Abstract Introduction FGFR structural variations and mutations present rare actionable alterations in pLGG. Objective To investigate clinical and laboratory characteristics of FGFR-altered LGG in children. Materials and Methods Retrospectively 20 pediatric patients with LGG harboring FGFR alteration revealed by DNA or RNA sequencing diagnosed between 2017-2025 were evaluated. Results The male-to-female ratio was 1:1,5. Median age at diagnosis was 7.4 years (range: 1.1–16.8). Localization included midline structures (13), cerebral hemisphere (5) and cerebellum (2). Metastatic disease was in 5 patients. There were 4 cases of gross total resection (GTR), 11 of partial tumor resection (PR) and 5 biopsies. The initial morphological diagnoses: pilocytic astrocytoma (14), dysembryoplastic neuroepithelial tumor (2), low-grade glioma (2), polymorphous low grade neuroepithelial tumor of the young (1), and glioneuronal tumor (1). Molecular alterations were: FGFR fusions (n = 9, predominantly, FGFR1::TACC1), point mutations (n = 7) and internal tandem duplications (n = 4). Four cases of FGFR1 and PIK3CA co-mutations were observed. All 4 patients who underwent GTR and 4 of 11 patients after PR remained progression -free without further intervention. 7 patients received chemotherapy (carboplatin and vincristine) and 2 patients received focal radiation as firstline treatment. Disease progression was observed in 9 of 20 patients. Six patients received targeted therapy at the time of progression : FGFR inhibitor (erdafitinib) in 3 cases, combination of mTOR and MEK inhibitors (everolimus and trametinib) in 2 cases, and monotherapy with mTOR inhibitor (everolimus) in 1 case. No progression was detected in the targeted therapy cohort. At the time of followup, 18 patients were alive and 2 patients died from complications (tumor hemorrhage after radiation and pneumonia). Median followup time achieved 3.3 years (0.4–8.6). Conclusion FGFR-altered tumors exhibit morphological and clinical variability. In cases with GTR, observation may be sufficient. In case of progressive disease different types of targeted therapy could be effective treatment option.

Under the auspices of the World Health Organization Classification of CNS Tumors (5th Edition), supratentorial ependymomas are divided into 2 main molecular groups, comprising tumors that are either ZFTA- or YAP1-fused with the majority harboring ZFTA::RELA fusion. ZFTA-rearranged ependymomas with non-canonical 3´ fusion partners have significant clinical, radiological, and histopathological variability. We report a 5-year-old girl with a left frontal lobe tumor harboring a ZFTA::YAP1 fusion. The patient presented with recurrent absence episodes aggravating to epileptic seizures. The histological appearance of the tumor was inconclusive and shared morphological features of ependymal and glioneuronal neoplasms. Despite the nominal presence of a ZFTA alteration typically associated with aggressive ependymal tumors, the lesion demonstrated prolonged indolent biological behavior. Gene expression assay revealed paradoxical activation of YAP/TAZ signaling and signature unambiguously correspondent to YAP1-activated ependymoma. To our knowledge, this is the first case report demonstrating the molecular background of ZFTA::YAP1-rearranged ependymoma. The case denies the binary classification of supratentorial ependymomas into ZFTA and YAP1 subtypes based entirely on the identity of 5′ partner gene involved in the rearrangement. The findings elaborate the concept of molecular pathogenesis for YAP1-rearranged tumors.

