (HLA)-presented peptidomes of 28 tumors and perform comparative immunopeptidome profiling against an in-house benign database. Medulloblastoma is shown to be a rich source of tumor-associated antigens, naturally presented on HLA class I and II molecules. Remarkably, most tumor-associated peptides and proteins are subgroup-specific, whereas shared presentation among all subgroups of medulloblastoma (WNT, SHH, Group 3 and Group 4) is rare. Functional testing of top-ranking novel candidate antigens demonstrates the induction of peptide-specific T cell responses, supporting their potential for T cell immunotherapy. This study is an in-depth mapping of naturally presented T cell antigens in medulloblastoma. Integration of immunopeptidomics, transcriptomics, and epigenetic data leads to the identification of a large set of actionable targets that can be further used for the translation into the clinical setting by facilitating the informed design of immunotherapeutic approaches to children with medulloblastoma.

A case of myxopapillary ependymoma with predominant giant cell morphology: A rare entity with comprehensive genomic profiling and review of literature

In the evolving landscape of ependymoma classification, which integrates histological, molecular, and anatomical context, we detail a rare case divergent from the usual histopathological spectrum. We present the case of a 37-year-old man with symptomatic spinal cord compression at the L3-L4 level. Neuroradiological evaluation revealed an intradural, encapsulated mass. Histologically, the tumor displayed atypical features: bizarre pleomorphic giant cells, intranuclear inclusions, mitotic activity, and a profusion of eosinophilic cytoplasm with hyalinized vessels, deviating from the characteristic perivascular pseudorosettes or myxopapillary patterns. Immunohistochemical staining bolstered this divergence, marking the tumor cells positive for glial fibrillary acidic protein and epithelial membrane antigen with a characteristic ring-like pattern, and CD99 but negative for Olig-2. These markers, alongside methylation profiling, facilitated its classification as a myxopapillary ependymoma (MPE), despite the atypical histologic features. This profile underscores the necessity of a multifaceted diagnostic process, especially when histological presentation is uncommon, confirming the critical role of immunohistochemistry and molecular diagnostics in classifying morphologically ambiguous ependymomas and exemplifying the histological diversity within MPEs.

Targeting EPHB2/ABL1 restores antitumor immunity in preclinical models of ependymoma

Ependymoma (EPN) is a common form of brain tumor in children, often resistant to available cytotoxic therapies. Molecular profiling studies have led to a better understanding of EPN subtypes and revealed a critical role of oncogenes ZFTA-RELA fusion and EPHB2 in supratentorial ependymoma (ST-EPN). However, the immune system's role in tumor progression and response to therapy remains poorly understood. New treatments for various molecular subtypes of EPN are desperately needed. Using ST-EPN-ZFTA subtype-specific syngeneic mouse models, we found an increased frequency of M2-like tumor-associated macrophages (TAMs), which proportionally increased with tumor size during tumor progression. Transcriptomic profiling of ST-EPN-ZFTA and analysis of a human EPN dataset revealed multiple protein kinases as potential druggable targets. By matching transcriptomic signatures with the target spectrum of FDA-approved drugs, we found that the multikinase inhibitor dasatinib potently inhibited the growth of EPN both in vitro and in vivo, mainly through blocking EPHB2 and ABL1. Treatment with dasatinib reprogrammed the EPN immune microenvironment by polarizing TAMs toward an M1-like phenotype and increasing CD8 T cell activation. Furthermore, dasatinib treatment induced complete regression of established EPN tumors in 78% of the animals and protected survivors against tumor recurrence. Depletion of CD8 cells compromised the durability of EPN responses and reduced overall survival. These data indicate that dasatinib has the potential to be an effective therapy for ST-EPN-ZFTA molecular subgroup of EPN and support further investigation of dasatinib in clinical trials.

Diagnostic impact of DNA methylation classification in adult and pediatric CNS tumors

Over the past decade, neuropathological diagnosis has undergone significant changes, integrating morphological features with molecular biomarkers. The molecular era has successfully refined neuropathological diagnostic accuracy; however, a substantial number of CNS tumor diagnoses remain challenging, particularly in children. DNA methylation classification has emerged as a powerful machine learning approach for clinical decision-making in CNS tumors. The aim of this study is to share our experience using DNA methylation classification in daily routine practice, illustrated through clinical cases. We employed a classification system to evaluate discrepancies between histo-molecular and DNA methylation diagnoses, with a specific focus on adult versus pediatric CNS tumors. In our study, we observed that 40% of cases fell into Class I, 47% into Class II, and 13% into Class III among the "matched cases" (≥ 0.84). In other words, DNA methylation classification confirmed morphological diagnoses in 63% of adult and 23% of pediatric cases. Refinement of diagnosis was particularly evident in the pediatric population (65% vs. 21% for the adult population, p = 0.006). Additionally, we discussed cases classified with low calibrated scores. In conclusion, our study confirms that DNA methylation classification provides significant added-value for CNS tumors diagnosis, particularly in pediatric cases.

Autophagy in brain tumors: molecular mechanisms, challenges, and therapeutic opportunities

Autophagy is responsible for maintaining cellular balance and ensuring survival. Autophagy plays a crucial role in the development of diseases, particularly human cancers, with actions that can either promote survival or induce cell death. However, brain tumors contribute to high levels of both mortality and morbidity globally, with resistance to treatments being acquired due to genetic mutations and dysregulation of molecular mechanisms, among other factors. Hence, having knowledge of the role of molecular processes in the advancement of brain tumors is enlightening, and the current review specifically examines the role of autophagy. The discussion would focus on the molecular pathways that control autophagy in brain tumors, and its dual role as a tumor suppressor and a supporter of tumor survival. Autophagy can control the advancement of different types of brain tumors like glioblastoma, glioma, and ependymoma, demonstrating its potential for treatment. Autophagy mechanisms can influence metastasis and drug resistance in glioblastoma, and there is a complex interplay between autophagy and cellular responses to stress like hypoxia and starvation. Autophagy can inhibit the growth of brain tumors by promoting apoptosis. Hence, focusing on autophagy could offer fresh perspectives on creating successful treatments.

Distinct relapse pattern across molecular ependymoma types

BACKGROUND

Ependymoma (EPN) is not a uniform disease but represents different disease types with biological and clinical heterogeneity. However, the pattern of when and where different types of EPN relapse is not yet comprehensively described.

METHODS

We assembled 269 relapsed intracranial EPN from pediatric (n = 233) and adult (n = 36) patients from European and Northern American cohorts and correlated DNA methylation patterns and copy-number alterations with clinical information.

