A rare case of paediatric astroblastoma with concomitant MN1-GTSE1 and EWSR1-PATZ1 gene fusions altering management

PATZ1-Rearranged Tumors of the Central Nervous System: Characterization of a Pediatric Series of Seven Cases

PATZ1-rearranged sarcomas are well-recognized tumors as part of the family of round cell sarcoma with EWSR1-non-ETS fusions. Whether PATZ1-rearranged central nervous system (CNS) tumors are a distinct tumor type is debatable. We thoroughly characterized a pediatric series of PATZ1-rearranged CNS tumors by chromosome microarray analysis (CMA), DNA methylation analysis, gene expression profiling and, when frozen tissue is available, optical genome mapping (OGM). The series consisted of 7 cases (M:F=1.3:1, 1-17 years, median 12). On MRI, the tumors were supratentorial in close relation to the lateral ventricles (intraventricular or iuxtaventricular), preferentially located in the occipital lobe. Two major histologic groups were identified: one (4 cases) with an overall glial appearance, indicated as "neuroepithelial" (NET) by analogy with the corresponding methylation class (MC); the other (3 cases) with a predominant spindle cell sarcoma morphology, indicated as "sarcomatous" (SM). A single distinct methylation cluster encompassing both groups was identified by multidimensional scaling analysis. Despite the epigenetic homogeneity, unsupervised clustering analysis of gene expression profiles revealed 2 distinct transcriptional subgroups correlating with the histologic phenotypes. Interestingly, genes implicated in epithelial-mesenchymal transition and extracellular matrix composition were enriched in the subgroup associated to the SM phenotype. The combined use of CMA and OGM enabled the identification of chromosome 22 chromothripsis in all cases suitable for the analyses, explaining the physical association of PATZ1 to EWSR1 or MN1. Six patients are currently disease-free (median follow-up 30 months, range 12-92). One patient of the SM group developed spinal metastases at 26 months from diagnosis and is currently receiving multimodal therapy (42 months). Our data suggest that PATZ1-CNS tumors are defined by chromosome 22 chromothripsis as causative of PATZ1 fusion, show peculiar MRI features (eg, relation to lateral ventricles, supratentorial frequently posterior site), and, although epigenetically homogenous, encompass 2 distinct histologic and transcriptional subgroups.

Neuroepithelial tumor with EWSR1::PATZ1 fusion: A literature review

We present the clinicopathological and molecular genetic characteristics of a neuroepithelial tumor (NET), EWSR1::PATZ1 fusion-positive with a literature review. This fusion has recently been discovered in rare central nervous system tumors and soft tissue sarcomas and was not included in the fifth edition of the WHO classifications. We identified this fusion in 2 NETs. The first case involved a 7-year-old girl and the second case occurred in a 53-year-old man; both presented with headaches and vomiting. The pediatric case initially showed an intermediate grade of the tumor, but upon recurrences, it transformed into a high-grade tumor with 2 relapses in 8.3 years. This case exhibited high mitotic activity (20/10 high-power fields), and a high Ki-67 index (21%). The TERT promoter (TERTp) mutation was present in both initial and recurrent tumors. In contrast, the adult case was a low-grade tumor with no mitotic activity or recurrence over 13.5 months after subtotal resection and gamma knife surgery. Interestingly, the pediatric case demonstrated a longer survival time compared to conventional glioblastoma. The TERTp mutation, similar to being a molecular signature in adult-type glioblastoma, could also be an indicator of high-grade behavior in PATZ1 fusion NET.

Early ependymal tumor with MN1-BEND2 fusion: a mostly cerebral tumor of female children with a good prognosis that is distinct from classical astroblastoma

PURPOSE

Review of the clinicopathologic and genetic features of early ependymal tumor with MN1-BEND2 fusion (EET MN1-BEND2), classical astroblastomas, and recently described related pediatric CNS tumors. I also briefly review general mechanisms of gene expression silencing by DNA methylation and chromatin remodeling, and genomic DNA methylation profiling as a powerful new tool for CNS tumor classification.

METHODS

Literature review and illustration of tumor histopathologic features and prenatal gene expression timelines.

RESULTS

Astroblastoma, originally descried by Bailey and Cushing in 1926, has been an enigmatic tumor. Whether they are of ependymal or astrocytic derivation was argued for decades. Recent genetic evidence supports existence of both ependymal and astrocytic astroblastoma-like tumors. Studies have shown that tumors exhibiting astroblastoma-like histology can be classified into discrete entities based on their genomic DNA methylation profiles, gene expression, and in some cases, the presence of unique gene fusions. One such tumor, EET MN1-BEND2 occurs mostly in female children, and has an overall very good prognosis with surgical management. It contains a gene fusion comprised of portions of the MN1 gene at chromosomal location 22q12.1 and the BEND2 gene at Xp22.13. Other emerging pediatric CNS tumor entities demonstrating ependymal or astroblastoma-like histological features also harbor gene fusions involving chromosome X, 11q22 and 22q12 breakpoint regions.