Maturation is an enigmatic property of neurogenic tumors, including neuroblastoma and brain tumors in the unique cases. Multiple factors (TrkA-signaling, microenvironment, telomerase and epigenetics) have been linked to the tumor maturation. We analyzed four cases of pediatric CNS tumors (medulloblastoma SHH-activated; ETMR; unspecified CNS embryonal tumor (ET-CNS); thalamic high-grade glioma, HGG) having undergone a morphologically verified maturation to ganglioglioma, pleomorphic xanthoastrocytoma or diffuse low-grade glioma in parallel with 23 cases of maturating extracranial neuroblastoma. The paired tumor samples were analyzed using targeted NGS and gene expression profiling by NanoString. The NanoString experiment revealed an identical shift of gene expression profile, all investigated tumors after maturation clustered together regardless of initial tumor type. MAPK (FDR=1.54×10-14), PI3K-AKT-mTOR (FDR=6.78×10-13) and TrkA signaling (FDR=2.72×10-11), cellular senescence (FDR=3.90×10-9) were predicted to be activated, while cell cycle control, DNA replication and repair (FDR respectively 1.53×10-14, 2.04×10-14 and 3.60×10-13) - repressed. Moreover, tumors completing the maturation similarly showed enhanced immunogenicity, mostly pronounced in MB and ETMR. Maturing cases of neurogenic tumors were enriched in genetic aberrations leading to MAPK cascade activation: mutations in BRAF (n=5), PTEN,PTPN11,HRAS or NF1, and a KCTD16::NTRK2 rearrangement (in neuroblastoma, ET-CNS and HGG, respectively). Genes encoding neurothophin receptors, epigenetic writers, erasers, and Kruppel-family transcription factors had similar dynamics of expression upon maturation in both CNS malignancies and neuroblastoma. NTRK1 expression was elevated at debut, whereas NTRK2 increased during maturation. Expression of negative epigenetic regulators HDAC2,HDAC10,DNMT3A and EZH2 similarly decreased in maturing tumors, while positive (SWI/SNF subunits) increased at the beginning of maturation and decreased upon the differentiation completion. KLF4, GLI1/3 expression significantly increased in the matured tumors. Central and peripheral neurogenic tumors share common mechanisms of maturation, which include maintenance of MAPK signaling via neurotrophins and consistent changes in expression of epigenetic modifiers and KLF-like transcription factors.

Despite the progress in understanding the pathogenesis of diffuse brainstem tumors, treatment of these neoplasms is usually empirical and conducted without morphological and molecular verification. Liquid biopsy is a minimally invasive technique providing data on tumor biology without standard biopsy. This method is based on analysis of cell-free nucleic acids (predominantly, extracellular DNA) in biological fluids with detection of specific mutations. Despite wide implementation in diagnosis and disease monitoring in extracranial malignancies, it is infrequently applied in neuro-oncology. OBJECTIVE:To estimate diagnostic value of liquid biopsy in detecting H3K27 and BRAF V600E mutations in patients with diffuse brainstem tumors. MATERIAL AND METHODS:Lumbar puncture with cerebrospinal fluid sampling was performed in 16 patients (5 children and 11 adults) with diffuse brainstem tumors verified by neuroimaging data. Cell-free DNA (cfDNA) was used in digital droplet PCR for determination of H3F3A K28M and BRAF V600E oncogenic missense variants. In 14 patients, investigation of cfDNA was performed in parallel with analysis of correspondent mutations in DNA derived from tumor tissue. RESULTS:None patient had BRAF V600E mutation. H3F3A K28M variant was detected in 5 CSF samples and 6 tumor specimens from patients who underwent surgical biopsy. Thus, overall sensitivity of the method in determination of H3F3A K28M variant was 92.9% (13/14). CONCLUSION:Liquid biopsy is highly informative for identifying the specific mutation H3F3A K28M and often verifies diffuse brainstem glioma without standard biopsy.