RESULTS

The cohort comprised the following molecular EPN types: PF-EPN-A (n = 177), ST-EPN-ZFTA (n = 45), PF-EPN-B (n = 31), PF-EPN-SE (n = 12), and ST-EPN-YAP (n = 4). First relapses of PF-EPN-B (PF: posterior-fossa) and PF-EPN-SE (SE: subependymoma) occurred later than of PF-EPN-A, ST-EPN-YAP (ST: supratentorial), or ST-EPN-ZFTA (median time to relapse: 4.3 and 6.0 years vs. 1.9/1.0/2.4 years; P < .01). Metastatic or combined recurrences in PF-EPN-B and -A more often involved the spinal cord than in ST-EPN-ZFTA (72.7% and 40.0 vs. 12.5%; P < .01). No distant relapses were observed in ST-EPN-YAP (n = 4) or PF-EPN-SE (n = 12). Post-relapse survival (PRS) was poor for PF-EPN-A and ST-EPN-ZFTA (5-year PRS: 44.5% ± 4.4%/47.8% ± 9.1%), whereas PF-EPN-B and PF-EPN-SE displayed a 5-year PRS of 89.5% ± 7.1%/90.0% ± 9.5% (P = .03). However, 10-year PRS for PF-EPN-B dropped to 45.8% ± 17.3%. Neither between the radiation field and relapse pattern nor between the radiation field and spinal involvement at relapse an impact was identified. Notably, all patients with relapsed ST-EPN-YAP did not receive upfront radiotherapy but were successfully salvaged using irradiation at relapse.

CONCLUSIONS

Relapse patterns of specific EPN types are different. Future clinical trials, treatment adaptions, duration of surveillance, and diagnostics should be planned to incorporate entity-specific relapse information.

Central nervous system tumors in adolescents and young adults: A Society for Neuro-Oncology Consensus Review on diagnosis, management, and future directions

Adolescents and young adults (AYAs; ages 15-39 years) are a vulnerable population facing challenges in oncological care, including access to specialized care, transition of care, unique tumor biology, and poor representation in clinical trials. Brain tumors are the second most common tumor type in AYA, with malignant brain tumors being the most common cause of cancer-related death. The 2021 WHO Classification for central nervous system (CNS) Tumors highlights the importance of integrated molecular characterization with histologic diagnosis in several tumors relevant to the AYA population. In this position paper from the Society for Neuro-Oncology (SNO), the diagnosis and management of CNS tumors in AYA is reviewed, focusing on the most common tumor types in this population, namely glioma, medulloblastoma, ependymoma, and CNS germ cell tumor. Current challenges and future directions specific to AYA are also highlighted. Finally, possible solutions to address barriers in the care of AYA patients are discussed, emphasizing the need for multidisciplinary and collaborative approaches that span the pediatric and adult paradigms of care, and incorporating advanced molecular testing, targeted therapy, and AYA-centered care.

Intradural extramedullary double primary ependymoma and meningioma rare condition: Case report and literature review

RATIONALE

Ependymomas are commonly prevalent intramedullary neoplasms in adults, with hardly any cases of exophytic extramedullary ependymoma being reported. Meningiomas, on the contrary, are one of the most common intradural extramedullary (IDEM) tumors. However, the occurrence of both IDEM tumors simultaneously is extremely rare.

PATIENT CONCERNS

A 63-year-old female who presented with pain and numbness in both lower limbs, and symptoms rapidly progressed over the past 5 months.

DIAGNOSIS

Based on the patient's clinical symptoms and imaging features, we conducted pathological examination and genetic testing, ultimately confirming that the patient had IDEM double primary ependymoma and meningioma.

INTERVENTIONS

Surgery was performed to remove double spinal tumors, decompress spinal nerve roots, and perform laminectomy, and she was treated with electrocardiogram monitoring, antibiotics, hemostasis, and antiedema therapy.

OUTCOMES

Histopathology confirmed World Health Organization grade II ependymoma at L2 and World Health Organization grade I meningioma at T12-L1. MYCN amplification and other genetic alterations were absent. Postoperative recovery was favorable, with no recurrence at 6-month follow-up.

LESSONS

This is the first reported case of IDEM double primary ependymoma and meningioma, highlighting the rarity of such cases and the importance of thorough diagnostic workup and surgical excision for IDEM tumors. Genetic analysis adds to the understanding of these rare tumors and guides management strategies.

Cortically Based Brain Tumors in Children: A Decision-Tree Approach in the Radiology Reading Room

Cortically based brain tumors in children constitute a unique set of tumors with variably aggressive biologic behavior. Because radiologists play an integral role on the multidisciplinary medical team, a clinically useful and easy-to-follow flow chart for the differential diagnoses of these complex brain tumors is essential. This proposed algorithm tree provides the latest insights into the typical imaging characteristics and epidemiologic data that differentiate the tumor entities, taking into perspective the 2021 World Health Organization's classification and highlighting classic as well as newly identified pathologic subtypes by using current molecular understanding.

Biglycan-driven risk stratification in ZFTA-RELA fusion supratentorial ependymomas through transcriptome profiling

Recent genomic studies have allowed the subdivision of intracranial ependymomas into molecularly distinct groups with highly specific clinical features and outcomes. The majority of supratentorial ependymomas (ST-EPN) harbor ZFTA-RELA fusions which were designated, in general, as an intermediate risk tumor variant. However, molecular prognosticators within ST-EPN ZFTA-RELA have not been determined yet. Here, we performed methylation-based DNA profiling and transcriptome RNA sequencing analysis of 80 ST-EPN ZFTA-RELA investigating the clinical significance of various molecular patterns. The principal types of ZFTA-RELA fusions, based on breakpoint location, demonstrated no significant correlations with clinical outcomes. Multigene analysis disclosed 1892 survival-associated genes, and a metagene set of 100 genes subdivided ST-EPN ZFTA-RELA into favorable and unfavorable transcriptome subtypes composed of different cell subpopulations as detected by deconvolution analysis. BGN (biglycan) was identified as the top-ranked survival-associated gene and high BGN expression levels were associated with poor survival (Hazard Ratio 17.85 for PFS and 45.48 for OS; log-rank; p-value < 0.01). Furthermore, BGN immunopositivity was identified as a strong prognostic indicator of poor survival in ST-EPN, and this finding was confirmed in an independent validation set of 56 samples. Our results indicate that integrating BGN expression (at mRNA and/or protein level) into risk stratification models may improve ST-EPN ZFTA-RELA outcome prediction. Therefore, gene and/or protein expression analyses for this molecular marker could be adopted for ST-EPN ZFTA-RELA prognostication and may help assign patients to optimal therapies in prospective clinical trials.

Lipomatous ependymoma with ZFTA: RELA fusion-positive: A case report

BACKGROUND

Ependymoma with lipomatous differentiation is a rare type of ependymoma. The ZFTA fusion-positive supratentorial ependymoma is a novel tumor type in the 2021 World Health Organization classification of central nervous system tumors. ZFTA fusion-positive lipomatous ependymoma has not been reported to date.

