Posterior Fossa Ependymoma Research Articles

ANGI-10. METRONOMIC 5 DRUG ANTI-ANGIOGENESIS THERAPY FOR RECURRENT EPENDYMOMA

Abstract Low dose continuous (metronomic) anti-angiogenesis therapy is a treatment regimen currently under investigation for chemo-refractory tumors to target tumor vasculature. This effect has been shown to improve survival in primary brain tumors such as medulloblastoma. The Dana Farber Antiangiogenic Chemotherapy Phase II Trial and MEMMAT trial are investigations into outcomes of metronomic anti-angiogenesis therapy for children with recurrent ependymoma, among other primary brain tumors. We retrospectively report 9 pediatric patients diagnosed between the ages of 1 and 8 with surgery and radiation refractory posterior fossa ependymoma that were treated with 5 drug metronomic anti-angiogenesis therapy including celecoxib, thalidomide, fenofibrate, and alternating low dose etoposide and cyclophosphamide. For one patient, we added bevacizumab every other week. 7 patients had anaplastic presentation of ependymoma. All patients either had gross total resection or multiple subtotal resections. Tumor markers include GFAP, S100, EMA, OLIG 2, CD99, and Ki-67. Side effects were primarily hematologic but also included muscle pain, constipation, and dizziness, however treatment was tolerated well overall. The primary reason for stopping treatment early was progression of disease, no patients stopped therapy for side effects. There was no change in response to therapy based on tumor markers found. 2-year survival was 78% and 2-year progression free survival was 56%. 3/9 patients have no recurrent disease, two of these patients had anaplastic ependymoma and 1 presented with metastatic disease to the spine. We show improved outcomes with a minimal side effect profile for metronomic anti-angiogenesis therapy in pediatric patients with recurrent ependymoma refractory to surgical and radiation therapy.

A Fully Automated Deep-Learning Model for Predicting the Molecular Subtypes of Posterior Fossa Ependymomas Using T2-Weighted Images.

We aimed to develop and validate a deep learning (DL) model to automatically segment posterior fossa ependymoma (PF-EPN) and predict its molecular subtypes [Group A (PFA) and Group B (PFB)] from preoperative MR images. We retrospectively identified 227 PF-EPNs (development and internal test sets) with available preoperative T2-weighted (T2w) MR images and molecular status to develop and test a 3D nnU-Net (referred to as T2-nnU-Net) for tumor segmentation and molecular subtype prediction. The network was externally tested using an external independent set [n = 40; subset-1 (n = 31) and subset-2 (n =9)] and prospectively enrolled cases [prospective validation set (n = 27)]. The Dice similarity coefficient was used to evaluate the segmentation performance. Receiver operating characteristic analysis for molecular subtype prediction was performed. For tumor segmentation, the T2-nnU-Net achieved a Dice score of 0.94 ± 0.02 in the internal test set. For molecular subtype prediction, the T2-nnU-Net achieved an AUC of 0.93 and accuracy of 0.89 in the internal test set, an AUC of 0.99 and accuracy of 0.93 in the external test set. In the prospective validation set, the model achieved an AUC of 0.93 and an accuracy of 0.89. The predictive performance of T2-nnU-Net was superior or comparable to that of demographic and multiple radiologic features (AUCs ranging from 0.87 to 0.95). A fully automated DL model was developed and validated to accurately segment PF-EPNs and predict molecular subtypes using only T2w MR images, which could help in clinical decision-making.

Ependimomas de fosa posterior de tipo lateral en la edad pediátrica

Background and aimsLateral-type posterior fossa ependymomas are a well-defined subtype of tumors both clinically and pathologically, with a poor prognosis. Their incidence is low and surgical management is challenging. The objective of the present work is to review our series of lateral-tye posterior fossa ependymomas and compare our results with those of previous series. Materials and methodsAmong 30 cases of ependymoma operated in our pediatric department in the last 10 years, we identified seven cases of lateral-type posterior fossa ependymomas. We then performed a retrospective, descriptive study. ResultsMean age of our patients was 3.75 years. Six cases presented with hydrocephalus. Mean tumor volume at diagnosis was 61cc. A complete resection was achieved in six cases and a near-total resection in one patient. Five patients transiently required a gastrostomy and a tracheostomy. Mean follow-up was 58 months. One case progressed along this period and eventually died. Four cases of hydrocephalus required a ventriculoperitoneal CSF shunt and two were managed with a third ventriculostomy. At last follow-up four patients carried a normal life and two displayed a mild restriction according to Lansky's scale. ConclusionsThe aim of surgical treatment in lateral-type posterior fossa ependymomas is complete resection. Neurological deficits associated to lower cranial nerve dysfunction are common but transient. Deeper genetic characterization of these tumors may identify risk factors that guide stratification of adjuvant therapies.