Background:Infant-type hemispheric gliomas (IHG) represent a novel entity, first codified in the WHO CNS 5 classification. Due to their rarity, as well as their neuroimaging and histopathologic heterogeneity, definitive diagnosis can be challenging. In the majority of cases, the tumors are large, and difficult to fully resect. The efficacy of standard cytotoxic chemotherapy remains unclear. IHGs frequently contain receptor tyrosine-kinase (RTK) gene fusions, denoting a potential vulnerability to targeted therapy by small-molecule RTK inhibitors. Methods:We report 15 patients with IHG receiving treatment during a 5-year period. Integrated diagnosis was achieved combining histopathology, DNA methylation profiling and RNA sequencing. Ten out of 15 patients received chemotherapy. Targeted therapy with entrectinib or lorlatinib was prescribed in 5 patients after progression and in 1 as first-line treatment. Results:The median follow-up was 1.5 years (range, 0.1-5.1 years). Six patients were asymptomatic despite large volumes and diagnosed during routine ultrasound screening. Neuroimaging revealed 2 general radiographic presentation, either cystic-solid or purely solid masses. These radiologic subtypes were not associated with differences in histology or clinical behavior, but demonstrated differential gene expression profiles. Standard cytotoxic chemotherapy was administered in 10 patients, in 6 of them disease progression was observed (all with residual tumor). RTK gene fusions were revealed in all cases. Six patients were treated with targeted therapies. All patients had an initial tumor response; following which 2 had disease progression. One-year event-free survival for the entire cohort was 47% (CI 27%-80%), 2-year overall survival was 61% (CI 39%-95%). Conclusions:IHGs are comprised of 2 radiologically and molecularly distinct groups. Huge cystic tumors are frequently associated with life-threating complications. The limited efficacy of the standard cytotoxic chemotherapy and presence of kinase fusion in nearly all cases render patients with IHG candidates for targeted therapies.

Pleomorphic xanthoastrocytoma (PXA) represents a rare glial brain tumor with variable prognosis. The majority of cases in adulthood harbor BRAFV600E mutation and CDKN2A homozygous deletion, while pediatric PXA remained poorly investigated. 42 pediatric patients with morphologically verified PXA (28 grade 2 and 14 grade 3) with median age of 9.9 years were investigated. Molecular studied included BRAF codon 600 allele-specific PCR, targeted RNA sequencing, DNA methylation assay. First-line management was conducted as per SIOP-LGG or HIT-HGG protocols depending on tumor grade. Targeted therapy was applied mostly after disease progression and first-line in two cases. Median of follow-up time achieved 4.0 years. Molecular genetic markers included BRAF V600E mutation in 25 cases (59.5%), CDKN2A deletion either homo or heterozygous in 23 (54.8%) and rearrangements of receptor tyrosine-kinase (RTK) genes (CCDC88A::ALK, SFPQ::ALK, NOS1AP::NTRK1, TPM3::NTRK1, NACC2::NTRK2, ETV6::NTRK2, VIM::NTRK3, GOPC::ROS1) in 8 patients (19.0%). Remarkably, four patients with RTK fusions aged >10 years did not matched any known DNA methylation class (DKFZ v.12.8) while others were perfectly consistent with MC PXA (>0.90). CDKN2A deletions were uniformly distributed between BRAF-mutated and RTK-fused cases. Patients with PXA grade 2 were observed after surgery and extent of tumor resection predicted survival (p=0.01). Radiation therapy of PXA grade 3 was not able to control the disease: 2-year progression-free survival (PFS) – 31% (95%CI14-70%). Targeted therapy was used in 15 cases (9 PXA grade 3 and 6 PXA grade 2) with combination of dabrafenib and trametinib in 12 and entrectinib in 3. This resulted in 2-year PFS 100% and 50.0%(95%CI27-93%) for PXA grade 2 and 3, respectively. PXA is a molecularly heterogenic tumor with high frequency of actionable genetic alterations. RTK fusions should be investigated in all BRAF-negative cases. Targeted therapy demonstrated promising results.