CASE SUMMARY

We reported a case of a 15-year-old Chinese male who had a sudden convulsion lasting approximately six minutes. Magnetic resonance imaging showed a round cystic shadow of approximately 1.9 cm × 1.5 cm × 1.9 cm under the right parieto-occipital cortex. Microscopic examination showed characteristic perivascular pseudorosettes and adipose differentiation in the cytoplasm. Immunohistochemical staining showed that the tumor cells were negative for cytokeratin, NeuN, Syn and p53, but positive for GFAP, vimentin and S-100 protein. Significant punctate intracytoplasmic EMA immunoreactivity was observed. The level of Ki-67 was about 5%. Genetic analysis revealed ZFTA: RELA fusion. A craniotomy with total excision of the tumor was performed. The follow-up time was 36 months, no evidence of disease recurrence was found in magnetic resonance imaging.

CONCLUSION

Based on these findings, the patient was diagnosed as a ependymoma with ZFTA fusion and lipomatous differentiation. This case report provides information on the microscopic morphological features of ependymoma with ZFTA fusion and lipomatous differentiation, which can help pathologists to make a definitive diagnosis of this tumor.

Clinicopathological profile of ependymomas with special reference to survival data - Experiences of a tertiary care center'

BACKGROUND AND AIMS

Ependymomas exhibit heterogeneity across age, location, histology, molecular nature and survival suggestive of an epigenetic component in its pathogenesis. The CNS WHO classification (2021) classifies ependymomas based on DNA methylation profiles. Studies suggest that molecular sub-types remain stable throughout the course of disease. Immunohistochemical expression of L1CAM, has been identified as a surrogate marker for ZFTA/c11orf95-RELA fusion in supratentorial ependymomas. This study aims at realising its utility specially in resource-poor setups.

MATERIALS AND METHODS

Forty-three histopathologically-proven cases of ependymoma under treatment over the period of three years were selected. Histopathological examination followed by routine IHC staining for GFAP, S-100, EMA and Ki-67 in all cases and L1CAM in the supratentorial ependymomas was done. We have followed-up almost all cases during our study period and was correlated with the IHC expression patterns and clinico-pathological parameters, including survival.

RESULTS

In our study the commonest location for ependymomas was spine in adults and posterior fossa in pediatric age group. Majority cases belonged to CNS WHO Grade 2 both in adults and in the paediatric age group. Supratentorial location of ependymomas with positive immuno-reactivity for L1CAM and a higher Ki-67 labelling index were associated with poor survival.

CONCLUSION

Our study revealed that L1CAM is an effective surrogate marker for supratentorial ependymomas possibly carrying the ZFTA Fusion gene product. The L1CAM immuno-reactivity also corresponded with the survival data. However, larger population-based studies are required to validate these results further.

Pediatric neuro-oncology: Highlights of the last quarter-century

The last quarter century has heralded dramatic changes in the field of pediatric neuro-oncology, with the era defined by profound developments in the understanding of the biological underpinnings of childhood central nervous system (CNS) tumors and translational therapeutics. Although there have been momentous strides forward in biologic, diagnostic, therapeutic, and experimental domains, considerable challenges remain and CNS tumors remain the leading cause of pediatric cancer-related mortality. Here, we review the significant advances in the field of pediatric neuro-oncology over the last 25 years and highlight ongoing hurdles facing future progress.

cIMPACT-NOW update 9: Recommendations on utilization of genome-wide DNA methylation profiling for central nervous system tumor diagnostics

Genome-wide DNA methylation signatures correlate with and distinguish central nervous system (CNS) tumor types. Since the publication of the initial CNS tumor DNA methylation classifier in 2018, this platform has been increasingly used as a diagnostic tool for CNS tumors, with multiple studies showing the value and utility of DNA methylation-based classification of CNS tumors. A Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy (cIMPACT-NOW) Working Group was therefore convened to describe the current state of the field and to provide advice based on lessons learned to date. Here, we provide recommendations for the use of DNA methylation-based classification in CNS tumor diagnostics, emphasizing the attributes and limitations of the modality. We emphasize that the methylation classifier is one diagnostic tool to be used alongside previously established diagnostic tools in a fully integrated fashion. In addition, we provide examples of the inclusion of DNA methylation data within the layered diagnostic reporting format endorsed by the World Health Organization (WHO) and the International Collaboration on Cancer Reporting. We emphasize the need for backward compatibility of future platforms to enable accumulated data to be compatible with new versions of the array. Finally, we outline the specific connections between methylation classes and CNS WHO tumor types to aid in the interpretation of classifier results. It is hoped that this update will assist the neuro-oncology community in the interpretation of DNA methylation classifier results to facilitate the accurate diagnosis of CNS tumors and thereby help guide patient management.

Advances towards potential cancer therapeutics targeting Hippo signaling

Decades of research into the Hippo signaling pathway have greatly advanced our understanding of its roles in organ growth, tissue regeneration, and tumorigenesis. The Hippo pathway is frequently dysregulated in human cancers and is recognized as a prominent cancer signaling pathway. Hence, the Hippo pathway represents an ideal molecular target for cancer therapies. This review will highlight recent advancements in targeting the Hippo pathway for cancer treatment and discuss the potential opportunities for developing new therapeutic modalities.

Intracranial ependymoma: A retrospective analysis of clinical features, treatment modalities, and long-term outcome

Objective

Ependymomas, rare neuroglial tumors originating from ependymal cells, can occur in the CNS and typically affect the brain's ventricles or spinal cord. Prognosis is influenced by tumor grade, location, resection extent, and preoperative Karnofsky Performance Status Scale (KPSS) scores. This study evaluates clinical features, treatment outcomes, and factors affecting prognosis in patients with intracranial ependymomas.

Methods

A retrospective review of 23 patients with intracranial ependymomas, treated from 2018 to 2023, was conducted. Data included demographics, clinical presentations, KPSS scores, imaging findings, and treatment details. Outcomes assessed were postoperative complications, recurrence rates, and functional status. Statistical analysis used SPSS version 26, with significance set at p < 0.05.

Results

The cohort was predominantly male (87.0%), with a mean age of 27 years. Tumors were mostly in the fourth ventricle (82.6%), with an average diameter of 68.9 mm. Complete resection was achieved in 87.0% of cases. Postoperative radiotherapy was given to 91.0% of grade 2 and all grade 3 tumors. Recurrence occurred in 17.4% of grade 2 ependymomas, but none of grade 3. The seven-month mortality rate was 4.3%. Higher preoperative KPSS scores correlated with better outcomes.