GLIOMA-02 HISTOPATHOLOGIC AND MOLECULAR PROFILE OF GLIOMAS: A 9-YEAR RETROSPECTIVE STUDY OF CASES DIAGNOSED IN LAGOS NIGERIA

Abstract BACKGROUND The diagnosis and management of patients with brain tumors currently uses WHO defined morphologic and molecular features. However, neuro-oncology practice in low resource settings relies solely on histomorphology. This study aims to reclassify glioma cases diagnosed in the Department of Anatomic and Molecular Pathology Lagos University Teaching Hospital using the WHO 2021 classification. METHODS Fifty-six cases of glioma diagnosed between 2013 to 2021 were evaluated. Morphologic diagnosis was reassessed. Five-micron sections were obtained for immunohistochemistry (IHC), and genetic testing (DNA and RNA) after manual macrodissection for tumor enrichment used 10-µm sections. IHC for IDH1-R132H, ATRX, BRAF-V600E, p53, Ki67 and H3-K27M and Oncoscan chromosomal microarray analysis were performed. NGS mutation/fusion analysis and EPIC methylation array profiling are in progress. RESULTS Of the 56 cases evaluated, median age was 22 years (range, 1-60); 71% were male. The initial morphologic diagnoses included 21 pilocytic astrocytoma, 11 glioblastoma, 9 ependymoma, 7 diffuse astrocytoma, 3 anaplastic astrocytoma, 2 high-grade gliomas, 1 oligodendroglioma, 1 diffuse midline glioma, and 1 pleomorphic xanthoastrocytoma (PXA). Histomorphologic re-evaluation revealed discordant diagnosis in 29% (16/56) of cases. Of the 56 cases, 73% (41/56) had usable DNA yield and 38% (21/56) had DNA yield of ≥750ng. Chromosomal microarray analysis was completed for 50% (28/56) cases. The revised WHO 2021 diagnosis was: 5 glioblastoma IDH-wildtype, 5 pilocytic astrocytoma, 4 glioma NEC, 3 posterior fossa ependymoma, group B, 3 PXA, 3 astrocytoma IDH-mutant, 2 pediatric low-grade gliomas, 2 supratentorial ependymoma, ZFTA fusion-positive, 1 posterior fossa ependymoma, group A. In 71% (20/28) of cases with molecular testing, diagnosis was revised using WHO 2021 criteria. CONCLUSION Most cases had usable DNA. Overall, histologic re-evaluation and molecular based on the WHO 2021 criteria refined the diagnosis in 48% (27/56) of cases.

"Soap bubble" sign as an imaging marker for posterior fossa ependymoma Group B.

To investigate the predictive value of the "soap bubble" sign on molecular subtypes (Group A [PFA] and Group B [PFB]) of posterior fossa ependymomas (PF-EPNs). MRI scans of 227 PF-EPNs (internal retrospective discovery set) were evaluated by two independent neuroradiologists to assess the "soap bubble" sign, which was defined as clusters of cysts of various sizes that look like "soap bubbles" on T2-weighted images. Two independent cohorts (external validation set [n = 31] and prospective validation set [n = 27]) were collected to validate the "soap bubble" sign. Across three datasets, the "soap bubble" sign was observed in 21 PFB cases (7.4% [21/285] of PF-EPNs and 12.9% [21/163] of PFB); none in PFA. Analysis of the internal retrospective discovery set demonstrated substantial interrater agreement (1st Rating: κ = 0.71 [0.53-0.90], 2nd Rating: κ = 0.83 [0.68-0.98]) and intrarater agreement (Rater 1: κ = 0.73 [0.55-0.91], Rater 2: κ = 0.74 [0.55-0.92]) for the "soap bubble" sign; all 13 cases positive for the "soap bubble" sign were PFB (p = 0.002; positive predictive value [PPV] = 100%, negative predictive value [NPV] = 44%, sensitivity = 10%, specificity = 100%). The findings from the external validation set and the prospective validation set were similar, all cases positive for the "soap bubble" sign were PFB (p < 0.001; PPV = 100%). The "soap bubble" sign represents a highly specific imaging marker for the PFB molecular subtype of PF-EPNs.