Introduction. Medulloblastoma (MB) is a clinically and biologically heterogeneous tumor of the central nervous system (CNS); however, current risk stratification criteria rely primarily on its clinical and morphological features. The aim of the study was to assess molecular and genetic characteristics of MB in standard risk group patients and analyze their impact on the clinical course of the disease and long-term treatment outcomes. Materials and methods. This retrospective study included 137 patients with standard-risk MB according to the criteria in the HIT-MED 2020. The study was approved by the Independent Ethics Committee and the Scientific Council of the Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology of Ministry of Healthcare of the Russian Federation. All the patients underwent molecular subgrouping (WNT, SHH, Group 3, or Group 4). Overall survival (OS), event-free survival (EFS), and relapse characteristics were assessed in relation to molecular subgroup, craniospinal irradiation (CSI) dose, and time to the start of radiotherapy. Results. Five-year OS and EFS rates for the entire cohort were 84% and 74%, respectively. The most favorable outcomes were observed in the WNT subgroup (OS 93%, EFS 86%); however, recurrences occurred in 14.6% of the patients, exclusively among those who received a CSI dose of 23.4 Gy. In the SHH subgroup, the recurrence rate was 39.1% and was associated with the presence of TP53 mutations. CSI dose escalation of did not improve survival in this subgroup. Patients in Group 3 had the poorest prognosis, with a high rate of early metastatic relapses, particularly among those treated with a CSI dose of 23.4 Gy. Patients in Group 4 had intermediate survival and a moderate recurrence rate (22%). Neither CSI dose nor the time to the start of radiation therapy had a significant impact on survival in the entire cohort. Conclusion. Molecular subgroups are an important prognostic factor even in patients with favorable clinical and morphological profiles. Our findings support the need to integrate molecular stratification into routine clinical practice and to be careful when considering de-escalation or intensification of treatment strategies in the standard-risk group.

Abstract BACKGROUND The prognosis for patients with pediatric high-grade glioma (pHGG) is poor despite aggressive multimodal therapy. Recent advances in understanding tumor biology facilitate utilization of targeted therapies (TT) in pediatric neuro-oncology. METHODS We analyzed the efficacy of targeted therapy in patients with progressive pHGG treated with TT according to molecularly-identified actionable events. Molecular characterization of the tumor included DNA panel and transcriptomic RNA sequencing. RESULTS Eighteen patients were included (median age 3.7 years, range 0.1-17.7) with anaplastic pleomorphic xanthoastrocytoma (n=10), infant-type hemispheric glioma (n=4), and diffuse high-grade glioma (n=4). Metastatic disease was present in 3/18 patients. Molecular genetic alterations included BRAF V600E mutations (n=8), NTRK1/2/3 fusions (n=4), ROS1 fusions (n=4), MET fusion (n=1), KIT P627L mutation (n=1). Eight patients received an NTRK/ALK/ROS1 inhibitor (entrectinib), seven patients received combination therapy with BRAF and MEK inhibitors (dabrafenib and trametinib), and one patient anti-BRAF monotherapy (dabrafenib). Two patients were treated with a multi-tyrosine kinase inhibitor (cabozantinib). The median duration of targeted therapy was 10.6 months (1-42). Most patients tolerated treatment well with no grade 4-5 toxicities. The overall response rate was 66% (12/18), including 4 complete (22%) and 8 partial responses (44%). At 12 months, PFS was 86% with dabrafenib/trametinib and 42% with entrectinib; at 18 months PFS was 44 % with dabrafenib plus trametinib and 42% with entrectinib. Three out of four patients with ROS1 rearranged glioma experienced disease progression on entrectinib after an initial good response in all cases; two of them subsequently received lorlatinib with clinical benefit. All four patients with NTRK1/2/3 rearranged gliomas remain on entrectinib therapy without signs of progression. Cabozantinib therapy resulted in prolonged complete and partial responses in both cases. CONCLUSIONS TT for patients with progressive pHGG is feasible and provides unexpectedly good clinical efficacy.