Conclusion

Complete tumor resection and postoperative radiotherapy are crucial for improved outcomes in ependymomas. Higher preoperative KPSS scores and tumor location significantly impact prognosis. Tumors in the lateral ventricles are associated with higher recurrence risks. These findings highlight the need for aggressive surgical management and personalized adjuvant therapy to enhance patient outcomes.

Sex Differences in Ependymoma Methylation by Methylation-Defined Subgroup

Ependymoma is the second most common malignant paediatric brain tumour composed of nine methylation-defined, clinically relevant subgroups. It is unclear if there are sex differences in methylation profiles within these subgroups which could guide future treatment options. We obtained available methylation data from the National Center for Biotechnology Information Gene Expression Omnibus (GEO). Differentially methylated probes (DMPs) between sexes were identified in each ependymoma sample and mapped to genes. Reactome pathways resulting from genes were identified. Survival was estimated for each sex within molecular subgroups. There were 492 cases included in the main analysis: PF-EPN-A (n = 238) PF-EPN-B (n = 52), PF-SE (n = 34), SP-MPE (n = 26), SP-EPN (n = 21), ST-EPN-RELA (n = 87), ST-EPN-YAP1 (n = 13) and ST-SE (n = 21). Females were observed to have better, but statistically nonsignificant, 5-year overall survival (OS) and better, marginally significant 5-year progression-free survival (PFS) than males. One subgroup, ST-EPN-RELA, showed significantly better OS in females. There was a difference in immune cell composition within tumour subgroups. One gene, RFTN1, was consistently differentially methylated by sex among all subgroups. There were biologic pathways identified from genes with differential methylation by sex in the following subgroups: PF-EPN-B, PF-SE, ST-EPN-RELA and ST-EPN-YAP1. Many of the identified pathways may be options for potential therapeutic targets.

Whole genome profiling of rare pediatric thoracic tumors elucidates a YAP1::LEUTX fusion in an unclassified biphasic embryonal neoplasm

Malignant biphasic tumors of the lungs are rare, more so in the pediatric population. Here, we present the whole-genome characterization of a pleuropulmonary blastoma Type III and an unclassified biphasic thoracic embryonal neoplasm. The pleuropulmonary blastoma harbored pathogenic DICER1 germline and somatic mutations, and additional somatic variants in TP53 and BCOR. The other malignant tumor demonstrated a t(11;19) balanced translocation with a YAP1::LEUTX fusion that was confirmed by fluorescence in situ hybridization. No DICER1 germline or somatic mutation was present. YAP1 and LEUTX have been implicated in tumorigenesis of various neoplasms, and YAP1 fusion genes are an emerging oncogenic entity in a variety of malignancies. In this study we highlight the importance of whole-genome characterization of rare and unclassified tumors to identify biologic mechanisms and potential therapeutic targets.

Demystifying the potential of lipid-based nanocarriers in targeting brain malignancies

Drug targeting for brain malignancies is restricted due to the presence of the blood-brain barrier (BBB) and blood-brain tumor barrier (BBTB), which act as barriers between the blood and brain parenchyma. Certainly, the limited therapeutic options for brain malignancies have made notable progress with enhanced biological understanding and innovative approaches, such as targeted therapies and immunotherapies. These advancements significantly contribute to improving patient prognoses and represent a promising shift in the landscape of brain malignancy treatments. A more comprehensive understanding of the histology and pathogenesis of brain malignancies is urgently needed. Continued research focused on unraveling the intricacies of brain malignancy biology holds the key to developing innovative and tailored therapies that can improve patient outcomes. Lipid nanocarriers are highly effective drug delivery systems that significantly improve their solubility, bioavailability, and stability while also minimizing unwanted side effects. Surface-modified lipid nanocarriers (liposomes, niosomes, solid lipid nanoparticles, nanostructured lipid carriers, lipid nanocapsules, lipid-polymer hybrid nanocarriers, lipoproteins, and lipoplexes) are employed to improve BBB penetration and uptake through various mechanisms. This systematic review illuminates and covers various topics related to brain malignancies. It explores the different methods of drug delivery used in treating brain malignancies and delves into the benefits, limitations, and types of brain-targeted lipid-based nanocarriers. Additionally, this review discusses ongoing clinical trials and patents related to brain malignancy therapies and provides a glance into future perspectives for treating this condition.

Supra-tentorial Ependymomas with ZFTA Fusion, YAP1 Fusion, and Astroblastomas, MN1-altered: Characteristic Imaging Features

PURPOSE

Supratentorial (ST) ependymoma subgroups are defined by two different fusions with different prognoses. Astroblastomas, MN1-altered, have ependymal-like histopathologic features and represent a differential diagnosis in children. We hypothesized that ZFTA-fused ependymoma and YAP1-fused ependymoma on the one hand, and astroblastoma, MN1-altered, on the other hand, show different MRI characteristics.

METHODS

We retrospectively analyzed the preoperative imaging of 45 patients with ST ependymoma or astroblastoma between January 2000 and September 2020, blinded to histomolecular grouping. Several characteristics, such as location, tumor volume, calcifications, solid/cystic component, and signal enhancement or diffusion were evaluated. We compared imaging characteristics according to their molecular subtype (ZFTA-fused, YAP1-fused, and astroblastoma, MN1-altered).

RESULTS

Thirty-nine patients were classified as having an ependymoma, 35 with a ZFTA fusion and four with a YAP1 fusion, and six as having an astroblastoma, MN1-altered. YAP1-fused ependymomas were more likely to involve at least 3 lobes than ZFTA-fused ependymomas. Astroblastomas were located in the frontal lobe in 100% of the tumors versus 49% of the ependymomas. Cerebral blood flow by arterial spin labeling was higher in astroblastomas than in ependymomas. There were no differences in the other characteristics between the molecular groups. All the tumors showed common features: intra-axial extra-ventricular tumors, very frequent contrast enhancement (39/43, 91%), a cystic/necrotic component (41/45, 91%), restricted diffusion (32/36, 89%), calcifications (15/18, 83%), and peri-tumoral edema (38/44, 86%).

CONCLUSION

The distinction between ST ependymoma subtypes and astroblastomas can be guided by several imaging features. These tumors share common imaging features that may help to differentiate ST ependymomas and astroblastomas from other pediatric ST tumors.

Histopathologic and molecular profile of gliomas diagnosed in Lagos, Nigeria

Background

The optimal diagnosis and management of patients with brain tumors currently uses the 2021 WHO integrated diagnosis of histomorphologic and molecular features. However, neuro-oncology practice in resource-limited settings usually relies solely on histomorphology. This study aimed to classify glioma cases diagnosed in the Department of Anatomic and Molecular Pathology, Lagos University Teaching Hospital, using the 2021 WHO CNS tumor classification.