Posterior fossa ependymomas in children and adolescents - the state of the art

Central nervous system tumors in pediatric patients represent the most frequent solid tumor type in this age group, especially ependymomas, which comprise 5% of childhood intracranial tumors, and occur mainly in the posterior fossa. The MEDLINE and ClinicalTrials databases were searched for studies on posterior fossa ependymomas, 64 studies met the search criteria. &#x0D; Symptoms include ataxia, vertigo, headache, vomiting, cranial nerve palsies, or papilledema, resulting from intracranial hypertension due to obstruction of CSF circulation. Imaging examination often reveals posterior fossa ependymomas in the fourth ventricle or cerebellopontine angle; they may extend through the foramina of Luschka, Magendie, and/or magnum. These tumors cause a significant mass effect, displacing rather than invading the hidbrain, and may involve vessels or cranial nerves, making surgical resection difficult. Various radiological features have been studied to distinguish between ependymomas and other histological types, as well as between ependymoma subtypes. &#x0D; The 2021 WHO classification of central nervous system tumors classifies ependymomas by location. Three types occur in the posterior fossa: subependymomas, PF-A, and PF-B. These are differentiated by the degree of DNA methylation and CpG islands, which can be assessed by immunohistochemical analysis with H3K27me3. &#x0D; The consensus on the treatment of posterior fossa ependymomas in children advocates the maximum possible surgical resection, followed by radiotherapy in patients &gt;1 year. Chemotherapy remains controversial, with no survival gain. Recent studies suggest molecular subgroups as an independent prognostic factor in posterior fossa ependymomas. The therapeutic challenge of ependymomas requires new treatment options, based on new technologies and molecular discoveries.

Posterior Fossa Tumors: Special Issue

This edition of APN is entirely dedicated to posterior fossa tumors. Very common in the daily routine of pediatric neurosurgeons, these tumors remain one of the most challenging pathologies we must face. The importance and complexity of the anatomical structures of the posterior fossa, associated with the enormous histological variety of neoplastic lesions in this region, make its therapeutic approach difficult and even more challenging. The degree of surgical resection plays a determining role in the prognosis and cure possibilities for the children with posterior fossa tumors; on the other hand, gross total resection is related to the much feared cerebellar mutism syndrome, related to serious cognitive and behavioral sequelae. Every pediatric neurosurgeon's nightmare, this subject deserves special attention in our edition. Ballestero and Juca review the literature, discuss the concepts of mutism, predisposing factors, pathophysiology, and available treatments.&#x0D; However, mutism prevention after surgical resection is essential. In addition to excellent mastery of microneurosurgery techniques and in-depth anatomical knowledge of the structures of the posterior fossa, pediatric neurosurgeons must use all the most advanced technologies to protect their patients and obtain the best results. Therefore, Kodangeski and Pinheiro discuss the use of electrophysiological monitoring during resection surgeries for posterior fossa tumors. Ahmed also emphasizes the importance of neuronavigation in these surgeries, as a significant tool to reduce morbidity and mortality.&#x0D; Around 70 to 90% of posterior fossa tumors present with hydrocephalus. The treatment of hydrocephalus before, during or after tumor resection is a very controversial subject, with different approaches among groups. Mandic retrospectively applies the success scores of endoscopic third ventriculocysternostomy in a group of patients with posterior fossa tumors and analyzes its efficiency.&#x0D; Costa pays special attention to posterior fossa ependymomas. Despite the explosion of genomic and epigenomic knowledge of these tumors in recent decades, surgery still plays an essential role in their treatment because the main objective as gross total resection represents a great technical challenge for the neurosurgeon.&#x0D; Besides to medulloblastomas, astrocytoma and ependymomas, more rarely other histological types can involve the posterior fossa and should be considered as differential diagnosis of these lesions. Therefore, Lopez presents clinical cases of choroid plexus papilloma and Rabelo Rodrigues reviews the cases of hemangioblastomas found in the literature.&#x0D; Even though posterior fossa tumors are predominant in children of preschool and school age, Dassi presents a series of cases in patients under two years of age, highlighting the histological characteristics and treatment strategies in this age group.&#x0D; The final result of this edition is a set of articles that highlight the complexity of posterior fossa tumors and the challenges of their treatment. Although these are the most common intracranial tumors in childhood and are part of the routine of every pediatric neurosurgery service, the war against those tumors has not been definitively won. We still lack greater understanding, and the exchange of experiences is increasingly necessary. We hope these articles can help all readers in their daily battles.&#x0D; Our special thanks to all the authors who worked on this edition and to the editorial staff who, with all their dedication, made it possible.&#x0D; Have an excellent read!