PURPOSE Midline low-grade gliomas (mLGGs) of early childhood have a poorer prognosis compared with tumors of other localizations and in older patients. LGGs are associated with aberrant activation of RAS-RAF-MEK pathway, and pharmacological inhibition of the pathway has therapeutic promise. The aim of this study was clinical and molecular characterization of infantile mLGGs, with emphasis on the efficacy of targeted kinase inhibition. PATIENTS AND METHODS This study enrolled 40 patients with mLGG age <3 years. The majority of the patients (30/40) received first-line chemotherapy (CT) as per International Society of Paediatric Oncology LGG 2004 guidelines. In all patients, molecular genetic investigation of tumor tissue by polymerase chain reaction and RNA sequencing was performed. The median follow-up was 3.5 years. RESULTS First-line CT failed in 24 of 30 recipients. The identified molecular profiles included KIAA1549::BRAF fusions in 26 patients, BRAF V600E in six patients, FGFR1::TACC1 fusions in two patients, and rare fusion transcripts in four patients. At disease progression, targeted therapy (TT) was initiated in 27 patients (22 patients received trametinib) on the basis of molecular findings. TT was administered for a median of 16 months, with partial response achieved in 12 of 26 (46%) patients in which response was evaluated. Severe adverse events were detected only on trametinib monotherapy: acute damage of GI or urinary mucosa complicated by hemorrhage and development of transfusion-dependent anemia in four patients and grade 3 skin toxicity in three patients. CONCLUSION mLGGs of early childhood are often aggressive tumors, resistant to CT, and frequently require alternative treatment. The majority of patients harbor druggable molecular targets and respond to molecular TT.

Intracranial mesenchymal tumors with rearrangements of the genes of the FET and CREB families were first described in the 2021 World Health Organization classification of tumors of the central nervous system. At the moment, the criteria for the diagnosis and treatment of these tumors have not been unambiguously defined. This article presents two exceptionally rare clinical cases of adolescent patients with IMT with the presence of gene rearrangement of the FET and CREB gene families, who were treated and examined at the Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology. The patients’ parents gave consent to the use of their children's data, including photographs, for research purposes and in publications.

Abstract We analyzed an infant cohort consisting of 14 patientswith hemispheric gliomas (hHGG, n=10 and DIGG, n=4) diagnosed at D. Rogachev Center between 2017and 2022. The hHGG cohort included nine females and one male ranging in age from one week to 22 months. RTK-fusions were detected in all (ROS1 - 4, ALK - 2,NTRK1 – 2, NTRK3 - 1, and EGFR - 1). In one of thesecases, the diagnosis was made retrospectively in a patient initially diagnosed with anaplastic ependymoma who died during treatment. Out of the nine remaining hHGG patients, four (ROS1 - 3, NTRK3-1) experienced rapid progressive disease (PD) duringconventional chemotherapy and one pt (ROS1) after RT. These five pts received targeted therapy with entrectinib with initial good responses in all cases (CR-2, PR-3); one of these patients (ROS1) experienced PD after 7 months of targeted therapy and died of disease. Molecular genetic analysis after the second operationin this case revealed an acquired ROS1 G2032R mutation. Treatment-related adverse events on entrectinib therapy were detected in two patients and included bone fractures and neutrophil count decrease in one case and decrease left ventricular ejection fraction in another patient. Median duration of targeted therapy was 7 months (range, 3-33). From those pts who received only chemotherapy – 2 pts are alive with CR and 1 pt died from complication of CT. All patients with DIGG are alive without signs of progression after surgery alone. Median follow-up time is 19 months (range, 5-64). Molecular genetic analysis revealed MAPK-pathway alterations in each case (rearrangements of NTRK1-1, ROS-1, RAF1-1, BRAF-1), respectively. Patients with infant hHGG demonstrate an aggressive course on conventional therapy, especially in cases with ROS1-positive tumors. Targeted therapy may be an effective treatment option but required close monitoring for toxicity and resistance.