Methods

Fifty-six brain tumors from 55 patients diagnosed with glioma between 2013 and 2021 were reevaluated for morphologic diagnosis. Molecular features were determined from formalin-fixed paraffin-embedded (FFPE) tissue using immunohistochemistry (IHC) for IDH1-R132H, ATRX, BRAF-V600E, p53, Ki67, and H3-K27M, OncoScan chromosomal microarray for copy number, targeted next generation sequencing for mutation and fusion and methylation array profiling.

Results

Of 55 central nervous system tumors, 3 were excluded from histomorphologic reevaluation for not being of glial or neuroepithelial origin. Of the remaining 52 patients, the median age was 20.5 years (range: 1 to 60 years), 38(73%) were males and 14(27%) were females. Seventy-one percent of the gliomas evaluated provided adequate DNA from archival FFPE tissue blocks. After applying the 2021 WHO diagnostic criteria the initial morphologic diagnosis changed for 35% (18/52) of cases. Diagnoses of 5 (9.6%) gliomas were upgraded, and 7 (14%) were downgraded.

Conclusions

This study shows that the incorporation of molecular testing can considerably improve brain tumor diagnoses in Nigeria. Furthermore, this study highlights the diagnostic challenges in resource-limited settings and what is at stake in the global disparities of brain tumor diagnosis.

Ependymal Tumors: Overview of the Recent World Health Organization Histopathologic and Genetic Updates with an Imaging Characteristic

The 2021 World Health Organization Classification of Tumors of the Central Nervous System (CNS5), introduced significant changes, impacting tumors ranging from glial to ependymal neoplasms. Ependymal tumors were previously classified and graded based on histopathology, which had limited clinical and prognostic utility. The updated CNS5 classification now divides ependymomas into 10 subgroups based on anatomic location (supratentorial, posterior fossa, and spinal compartment) and genomic markers. Supratentorial tumors are defined by zinc finger translocation associated (ZFTA) (formerly v-rel avian reticuloendotheliosis viral oncogene [RELA]), or yes-associated protein 1 (YAP1) fusion; posterior fossa tumors are classified into groups A (PFA) and B (PFB), spinal ependymomas are defined by MYCN amplification. Subependymomas are present across all these anatomic compartments. The new classification kept an open category of "not elsewhere classified" or "not otherwise specified" if no pathogenic gene fusion is identified or if the molecular diagnosis is not feasible. Although there is significant overlap in the imaging findings of these tumors, a neuroradiologist needs to be familiar with updated CNS5 classification to understand tumor behavior, for example, the higher tendency for tumor recurrence along the dural flap for ZFTA fusion-positive ependymomas. On imaging, supratentorial ZFTA-fused ependymomas are preferentially located in the cerebral cortex, carrying predominant cystic components. YAP1-MAMLD1-fused ependymomas are intra- or periventricular with prominent multinodular solid components and have significantly better prognosis than ZFTA-fused counterparts. PFA ependymomas are aggressive paramedian masses with frequent calcification, seen in young children, originating from the lateral part of the fourth ventricular roof. PFB ependymomas are usually midline, noncalcified solid-cystic masses seen in adolescents and young adults arising from the fourth ventricular floor. PFA has a poorer prognosis, higher recurrence, and higher metastatic rate than PFB. Myxopapillary spinal ependymomas are now considered grade II due to high recurrence rates. Spinal-MYCN ependymomas are aggressive tumors with frequent leptomeningeal spread, relapse, and poor prognosis. Subependymomas are noninvasive, intraventricular, slow-growing benign tumors with an excellent prognosis. Currently, the molecular classification does not enhance the clinicopathologic understanding of subependymoma and myxopapillary categories. However, given the molecular advancements, this will likely change in the future. This review provides an updated molecular classification of ependymoma, discusses the individual imaging characteristics, and briefly outlines the latest targeted molecular therapies.

The medical and functional burden of surviving childhood ependymoma: A population-based study in Ontario, Canada

BACKGROUND

Few studies have characterized the burden of late effects among childhood ependymoma survivors. To address this gap, we examined these sequelae using real-world health services data in a population-based ependymoma survivor cohort.

METHODS

All individuals younger than 18 years diagnosed with an ependymoma in Ontario, Canada between 1987 and 2015 who had survived at least 5 years from their latest pediatric cancer event (index date) were matched 1:5 with population controls. Following linkage with provincial health services data, the cumulative incidences of multiple medical and functional outcomes between survivors and controls were compared.

RESULTS

Among 96 survivors, 77.1% had been irradiated and 9.4% had received cisplatin. At 10 years post-index, survivors were at significantly higher risk of all-cause mortality (7.1%, 95% confidence interval [CI]: 1.0-13.3 vs. 0.3%, 95% CI: 0.0-1.0; p = .0002), non-obstetric hospitalization (45.1%, 95% CI: 32.6-56.7 vs. 10.6%, 95% CI: 7.6-14.1; p < .0001), stroke (6.5%, 95% CI: 2.3-13.7 vs. 0%; p < .0001), severe hearing loss requiring an amplification device (7.5%, 95% CI: 2.7-15.7 vs. 0%; p < .0001), receiving homecare service (27.6%, 95% CI: 18.5-37.5 vs. 7.7%, 95% CI: 5.3-10.7; p < .0001), and submitting a disability support prescription claim (24.0%, 95% CI: 14.8-34.3 vs. 5.4%, 95% CI: 3.5-7.8; p < .0001) compared to controls.

CONCLUSIONS

Pediatric ependymoma survivors are highly vulnerable to severe late sequelae, including death, stroke, severe hearing loss, and disability. Urgent efforts are needed to improve risk-stratification approaches that mitigate exposure to toxic therapies for children with lower risk disease. Interventions to prevent or decrease the risk of developing late sequelae are critical to optimizing survivor long-term health.

The emerging role of artificial intelligence in neuropathology: Where are we and where do we want to go?

The field of neuropathology, a subspecialty of pathology which studies the diseases affecting the nervous system, is experiencing significant changes due to advancements in artificial intelligence (AI). Traditionally reliant on histological methods and clinical correlations, neuropathology is now experiencing a revolution due to the development of AI technologies like machine learning (ML) and deep learning (DL). These technologies enhance diagnostic accuracy, optimize workflows, and enable personalized treatment strategies. AI algorithms excel at analyzing histopathological images, often revealing subtle morphological changes missed by conventional methods. For example, deep learning models applied to digital pathology can effectively differentiate tumor grades and detect rare pathologies, leading to earlier and more precise diagnoses. Progress in neuroimaging is another helpful tool of AI, as enhanced analysis of MRI and CT scans supports early detection of neurodegenerative diseases. By identifying biomarkers and progression patterns, AI aids in timely therapeutic interventions, potentially slowing disease progression. In molecular pathology, AI's ability to analyze complex genomic data helps uncover the genetic and molecular basis of neuropathological conditions, facilitating personalized treatment plans. AI-driven automation streamlines routine diagnostic tasks, allowing pathologists to focus on complex cases, especially in settings with limited resources. This review explores AI's integration into neuropathology, highlighting its current applications, benefits, challenges, and future directions.