Imaging features to distinguish posterior fossa ependymoma subgroups.

Posterior fossa ependymoma group A (EPN_PFA) and group B (EPN_PFB) can be distinguished by their DNA methylation and give rise to different prognoses. We compared the MRI characteristics of EPN_PFA and EPN_PFB at presentation. Preoperative imaging of 68 patients with posterior fossa ependymoma from two centers was reviewed by three independent readers, blinded for histomolecular grouping. Location, tumor extension, tumor volume, hydrocephalus, calcifications, tissue component, enhancement or diffusion signal, and histopathological data (cellular density, calcifications, necrosis, mitoses, vascularization, and microvascular proliferation) were compared between the groups. Categorical data were compared between groups using Fisher's exact tests, and quantitative data using Mann-Whitney tests. We performed a Benjamini-Hochberg correction of the p values to account for multiple tests. Fifty-six patients were categorized as EPN_PFA and 12 as EPN_PFB, with median ages of 2 and 20years, respectively (p = 0.0008). The median EPN_PFA tumoral volume was larger (57 vs 29 cm3, p = 0.003), with more pronounced hydrocephalus (p = 0.002). EPN_PFA showed an exclusive central position within the 4th ventricle in 61% of patients vs 92% for EPN_PFB (p = 0.01). Intratumor calcifications were found in 93% of EPN_PFA vs 40% of EPN_PFB (p = 0.001). Invasion of the posterior fossa foramina was mostly found for EPN_PFA, particularly the foramina of Luschka (p = 0.0008). EPN_PFA showed whole and homogeneous tumor enhancement in 5% vs 75% of EPN_PFB (p = 0.0008). All mainly cystic tumors were EPN_PFB (p = 0.002). The minimal and maximal relative ADC was slightly lower in EPN_PFA (p = 0.02 and p = 0.01, respectively). Morphological characteristics from imaging differ between posterior fossa ependymoma subtypes and may help to distinguish them preoperatively. This study provides a tool to differentiate between group A and group B ependymomas, which will ultimately allow the therapeutic strategy to be adapted in the early stages of patient management. • Posterior fossa ependymoma subtypes often have different imaging characteristics. • Posterior fossa ependymomas group A are commonly median or lateral tissular calcified masses, with incomplete enhancement, affecting young children and responsible for pronounced hydrocephalus and invasion of the posterior fossa foramina. • Posterior fossa ependymomas group B are commonly median non-calcified masses of adolescents and adults, predominantly cystic, and minimally invasive, with total and homogeneous enhancement.

A Pediatric Case of Extraneural Subcutaneous Metastasis of Ependymoma.

Ependymoma is the third most common brain tumor in children. Extracranial metastases of ependymomas are uncommon. A 21-month-old Japanese boy was diagnosed to be brain dead due to a posterior fossa (PF) brain tumor. Surgical resection of the tumor was not performed. Twenty-seven months later, he developed a truncal subcutaneous tumor, which was pathologically diagnosed as PF ependymoma group A. We observed the intracranial recurrence of the brain tumor, an invasion to the left orbit, and a neoplasm in his liver before he died. This case suggests that PF ependymoma group A can metastasize extracranially to various organs.

Mapping pediatric brain tumors to their origins in the developing cerebellum.

Distinguishing the cellular origins of childhood brain tumors is key for understanding tumor initiation and identifying lineage-restricted, tumor-specific therapeutic targets. Previous strategies to map the cell-of-origin typically involved comparing human tumors to murine embryonal tissues, which is potentially limited due to species-specific differences. The aim of this study was to unravel the cellular origins of the 3 most common pediatric brain tumors, ependymoma, pilocytic astrocytoma, and medulloblastoma, using a developing human cerebellar atlas. We used a single-nucleus atlas of the normal developing human cerebellum consisting of 176 645 cells as a reference for an in-depth comparison to 4416 bulk and single-cell transcriptome tumor datasets, using gene set variation analysis, correlation, and single-cell matching techniques. We find that the astroglial cerebellar lineage is potentially the origin for posterior fossa ependymomas. We propose that infratentorial pilocytic astrocytomas originate from the oligodendrocyte lineage and MHC II genes are specifically enriched in these tumors. We confirm that SHH and Group 3/4 medulloblastomas originate from the granule cell and unipolar brush cell lineages. Radiation-induced gliomas stem from cerebellar glial lineages and demonstrate distinct origins from the primary medulloblastoma. We identify tumor genes that are expressed in the cerebellar lineage of origin, and genes that are tumor specific; both gene sets represent promising therapeutic targets for future study. Based on our results, individual cells within a tumor may resemble different cell types along a restricted developmental lineage. Therefore, we suggest that tumors can arise from multiple cellular states along the cerebellar "lineage of origin."