CONCLUSIONS

Genomic DNA profiling has facilitated discovery of several new CNS tumor entities, however, traditional methods, such as immunohistochemistry, DNA or RNA sequencing, and cytogenetic studies, including fluorescence in situ hybridization, remain necessary for their accurate biological classification and diagnosis.

Case report: A unique presentation of a high-grade neuroepithelial tumor with EWSR1::PATZ1 fusion with diagnostic, molecular, and therapeutic insights

Background

EWSR1::PATZ1 fusion tumors are exceedingly rare in the central nervous system with only 14 prior cases documented. PATZ1 fusion neuroepithelial tumors are beginning to be recognized as a distinct molecular class of neoplasms that most often occur in children and young adults. These tumors are polyphenotypic, show diverse morphologic features, may be low- or high-grade, and tend to have an intermediate prognosis.

Case presentation

Herein, we present an unusual case of a high-grade neuroepithelial tumor in a young man with an EWSR1::PATZ1 fusion. This case is unique because the tumor appears to have undergone high-grade transformation from a persistent low-grade glioma, which has yet to be reported. Furthermore, this case is the first to document concurrent RB1 loss, SMAD4 loss, and TP53 inactivation in this tumor type, which correlates with high-grade transformation. Fortunately, this patient is alive 2.5 years after treatment and 18.5 years after initial presentation, which provides a unique window into how these tumors clinically behave over a long follow-up period. Finally, we discuss the altered molecular pathways that are a result of the EWSR1::PATZ1 fusion and discuss potential therapeutic targets.

Conclusion

Awareness of the emerging entity of PATZ1 fusion neuroepithelial tumors is important not only for accurate diagnostic and prognostic purposes but also for predicting response to therapy.

Heterogeneous clinicopathological findings and patient-reported outcomes in adults with MN1-altered CNS tumors: A case report and systematic literature review

The uncommon MN1-altered primary central nervous system (CNS) tumors were recently added to the World Health Organization 2021 classification under the name Astroblastoma, MN1-altered. Another term used to describe them, "High-grade neuroepithelial tumor with MN1 alteration" (HGNET-MN1), makes reference to their distinct epigenetic profile but is currently not a recommended name. Thought to occur most commonly in children and predominantly in females, MN1-altered CNS tumors are associated with typical but not pathognomonic histological patterns and are characterized by a distinct DNA methylation profile and recurrent fusions implicating the MN1 (meningioma 1) gene. Diagnosis based on histological features alone is challenging: most cases with morphological features of astroblastoma (but not all) show these molecular features, whereas not all tumors with MN1 fusions show astroblastoma morphology. There is large variability in reported outcomes and detailed clinical and therapeutic information is frequently missing. Some patients experience multiple recurrences despite multimodality treatment, whereas others experience no recurrence after surgical resection alone, suggesting large clinical and biological heterogeneity despite unifying epigenetic features and recurrent fusions. In this report, we present the demographics, tumor characteristics, treatment, and outcome (including patient-reported outcomes) of three adults with MN1-altered primary CNS tumors diagnosed via genome-wide DNA methylation and RNA sequencing. All three patients were females and two of them were diagnosed as young adults. By reporting our neuropathological and clinical findings and comparing them with previously published cases we provide insight into the clinical heterogeneity of this tumor. Additionally, we propose a model for prospective, comprehensive, and systematic collection of clinical data in addition to neuropathological data, including standardized patient-reported outcomes.

MN1 altered astroblastoma with APC and LRP1B gene mutations: a unique variant in the cervical spine of a pediatric patient

PURPOSE

Astroblastomas (AB) are high-grade neoplasms which typically occur within the cerebral hemisphere. However, given the rarity of this neoplasm and the number of variants, the relevance of this molecular makeup is unknown. We sought to describe the clinical presentation, treatment, and pathological analysis of a novel MN1 (meningioma 1) cervical spinal cord astroblastoma variant presenting in a pediatric patient.

METHODS

A retrospective review of electronic medical records was performed with an emphasis on neuroimaging, perioperative course, and pathological analysis.