Transcriptomic landscape identifies two unrecognized ependymoma subtypes and novel pathways in medulloblastoma

Medulloblastoma and ependymoma are prevalent pediatric central nervous system tumors with significant molecular and clinical heterogeneity. We collected bulk RNA sequencing data from 888 medulloblastoma and 370 ependymoma tumors to establish a comprehensive reference landscape. Following rigorous batch effect correction, normalization, and dimensionality reduction, we constructed a unified landscape to explore gene expression, signaling pathways, gene fusions, and copy number variations. Our analysis revealed distinct clustering patterns, including two primary ependymoma compartments, EPN-E1 and EPN-E2, each with specific gene fusions and molecular signatures. In medulloblastoma, we achieved precise stratification of Group 3/4 tumors by subtype and in SHH tumors by patient age. Our landscape serves as a vital resource for identifying biomarkers, refining diagnoses, and enables the mapping of new patients' bulk RNA-seq data onto the reference framework to facilitate accurate disease subtype identification. The landscape is accessible via Oncoscape, an interactive platform, empowering global exploration and application.

Advancements of anticancer agents by targeting the Hippo signalling pathway: biological activity, selectivity, docking analysis, and structure-activity relationship

The Hippo signalling pathway is prominent and governs cell proliferation and stem cell activity, acting as a growth regulator and tumour suppressor. Defects in Hippo signalling and hyperactivation of its downstream effector's Yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ) play roles in cancer development, implying that pharmacological inhibition of YAP and TAZ activity could be an effective cancer treatment strategy. Conversely, YAP and TAZ can also have beneficial effects in promoting tissue repair and regeneration following damage, therefore their activation may be therapeutically effective in certain instances. Recently, a complex network of intracellular and extracellular signalling mechanisms that affect YAP and TAZ activity has been uncovered. The YAP/TAZ-TEAD interaction leads to tumour development and the protein structure of YAP/TAZ-TEAD includes three interfaces and one hydrophobic pocket. There are clinical and preclinical trial drugs available to inhibit the hippo signalling pathway, but these drugs have moderate to severe side effects, so researchers are in search of novel, potent, and selective hippo signalling pathway inhibitors. In this review, we have discussed the hippo pathway in detail, including its structure, activation, and role in cancer. We have also provided the various inhibitors under clinical and preclinical trials, and advancement of small molecules their detailed docking analysis, structure-activity relationship, and biological activity. We anticipate that the current study will be a helpful resource for researchers.

Risk-Stratified Radiotherapy in Pediatric Cancer

While the cure rate of cancer in children has markedly improved in the last few decades, late effects continue to be a problem in survivors. Radiotherapy, which is a major component of treatment in many cancers, is one of the major agents responsible for late toxicity. In the past decade, radiotherapy has been omitted in patients achieving excellent response to chemotherapy, such as in Hodgkin lymphoma and some Wilms tumors with lung metastases. Likewise, response to chemotherapy has been used to determine whether lower doses of radiation can be delivered in intracranial germinoma and pediatric nasopharyngeal carcinoma. Molecular subtyping in medulloblastoma is currently being employed, and in WNT-pathway M0 tumors, the reduction in radiotherapy dose to the craniospinal axis and tumor bed is currently being investigated. Finally, dose escalation was recently evaluated in patients with rhabdomyosarcoma > 5 cm who do not achieve a complete response to initial 9 weeks of chemotherapy as well as for unresectable Ewing sarcoma patients to improve local control.

H3K27me3 Loss in Central Nervous System Tumors: Diagnostic, Prognostic, and Therapeutic Implications

Central nervous system (CNS) tumors represent a formidable clinical challenge due to their molecular complexity and varied prognostic outcomes. This review delves into the pivotal role of the epigenetic marker H3K27me3 in the development and treatment of CNS tumors. H3K27me3, specifically the trimethylation of lysine 27 on the histone H3 protein, plays a crucial role in regulating gene expression and maintaining chromatin architecture (e.g., in X-chromosome inactivation). Notably, a reduction in H3K27me3 levels, frequently tied to mutations in the H3 gene family such as H3F3A and HIST1H3B, is evident in diverse brain tumor variants, including the diffuse midline glioma characterized by the H3K27M mutation and certain pediatric high-grade gliomas. The loss of H3K27me3 has been linked to more aggressive behavior in meningiomas, with the trimethylation loss associated with significantly shorter recurrence-free survival (RFS) among grade 2 meningiomas, albeit not within grade 1 tumors. Pediatric posterior fossa ependymomas characterized by a lowered H3K27me3 and DNA hypomethylation exhibit poor prognosis, underscoring the prognostic significance of these epigenetic alterations in CNS tumors. Comprehending the role of H3K27me3 in CNS tumors is vital for advancing diagnostic tools and therapeutic interventions, with the goal of enhancing patient outcomes and quality of life. This review underscores the importance of ongoing investigations into H3K27me to refine and optimize management strategies for CNS tumors, paving the way for improved personalized medicine practices in oncology.

The Epigenetic Hallmarks of Cancer

Cancer is a complex disease in which several molecular and cellular pathways converge to foster the tumoral phenotype. Notably, in the latest iteration of the cancer hallmarks, "nonmutational epigenetic reprogramming" was newly added. However, epigenetics, much like genetics, is a broad scientific area that deserves further attention due to its multiple roles in cancer initiation, progression, and adaptive nature. Herein, we present a detailed examination of the epigenetic hallmarks affected in human cancer, elucidating the pathways and genes involved, and dissecting the disrupted landscapes for DNA methylation, histone modifications, and chromatin architecture that define the disease. Significance: Cancer is a disease characterized by constant evolution, spanning from its initial premalignant stages to the advanced invasive and disseminated stages. It is a pathology that is able to adapt and survive amidst hostile cellular microenvironments and diverse treatments implemented by medical professionals. The more fixed setup of the genetic structure cannot fully provide transformed cells with the tools to survive but the rapid and plastic nature of epigenetic changes is ready for the task. This review summarizes the epigenetic hallmarks that define the ecological success of cancer cells in our bodies.