Challenges in Treating Childhood Infratentorial Ependymoma: A Low- and Middle-Income Country Experience

Patients and physicians in low and middle-income countries (LMICs) face challenges due to limited expertise and suboptimal access to appropriate diagnostic and treatment modalities. We report our experience in treating posterior fossa ependymoma (PFE) at MAHAK, a charity organization in Iran. The radiation oncology department is the only one exclusively dedicated to childhood cancer in the whole country. Pediatric patients with PFE and referred to MAHAK between November 2008 and January 2016 were identified. Details on investigations and management done before referral were collected. Management at MAHAK and patients outcome were analyzed. Out of 80 patients diagnosed as having ependymoma, 54 with PFE were identified. Fortythree received adjuvant radiotherapy and 11 patients were irradiated initially after recurrence. At a median follow-up of 5.1 years (range 0.3-9.7), the latter group had the worst outcome with a 5year overall survival (OS) of 27% (95% CI: 7-54). Patients who started radiotherapy within 77 days after initial surgery had a better outcome compared to those who started later (5-year OS: 74% vs 32%, p=0.05). Compliance with follow-up recommendations was poor. Only 22% of the patients had at least two IQ test assessments and 50% showed some decline over time. Three cases of growth hormone deficiency were detected but no one received replacement therapy. Access to pediatric neurosurgery, anesthesia, and timely radiotherapy are among the most challenging obstacles to be overcome in LMICs. Our series confirms that chemotherapy is not an appropriate option for delaying radiotherapy, especially in young children. The importance of long-term follow-up should be acknowledged by the parents and medical team.

EPEN-11. CHARACTERIZATION OF THE SPATIAL ARCHITECTURE OF INTRATUMORAL CELL STATES IN PEDIATRIC HIGH-RISK EPENDYMOMA

Abstract By single-cell analyses, we previously uncovered distinct intratumoral transcriptomic ependymoma (EPN) cell states and developmental trajectories correlating with molecular subtype and biological behavior. However, the relation of these cell states to characteristic EPN tissue architecture and tumor microenvironment remains widely unknown. We aimed to characterize the spatial architecture and elucidate regulatory circuits in EPN via spatial transcriptomics (10X Visium) of tumor specimens matching our previously generated single-cell transcriptome data spanning all EPN subtypes (ZFTA, YAP1, PFA, PFB). We investigated whether spatially restricted cell-cell interactions correlate with our previously identified cell states. Analyses revealed distinct spatially resolved cell populations in supratentorial and posterior fossa EPN. All subgroups showed several (5-9) spatially discrete cell clusters. Via non-negative matrix factorization (NMF), cell-specific spatial clusters emerged correlating with previous single-cell programs. ZFTA EPN highly correlates with ZFTA-specific metaprograms whereas all other subgroups did not show ZFTA-specific gene expression. Explicit genes such as DLK1 are exclusively upregulated in ZFTA EPN indicating spatially distinct aberrant Notch pathway signaling. Interestingly, this subgroup revealed spatial zones with upregulation of metabolic genes and endothelial markers anti-correlating with a ZFTA-specific program. Ependymal and neuronal-precursor-like signatures were enriched in our unique YAP1 EPN sample in a spatially restricted pattern, whereas GFAP was ubiquitously expressed. PFA was characterized by a neural stem cell (NSC)-like niche accompanied by metabolic and immune-reactive gene signatures. PFB showed a similar cell niche associated with NSC-like and glial-progenitor-like genes enriched simultaneously, further highlighting the NSC characteristic of posterior fossa tumors. Ependymal signatures were absent in PFA and present in PFB indicating more differentiated cell populations in PFB. Summarizing, we confirm presence of distinct intratumoral cell states within ependymoma tissue and reveal their spatial organization. In depth analysis and functional validation in matched ependymoma models will enable interrogation of underlying tumor promoting signaling events driving intratumoral developmental trajectories.