RESULTS

An 11-month-old male with no significant history presented with two weeks of neck stiffness and cervicalgia. Neurologically, the patient was intact without signs of infection or trauma. Cervical CT was unremarkable. A subsequent MRI demonstrated a heterogeneously enhancing intramedullary lesion extending from the craniocervical junction to T4. The patient was treated with perioperative steroids and underwent C1-C3 laminectomies and C4-T4 laminotomies for tumor resection. Upon completion of the durotomy, an exophytic gray-red tumor was appreciated within the epidural space and gross total resection was achieved (no change on intraoperative neurophysiological monitoring) and confirmed on post-operative imaging. Immunohistochemical analysis was consistent with an astroblastoma with atypical diffuse positivity of CD56, CD99, and nuclear OLIG2. Molecular analysis revealed not only MN1 alterations but also changes in genes encoding APC and LRP1B. Both alterations were not previously documented to be associated with an astroblastoma.

CONCLUSION

Our case represents the first report of an infant with an MN1 astroblastoma with APC and LRP1B gene alterations in the cervical spine. Gross total resection paired with a detailed histopathologic analysis is vital for optimizing adjuvant treatment.

An EWSR1-EZHIP fusion in a cerebral hemisphere astroblastoma

Astroblastomas are considered extremely rare tumors and have not been formally graded. While gene mutations are used to diagnose these tumors, further research is needed for proper diagnosis and classification. This report presents a case of astroblastoma in a 44-year-old woman. A tumor was found to have histology consistent with astroblastoma, with no MN1 gene changes. Several mutations were present, and fusion of the EWSR1 and EZHIP genes was noted, which has never been reported before in the literature. Fusions of the EWSR1 gene could be characteristics of astroblastomas, in addition to MN1 alterations, and identification of these mutations could help in the diagnosis of these rare tumors.

The NHS England 100,000 Genomes Project: feasibility and utility of centralised genome sequencing for children with cancer

BACKGROUND

Whole-genome sequencing (WGS) of cancers is becoming an accepted component of oncological care, and NHS England is currently rolling out WGS for all children with cancer. This approach was piloted during the 100,000 genomes (100 K) project. Here we share the experience of the East of England Genomic Medicine Centre (East-GMC), reporting the feasibility and clinical utility of centralised WGS for individual children locally.

METHODS

Non-consecutive children with solid tumours were recruited into the pilot 100 K project at our Genomic Medicine Centre. Variant catalogues were returned for local scrutiny and appraisal at dedicated genomic tumour advisory boards with an emphasis on a detailed exploration of potential clinical value.

RESULTS

Thirty-six children, representing one-sixth of the national 100 K cohort, were recruited through our Genomic Medicine Centre. The diagnoses encompassed 23 different solid tumour types and WGS provided clinical utility, beyond standard-of-care assays, by refining (2/36) or changing (4/36) diagnoses, providing prognostic information (8/36), defining pathogenic germline mutations (1/36) or revealing novel therapeutic opportunities (8/36).

CONCLUSION

Our findings demonstrate the feasibility and clinical value of centralised WGS for children with cancer. WGS offered additional clinical value, especially in diagnostic terms. However, our experience highlights the need for local expertise in scrutinising and clinically interpreting centrally derived variant calls for individual children.

The oncogenic fusion landscape in pediatric CNS neoplasms

Pediatric neoplasms in the central nervous system (CNS) are the leading cause of cancer-related deaths in children. Recent developments in molecular analyses have greatly contributed to a more accurate diagnosis and risk stratification of CNS tumors. Additionally, sequencing studies have identified various, often entity specific, tumor-driving events. In contrast to adult tumors, which often harbor multiple mutated oncogenic drivers, the number of mutated genes in pediatric cancers is much lower and many tumors can have a single oncogenic driver. Moreover, in children, much more than in adults, fusion proteins play an important role in driving tumorigenesis, and many different fusions have been identified as potential driver events in pediatric CNS neoplasms. However, a comprehensive overview of all the different reported oncogenic fusion proteins in pediatric CNS neoplasms is still lacking. A better understanding of the fusion proteins detected in these tumors and of the molecular mechanisms how these proteins drive tumorigenesis, could improve diagnosis and further benefit translational research into targeted therapies necessary to treat these distinct entities. In this review, we discuss the different oncogenic fusions reported in pediatric CNS neoplasms and their structure to create an overview of the variety of oncogenic fusion proteins to date, the tumor entities they occur in and their proposed mode of action.

Neuroimaging of astroblastomas: A case series and systematic review

BACKGROUND AND PURPOSE

Astroblastoma is a rare type of glial tumor, histologically classified into two types with different prognoses: high and low grade. We aimed to investigate the CT and MRI findings of astroblastomas by collecting studies with analyzable neuroimaging data and extracting the imaging features useful for tumor grading.