Comparison of DNA methylation based classification models for precision diagnostics of central nervous system tumors

As part of the advancement in therapeutic decision-making for brain tumor patients at St. Jude Children's Research Hospital (SJCRH), we developed three robust classifiers, a deep learning neural network (NN), k-nearest neighbor (kNN), and random forest (RF), trained on a reference series DNA-methylation profiles to classify central nervous system (CNS) tumor types. The models' performance was rigorously validated against 2054 samples from two independent cohorts. In addition to classic metrics of model performance, we compared the robustness of the three models to reduced tumor purity, a critical consideration in the clinical utility of such classifiers. Our findings revealed that the NN model exhibited the highest accuracy and maintained a balance between precision and recall. The NN model was the most resistant to drops in performance associated with a reduction in tumor purity, showing good performance until the purity fell below 50%. Through rigorous validation, our study emphasizes the potential of DNA-methylation-based deep learning methods to improve precision medicine for brain tumor classification in the clinical setting.

Novel case of ependymoma-like tumor with mesenchymal differentiation harboring ZFTA::RELA fusion in an adult

High-grade supratentorial tumors harboring ZFTA::NCOA1/2 fusion in infants presenting with mixed histology of embryonal-appearing components resembling ependymoma and mesenchymal sarcomatous components have recently been reported as ependymoma-like tumors with mesenchymal differentiation (ELTMDs). In contrast, we describe herein a pathologically similar case with a novel ZFTA::RELA fusion in an adult. A frontal lobe lesion was resected from a 30-year-old woman and displayed mixed components on pathological examination, showing ependymoma-like and sarcomatous parts. The absence of perivascular pseudorosettes was inconsistent with a diagnosis of ependymoma. Fluorescence in situ hybridization analysis confirmed ZFTA::RELA fusion. The DKFZ methylation classifier (v12.8) did not categorize this case among established methylation classes. In addition, t-distributed stochastic neighbor embedding analysis using DNA methylation data revealed that the present case was distant from ependymomas but close to two previously reported cases of ELTMD involving ZFTA::NCOA1/2 fusion. Taken together, we concluded that this tumor should be considered under the entity of ELTMD. This represents the first description of an adult patient with ELTMD harboring ZFTA::RELA fusion analyzed by DNA methylation profiling, supporting the establishment of ELTMD as a possible new tumor type.

Survival Factors in 1580 Adults with Spinal Ependymoma: Insights from a Multicenter Oncology Database

BACKGROUND

Using a multi-institutional oncology database, we investigate the survival rates and the impacts of demographic, clinical, and management characteristics on overall survival among adult patients diagnosed with spinal ependymoma.

METHODS

Utilizing the SEER registry, patients with histologically or radiologically confirmed ependymomas were included. Factors impacting overall survival were analyzed using Kaplan-Meier survival curves and log-rank statistical analyses.

RESULTS

A total of 1,580 patients were included. Their mean ± standard deviation age was 46.68 ± 15.96 years, and 51.1% were women. Gross total resection (GTR) was achieved in 66.4% of patients. The 5- and 10-year survival rates were 96.7% and 95.4%, respectively. A multivariable backward Cox regression showed that age ≥65 years was a significant predictor for mortality (hazard ratio [HR]: 3.93; 95% confidence interval [CI]: 2.21-7.00; P < 0.001). Likewise, tumor grade 3 (HR: 6.36; 95% CI: 1.95-20.76; P = 0.002), tumor grade 4 (HR: 7.74; 95% CI: 3.97-15.11; P < 0.001), presence of extra-neural metastasis (HR: 13.81; 95% CI: 3.67-51.96; P < 0.001), and receiving radiotherapy (HR: 2.50; 95% CI: 1.50-4.19; P < 0.001) were significant risk factors for mortality, while GTR was significantly associated with improved overall survival compared with subtotal resection or nonsurgical management (HR: 0.42; 95% CI: 0.25-0.73; P = 0.002). There were no significant effects for gender, race, marital status, income, residential area, chemotherapy, tumor size, and the presence of other benign or malignant tumors on the survival hazards (P > 0.05 for each).

CONCLUSION

Early diagnosis and surgical management of spinal ependymomas, such as GTR, were associated with remarkable survival benefits. Old age, high-grade spinal ependymoma, and extra-neural metastasis were associated with worse overall survival, whereas radiotherapy's role remains unclear.

Specifics of spinal neuropathology in the molecular age

Tumors located in the spinal cord and its coverings can be diagnostically challenging and require special consideration regarding treatment options. During the last decade, important advances regarding the molecular characterization of central and peripheral nervous system tumors were achieved, resulting in improved diagnostic precision, and understanding of the tumor spectrum of this compartment. In particular, array-based global DNA methylation profiling has emerged as a valuable tool to delineate biologically and clinically relevant tumor subgroups and has been incorporated in the current WHO classification for central nervous system tumors of 2021. In addition, several genetic drivers have been described, which may also help to define distinct tumor types and subtypes. Importantly, the current molecular understanding not only sharpens diagnostic precision but also provides the opportunity to investigate both targeted therapies as well as risk-adapted changes in treatment intensity. Here, we discuss the current knowledge and the clinical relevance of molecular neuropathology in spinal tumor entities.

Case report on an extremely rare type of ependymoma arising from the thigh

INTRODUCTION

Ependymomas are neuroepithelial neoplasms of the central nervous system that arise from the precursor cells lining the ventricular system and the central canal of the spinal cord. Herein, we report a case of an extremely rare type of ependymoma arising from the thigh. Then, a literature review was performed.

PRESENTATION OF CASE

An 87-year-old female Japanese patient presented with a chief complaint of a mass on the medial aspect of her right thigh. Pathology revealed a grade 2 extra-neural ependymoma. PET-CT and brain MRI showed no neoplastic lesions in the central nervous system, and the tumor was localized only in the right thigh. The tumor was growing and was treated as a low-grade tumor with extensive resection and postoperative adjuvant radiotherapy. The patient has been alive for 3 years, without postoperative recurrence or complications.

DISCUSSION

This case presents a rare extra-neural ependymoma of central nervous system origin arising in the thigh. The pathogenesis is unknown, but a search for neoplastic lesions in the cerebrospinal cord is warranted. Extra-neural ependymomas should be treated as low-grade tumors because they are more prone to recurrence and metastasis than ordinary ependymomas.

CONCLUSION

We experienced an extremely rare extra-neural ependymoma arising in the thigh. A search for tumors in the central nervous system region of the cerebrospinal cord, previous literature, and clinical, imaging, and pathological findings should be consulted to determine a treatment strategy.

Conditional survival estimates for ependymomas reveal the dynamic nature of prognostication

BACKGROUND

Traditional survival analysis is frequently used to assess the prognosis of ependymomas (EPNs); however, it may not provide additional survival insights for patients who have survived for several years. Thus, the conditional survival (CS) pattern of this disease is yet to be further investigated. This study aimed to evaluate the improvement of survival over time using CS analysis and develop a CS-based nomogram model for real-time dynamic survival estimation for EPN patients.