Posterior fossa ependymoma in children: A long-term single-center experience

IntroductionEpendymomas in the posterior fossa have poor prognosis. This study reports a single-center pediatric series, focusing on the value of surgical resection. Material and methodsA single-center retrospective study included all patients operated on by the senior author (CM) for posterior fossa ependymoma from 2002 to 2018. Medical and surgical data were extracted from the hospital's medical database. ResultsThirty-four patients were included. Age ranged from 6 months to 18 years, with a median of 4.7 years. Fourteen patients underwent initial endoscopic third ventriculocisternostomy before the direct surgical resection. Surgical removal was complete in 27 patients. There were 32 surgeries for second-look, local recurrence or metastasis despite complementary chemotherapy and/or radiotherapy. Twenty patients were WHO grade 2 and 14 grade 3. Sixteen patients showed recurrence (47%). Overall survival was 61.8% at a mean 10.1 years’ follow-up. Morbidities comprised facial nerve palsy, swallowing disorder, and transient cerebellar syndrome. Fifteen patients had normal schooling, 6 had special assistance; 4 patients reached university, 3 of whom experienced difficulties. Three patients had a job. ConclusionPosterior fossa ependymomas are aggressive tumors. Complete surgical removal is the most important prognostic factor, despite risk of sequelae. Complementary treatment is mandatory, but no targeted therapy has so far proved effective. It is important to continue the search for molecular markers in order to improve outcomes.

Survival analysis and prognostic factors in posterior fossa ependymomas in children and adolescents.

In this study, the authors aimed to analyze the overall survival (OS) and progression-free survival (PFS) of patients younger than 18 years of age who were diagnosed with posterior fossa ependymomas, and to identify prognostic factors such as the degree of resection, tumor topography, and involvement of the lesion in the hindbrain. The authors performed a retrospective cohort study of patients younger than 18 years of age, treated beginning in 2000, with a diagnosis of posterior fossa ependymoma. Ependymomas were separated into three groups: tumors restricted to the fourth ventricle, tumors inside the fourth ventricle and exiting from the foramen of Luschka, and tumors inside the fourth ventricle and completely surrounding the hindbrain. Furthermore, the tumors were classified by molecular group using the staining method for H3K27me3. Statistical analysis was performed using Kaplan-Meier survival curves, with p < 0.05 considered statistically significant. Of 1693 patients who underwent surgical treatment between January 2000 and May 2021, 55 patients who met the inclusion criteria were included. The median age at diagnosis was 2.98 years. The median OS was 44 months, and the survival rates at 1, 5, and 10 years were 92.5%, 49.1%, and 38.3%, respectively. The cases were assigned to two posterior fossa ependymoma molecular groups: 35 (63.6%) cases to group A and 8 (14.5%) to group B. The median ages in groups A and B were 2.94 and 2.85 years and the median OS values were 44 and 38 months, respectively (p = 0.9245). Statistical analysis was performed on multiple variables, including age, sex, histological grade, Ki-67 expression, tumor volume, extent of resection, and adjuvant therapies. The median PFS of patients with dorsal-only involvement was 28 months; for dorsolateral involvement, it was 15 months; and for total involvement, it was 9.5 months (p = 0.0464). No statistically significant difference was found for OS. There was a statistically significant difference between the proportion of patients in whom gross-total resection was achieved in the dorsal-only involvement group (73.1%, 19/26) and those in the total involvement group (0%, 0/6) (p = 0.0019). This study confirmed that the extent of resection has an impact on OS and PFS. The authors found that adjuvant radiotherapy resulted in a higher OS but did not prevent progression, that the pattern of involvement of the brainstem in the tumor at diagnosis could elicit important information regarding the patient's prognosis regarding PFS, and that the total involvement of the rhombencephalon impaired the gross-total resection of these tumors.

Drug Repurposing in Pediatric Brain Tumors: Posterior Fossa Ependymoma and Diffuse Midline Glioma under the Looking Glass.