METHODS

We searched for reports of pathologically proven astroblastomas with analyzable neuroimaging data using PubMed, Scopus, and Embase. Sixty-five studies with 71 patients with astroblastomas met the criteria for a systematic review. We added eight patients from our hospital, resulting in a final study cohort of 79 patients. The proportion of high-grade tumors was compared in groups based on the morphology (typical and atypical) using Fisher's exact test.

RESULTS

High- and low-grade tumors were 35/71 (49.3%) and 36/71 (50.7%), respectively. There was a significant difference in the proportion of high-grade tumors based on the tumor morphology (typical morphology: high-grade = 33/58 [56.9%] vs. atypical morphology, 2/13 [15.4%], p = .012). The reviews of neuroimaging findings were performed using the images included in each article. The articles had missing data due to the heterogeneity of the collected studies.

CONCLUSIONS

Detailed neuroimaging features were clarified, including tumor location, margin status, morphology, CT attenuation, MRI signal intensity, and contrast enhancement pattern. The classification of tumor morphology may help predict the tumor's histological grade, contributing to clinical care and future oncologic research.

PATZ1 fusions define a novel molecularly distinct neuroepithelial tumor entity with a broad histological spectrum

Large-scale molecular profiling studies in recent years have shown that central nervous system (CNS) tumors display a much greater heterogeneity in terms of molecularly distinct entities, cellular origins and genetic drivers than anticipated from histological assessment. DNA methylation profiling has emerged as a useful tool for robust tumor classification, providing new insights into these heterogeneous molecular classes. This is particularly true for rare CNS tumors with a broad morphological spectrum, which are not possible to assign as separate entities based on histological similarity alone. Here, we describe a molecularly distinct subset of predominantly pediatric CNS neoplasms (n = 60) that harbor PATZ1 fusions. The original histological diagnoses of these tumors covered a wide spectrum of tumor types and malignancy grades. While the single most common diagnosis was glioblastoma (GBM), clinical data of the PATZ1-fused tumors showed a better prognosis than typical GBM, despite frequent relapses. RNA sequencing revealed recurrent MN1:PATZ1 or EWSR1:PATZ1 fusions related to (often extensive) copy number variations on chromosome 22, where PATZ1 and the two fusion partners are located. These fusions have individually been reported in a number of glial/glioneuronal tumors, as well as extracranial sarcomas. We show here that they are more common than previously acknowledged, and together define a biologically distinct CNS tumor type with high expression of neural development markers such as PAX2, GATA2 and IGF2. Drug screening performed on the MN1:PATZ1 fusion-bearing KS-1 brain tumor cell line revealed preliminary candidates for further study. In summary, PATZ1 fusions define a molecular class of histologically polyphenotypic neuroepithelial tumors, which show an intermediate prognosis under current treatment regimens.

A pediatric cerebral tumor with MN1 alteration and pathological features mimicking carcinoma metastasis: may the terminology "high grade neuroepithelial tumor with MN1 alteration" still be relevant?

INTRODUCTION

Astroblastoma, MN1-altered (old name: high-grade neuroepithelial tumor/HGNET with MN1 alteration) is a recently described central nervous system tumor mostly affecting pediatric patients and profoundly young girls. Differential pathological diagnoses of these tumors include ependymoma, pleomorphic xanthoastrocytoma, embryonal tumor with multilayered rosettes, meningioma, and even glioblastoma. As the treatment approaches to these tumors differ, it is essential to increase the awareness about these tumors in the neurosurgical community.

CLINICAL PRESENTATION

A 7-year-old female patient admitted with a 7-day history of headache, nausea, and vomiting. A contrasted MRI scan revealed a left parietal 4 × 4 × 5 cm mass with central necrosis and peripheral contrast enhancement. The tumor's histopathological findings were suggestive of a metastatic carcinoma with unknown primary, yet further genetic analysis revealed MN1 alteration. Peculiarly, the tumor pathomorphological features were not compatible with astroblastomas and exerted features strongly indicating a metastatic cancer; however, systemic PET and whole-body MRI failed to detect a primary malignancy.

OUTCOME AND CONCLUSIONS

Eighteen months after gross-total tumor resection, an in-field and out-field multifocal recurrence developed which required a second surgery and subsequent chemo-radiotherapy. The patient is doing well for 1 year after the second treatment regimen at the time of this report. Despite the final cIMPACT6 classification in 2020 advised to define all MN1 altered brain tumors as astroblastomas, there exist prognostic differences in MN1-altered tumors with and without morphological features of astroblastoma. Rare morphological variants of MN1-altered tumors shall be recognized for their future prognostic and clinical classification. HGNET with MN1 alteration seems still be a more proper definition of such malignancies as an umbrella term.