METHODS

Data on patients with EPN were collected from the Surveillance, Epidemiology, and End Results (SEER) database. In order to construct and validate the model effectively, the selected patients were randomly divided at 7:3 ratio. CS is defined as the probability of surviving for a specified time period (y years) after initial diagnosis, given that the patient has survived x years. The CS pattern of EPN patients were explored. Then, the least absolute shrinkage and selection operator (LASSO) regression method with tenfold cross-validation was employed to identify prognostic predictors. Multivariate Cox regression was employed to develop a CS-based nomogram model, and we used this model to quantify EPN patient risk. Finally, the performance of the prediction model was also evaluated and verified.

RESULTS

In total, 1829 patients diagnosed with EPN were included in the study, with 1280 and 549 patients in the training and validation cohorts, respectively. The CS analysis demonstrated that patients' OS saw gradual improvements over time. With each additional year of survival post-diagnosis, the 10-year survival rate of EPN patients saw an increase, updating from 74% initially to 79%, 82%, 85%, 87%, 89%, 91%, 93%, 96%, and 98% (after surviving for 1-9 years, respectively). The LASSO regression model, which implements tenfold cross-validation, identified 7 significant predictors (age, tumor grade, tumor site, tumor extension, tumor size, surgery and radiotherapy) to develop a CS-based nomogram model. And further risk stratification was conducted based on nomogram model for these patients. Furthermore, this survival prediction model was successfully validated.

CONCLUSION

This study described the CS pattern of EPN patients and highlighted the gradual improvement of survival observed over time for long-term survivors. We also developed the first novel CS-nomogram model that enabled individualized and real-time prognosis prediction. But patients must be counselled that individual circumstances may not always accurately reflect the findings of the nomogram.

Predicting response to chemotherapy in brain tumor patients based on MRI features

Chemotherapy in brain tumors is tailored based on tumor type, grade, and molecular markers, which are crucial for predicting responses and survival outcomes. This review summarizes the role of chemotherapy in gliomas, glioneuronal and neuronal tumors, ependymomas, choroid plexus tumors, medulloblastomas, and meningiomas, discussing standard treatment protocols and recent developments in targeted therapies.Furthermore, the studies reporting the integration of MRI-based radiomics and deep learning models for predicting treatment outcomes are reviewed. Advances in MRI-based radiomics and deep learning models have significantly enhanced the prediction of chemotherapeutic benefits, survival prediction following chemotherapy, and differentiating tumor progression with psuedoprogression. These non-invasive techniques offer valuable insights into tumor characteristics and treatment responses, facilitating personalized therapeutic strategies. Further research is warranted to refine these models and expand their applicability across different brain tumor types.

Impact of Molecular Subgroups on Prognosis and Survival Outcomes in Posterior Fossa Ependymomas: A Retrospective Study of 412 Cases

BACKGROUND AND OBJECTIVES

Posterior fossa ependymomas (PFEs) are rare brain tumors classified as PF-EPN-A (PFA) and PF-EPN-B (PFB) subgroups. The study aimed to evaluate the prognosis and survival outcomes in PFEs, with a focus on the impact of molecular subgroups.

METHODS

A retrospective study was conducted on 412 patients with PFEs. Kaplan-Meier survival analyses were conducted to evaluate the overall survival (OS) and progression-free survival. Cox regression analyses were conducted to assess the prognostic factors. A nomogram was developed to predict the OS rates of PFEs.

RESULTS

The study revealed significant differences between PFA and PFB in patient and tumor characteristics. PFAs were associated with poorer OS (hazard ratios [HR] 3.252, 95% CI 1.777-5.950, P < .001) and progression-free survival (HR 4.144, 95% CI 2.869-5.985, P < .001). World Health Organization grade 3 was associated with poorer OS (HR 2.389, 95% CI 1.236-4.617, P = .010). As for treatment patterns, gross total resection followed by radiotherapy or the combination of radiotherapy and chemotherapy yielded the most favorable OS for PFA ( P = .025 for both), whereas gross total resection followed by radiotherapy rather than observation showed improved OS for PFB ( P = .046). The nomogram demonstrated a high degree of accuracy and discrimination capacity for the prediction of OS rates for up to 10 years. In addition, 6 cases of PFA (3.51%) with H3K27M mutations were identified.

CONCLUSION

PFAs demonstrate worse prognosis and survival outcomes compared with PFBs. Both PFAs and PFBs necessitate maximal resection followed by intensive adjuvant therapies in long-term effects.

Morphology-based molecular classification of spinal cord ependymomas using deep neural networks

Based on DNA-methylation, ependymomas growing in the spinal cord comprise two major molecular types termed spinal (SP-EPN) and myxopapillary ependymomas (MPE(-A/B)), which differ with respect to their clinical features and prognosis. Due to the existing discrepancy between histomorphogical diagnoses and classification using methylation data, we asked whether deep neural networks can predict the DNA methylation class of spinal cord ependymomas from hematoxylin and eosin stained whole-slide images. Using explainable AI, we further aimed to prospectively improve the consistency of histology-based diagnoses with DNA methylation profiling by identifying and quantifying distinct morphological patterns of these molecular ependymoma types. We assembled a case series of 139 molecularly characterized spinal cord ependymomas (nMPE = 84, nSP-EPN = 55). Self-supervised and weakly-supervised neural networks were used for classification. We employed attention analysis and supervised machine-learning methods for the discovery and quantification of morphological features and their correlation to the diagnoses of experienced neuropathologists. Our best performing model predicted the DNA methylation class with 98% test accuracy and used self-supervised learning to outperform pretrained encoder-networks (86% test accuracy). In contrast, the diagnoses of neuropathologists matched the DNA methylation class in only 83% of cases. Domain-adaptation techniques improved model generalization to an external validation cohort by up to 22%. Statistically significant morphological features were identified per molecular type and quantitatively correlated to human diagnoses. The approach was extended to recently defined subtypes of myxopapillary ependymomas (MPE-(A/B), 80% test accuracy). In summary, we demonstrated the accurate prediction of the DNA methylation class of spinal cord ependymomas (SP-EPN, MPE(-A/B)) using hematoxylin and eosin stained whole-slide images. Our approach may prospectively serve as a supplementary resource for integrated diagnostics and may even help to establish a standardized, high-quality level of histology-based diagnostics across institutions-in particular in low-income countries, where expensive DNA-methylation analyses may not be readily available.

Cytological features of ependymal and choroid plexus tumours

Ependymal and choroid plexus tumours arise in anatomically related regions. Their intraoperative differential diagnosis is large and depends on factors such as age, tumour site and clinical presentation. Squash cytology can provide valuable information in this context. Cytological features of conventional ependymomas, subependymomas and myxopapillary ependymomas as well as choroid plexus tumours are reviewed and illustrated. Differential diagnostic considerations integrating morphological and clinical information are discussed.