Tumors of the Central Nervous System (CNS) represent the leading cause of cancer-related deaths in children. Current treatment options are not curative for most malignant histologies, and intense preclinical and clinical research is needed to develop more effective therapeutic interventions against these tumors, most of which meet the FDA definition for orphan diseases. Increased attention is being paid to the repositioning of already-approved drugs for new anticancer indications as a fast-tracking strategy for identifying new and more effective therapies. Two pediatric CNS tumors, posterior fossa ependymoma (EPN-PF) type A and diffuse midline glioma (DMG) H3K27-altered, share loss of H3K27 trimethylation as a common epigenetic hallmark and display early onset and poor prognosis. These features suggest a potentially common druggable vulnerability. Successful treatment of these CNS tumors raises several challenges due to the location of tumors, chemoresistance, drug blood-brain barrier penetration, and the likelihood of adverse side effects. Recently, increasing evidence demonstrates intense interactions between tumor cell subpopulations and supportive tumor microenvironments (TMEs) including nerve, metabolic, and inflammatory TMEs. These findings suggest the use of drugs, and/or multi-drug combinations, that attack both tumor cells and the TME simultaneously. In this work, we present an overview of the existing evidence concerning the most preclinically validated noncancer drugs with antineoplastic activity. These drugs belong to four pharmacotherapeutic classes: antiparasitic, neuroactive, metabolic, and anti-inflammatory. Preclinical evidence and undergoing clinical trials in patients with brain tumors, with special emphasis on pediatric EPN-PF and DMG, are summarized and critically discussed.

3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma

Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains (‘neo-TADs’) caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.

Identification of HDAC4 as a potential therapeutic target and prognostic biomarker for ZFTA-fused ependymomas.

Members of the HDAC family are predictive biomarkers and regulate the tumorigenesis in several cancers. However, the role of these genes in the biology of intracranial ependymomas (EPNs) remains unexplored. Here, an analysis of eighteen HDACs genes in an EPN transcriptomic dataset, revealed significantly higher levels of HDAC4 in supratentorial ZFTA fusion (ST-ZFTA) compared with ST-YAP1 fusion and posterior fossa EPNs, while HDAC7 and SIRT2 were downregulated in ST-ZFTA. HDAC4 was also overexpressed in ST-ZFTA as measured by single-cell RNA-Seq, quantitative real time-polymerase chain reaction, and immunohistochemistry. Survival analyses showed a significantly worse outcome for EPNs with higher HDAC4 and SIRT1 mRNA levels. Ontology enrichment analysis showed an HDAC4-high signature consistent with viral processes while collagen-containing extracellular matrix and cell-cell junction were enriched in those with an HDAC4-low signature. Immune gene analysis demonstrated a correlation between HDAC4 expression and low levels of NK resting cells. Several small molecules compounds targeting HDAC4 and ABCG2, were predicted by in silico analysis to be effective against HDAC4-high ZFTA. Our results provide novel insights into the biology of the HDAC family in intracranial ependymomas and reveal HDAC4 as a prognostic marker and potential therapeutic target in ST-ZFTA.

Abstract 3523: A systematic comparison of molecular features shared by H3K27-altered diffuse midline gliomas and posterior fossa A ependymomas

Abstract In children, brain tumors account for the highest mortality rates of all malignancies, and in contrast to adult brain cancers, pediatric tumors often arise in infratentorial regions. Two tumors in particular, H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs) arise from structures around the fourth ventricle, and strikingly, both tumors exhibit a global decrease in the histone mark histone 3, lysine 27 tri-methylation (H3K27me3) that is associated with transcriptional repression. H3K27-altered DMGs primarily are found primarily in the pons and exhibit by lysine-to-methionine mutations at H3K27 (H3K27M). This missense mutation results in inhibition of the catalytic activity of the polycomb repressive complex 2 (PRC2) which mediates H3K27me3 deposition. PFAs are found in the lateral recess of the fourth ventricle and the cerebellum and demonstrate overexpression of EZH inhibitory protein (EZHIP). EZHIP contains a domain with striking resemblance to the mutant H3K27M histone tail and similarly blocks PRC2 activity. Although H3K27me3 levels are dramatically reduced in both areas, select genes retain H3K27me3 in both tumor types. Increasingly, data have emerged demonstrating that cases of PFAs actually harbor H3K27M mutations and cases of H3-wildtype DMGs in fact overexpress EZHIP. The neighboring origins and overlapping recurrent H3K27me3-modulating alterations observed in these two pediatric brain tumors suggest certain populations of cells in the developing hindbrain may be particularly prone to malignant transformation in the setting of PRC2 inhibition. A systematic comparison of genomic, transcriptomic, and epigenomic datasets for both tumors identified key molecular similarities between subsets of DMGs and PFAs and highlighted how developmental signatures may be preserved in tumor expression profiles. Specifically, these analyses identify shared copy-number profiles between PFAs and different subtypes of DMGs and demonstrate that the Activin A Receptor Type 1 (ACVR1), a gene with recurrent activating mutations in H3K27-altered DMGs, is overexpressed in a subset PFAs with worse survival outcomes. Additionally, interrogation of the H3K27me3 and enhancer landscapes identified critical genes with similar chromatin profiles and revealed heterogeneity in repression of H3K27me3-marked genes that correlated with patterns of inferred anatomic origins for each tumor. Moreover, one of these genes, cellular retinoic acid binding partner 1 (CRABP1) showed enrichment in progenitor cell types in single-cell transcriptomic datasets. Together, these analyses characterize the common and unique molecular features of H3K27-altered DMGs and PFAs and shed light on the cellular contexts of the developing hindbrain that lead to development of each tumor. Citation Format: Matthew Pun, Drew Pratt, Patricia R. Nano, Piyush K. Joshi, Li Jiang, Bernhard Englinger, Arvind Rao, Marcin Cieslik, Arul M. Chinnaiyan, Kenneth Aldape, Stefan Pfister, Mariella G. Filbin, Aparna Bhaduri, Sriram Venneti. A systematic comparison of molecular features shared by H3K27-altered diffuse midline gliomas and posterior fossa A ependymomas. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3523.

Posterior fossa tumors in children: An update and new concepts.

Posterior fossa tumors account for approximately half of the central nervous system tumors in children. Major technological advances, mainly in the fields of molecular biology and neuroimaging, have modified their classification, leading to a more detailed description of these entities. Into the classic taxonomy, used for many years, new concepts have been incorporated at times eliminating or modifying former ones. A literature search was conducted in PubMed using the medical subject headings involving the five most common pediatric posterior fossa tumors: diffuse midline glioma, medulloblastoma, ependymoma, atypical teratoid/rhabdoid tumor, and pilocytic astrocytoma. Only English published articles in the past 11 years that provided technological, neuroimaging, and molecular biology insight into posterior fossa tumors in children were considered. Substantial changes have been introduced in the nomenclature of pediatric posterior fossa tumors. Diffuse midline gliomas are named based on alterations in histone H3. Molecular rearrangements of medulloblastomas are more important in defining the prognosis than histological variants; therefore, these tumors are currently named based on their molecular subgroups. Posterior fossa ependymomas and atypical teratoid rhabdoid tumor classification have incorporated new groups based on different genetic profiles. Pilocytic astrocytoma has been placed in a new category that distinguishes circumscribed from diffuse entities. Advances in molecular biology and neuroimaging have substantially changed the way pediatric neoplasms are studied. The classical taxonomy has been modified leading to more accurate classifications that are based on the genetic alterations.

Common molecular features of H3K27M DMGs and PFA ependymomas map to hindbrain developmental pathways

Globally decreased histone 3, lysine 27 tri-methylation (H3K27me3) is a hallmark of H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs). H3K27-altered DMGs are largely characterized by lysine-to-methionine mutations in histone 3 at position 27 (H3K27M). Most PFAs overexpress EZH inhibitory protein (EZHIP), which possesses a region of similarity to the mutant H3K27M. Both H3K27M and EZHIP inhibit the function of the polycomb repressive complex 2 (PRC2) responsible for H3K27me3 deposition. These tumors often arise in neighboring regions of the brainstem and posterior fossa. In rare cases PFAs harbor H3K27M mutations, and DMGs overexpress EZHIP. These findings together raise the possibility that certain cell populations in the developing hindbrain/posterior fossa are especially sensitive to modulation of H3K27me3 states. We identified shared molecular features by comparing genomic, bulk transcriptomic, chromatin-based profiles, and single-cell RNA-sequencing (scRNA-seq) data from the two tumor classes. Our approach demonstrated that 1q gain, a key biomarker in PFAs, is prognostic in H3.1K27M, but not H3.3K27M gliomas. Conversely, Activin A Receptor Type 1 (ACVR1), which is associated with mutations in H3.1K27M gliomas, is overexpressed in a subset of PFAs with poor outcome. Despite diffuse H3K27me3 reduction, previous work shows that both tumors maintain genomic H3K27me3 deposition at select sites. We demonstrate heterogeneity in shared patterns of residual H3K27me3 for both tumors that largely segregated with inferred anatomic tumor origins and progenitor populations of tumor cells. In contrast, analysis of genes linked to H3K27 acetylation (H3K27ac)-marked enhancers showed higher expression in astrocytic-like tumor cells. Finally, common H3K27me3-marked genes mapped closely to expression patterns in the human developing hindbrain. Overall, our data demonstrate developmentally relevant molecular similarities between PFAs and H3K27M DMGs and support the overall hypothesis that deregulated mechanisms of hindbrain development are central to the biology of both tumors.