Background Choroid plexus carcinomas (CPCs) are rare aggressive pediatric tumors of the brain with no treatment standards. Genetic profiling of CPCs is often confined to possible association with Li-Fraumeni syndrome, though only about a half of CPCs develop from syndromic predispositions. Whole-chromosome gains and losses typical of CPCs reflect genomic instability of these tumors, but only partially explain the aggressive clinical course. Methods This retrospective study enrolled 25 pediatric patients with CPC, receiving treatment between January 2009 and June 2022. Molecular-genetic testing was performed for 20 cases with available tumor tissue and encompassed mutational status, chromosomal aberrations, and gene expression profiles. We analyzed several factors presumably influencing the outcomes, including molecular profiles and clinical parameters. The median follow-up constituted 5.2 years (absolute range 2.8-12.6 years). Results All studied CPCs had smooth mutational profiles with the only recurrent event being TP53 variants, either germline or somatic, encountered in 13 cases. Unbalanced whole-chromosome aberrations, \nnotably multiple monosomies, were highly typical. In 7 tumors, chromosome losses were combined with complex genomic rearrangements: segmental gains and losses or signs of chromothripsis. This phenomenon was associated with extremely low 5-year survival: 20.0 +/- 17.9% vs 85.7 +/- 13.2%; P = .009. Transcriptomically, the cohort split into 2 polar clusters Ped_CPC1 and Ped_CPC2 differing by survival: 31.3 +/- 17.8% vs 100%; P = .012. Conclusion CPCs split into at least 2 molecular subtypes distinguished both genomically and transcriptomically. Clusterization of the tumors into Ped_CPC1 and Ped_CPC2 significantly correlates with survival. The distinction may prove relevant in clinical trials for dedicated and patient-oriented optimization of clinical protocols for these rare tumors.

An 11-year-old previously healthy girl presented with acute cerebral symptoms in the form of headache and vomiting two to three times a day, bringing relief. MRI of the brain revealed a pathological cystic formation in the left frontoparietal region, of an oval shape with clear, partly uneven outlines and a total size of 35 × 44 × 31 mm, intensively accumulating the contrast agent along the periphery. The lesion exerted a pronounced mass effect, displacing the median structures to the right by 9 mm and squeezing the left lateral ventricle (Figure 1). The patient underwent gross total resection. MRI of the brain and spinal cord showed no metastatic spread of the tumor. Cytological examination of the cerebrospinal fluid revealed no malignant cells. The patient received proton therapy on the resected tumor bed to a total focal dose of 59.4 Gy. Follow-up MRI and 11C-methionine PET/CT scans verified a remission of the main disease, lasting 1.6 years (Box 1). Access at https://isn-slidearchive.org/?col=ISN&fol=Archive&file=BPA-22-06-167.svs Morphological examination revealed a malignant tumor composed of ovoid cells with abundant eosinophilic cytoplasm, forming perivascular pseudorosettes and suggesting a differential diagnosis between ependymoma and astroblastoma. The tumor showed high mitotic activity (up to 5 mitotic figures in 10 visual fields at magnification 400×), microvascular proliferation and necrosis, Figure 2A. Immunohistochemically, the tumor cells tested positive for GFAP, S100, dot-like EMA, focal Synaptophysin and preserved INI1 expression, Figure 2B. Single nuclei were positive for Olig2. Immunohistochemical tests for Chromogranin A, Myelin Basic Protein, Neurofilament, Desmin, Myogenin, and MyoD1 were negative. The Ki67 proliferation index reached 20%. The morphological and immunohistochemical findings suggested a diagnosis of anaplastic ependymoma. The putative diagnosis of supratentorial ependymoma was questioned by genetic examination of the tumor tissue, which identified no ZFTA::RELA or YAP1::MAMLD1 fusions by PCR. High-throughput genomic sequencing revealed no mutations with established clinical or diagnostic significance in H3F3A, BRAF, IDH1/2, TP53, PDGFRA, TERT, or CDKN2A/B. DNA methylation profiling was thereafter performed, but results were of intermediate confidence; the tumor was classified as Neuroepithelial Tumor, PATZ1 fusion-positive with borderline score (0.79052) according to the DKFZ Brain Tumor Classifier version v12.5. The highly recurrent MN1::PATZ1 fusion was subsequently revealed by RNA sequencing (TruSeq RNA exome, Illumina), Figure 2D. The formation of the chimeric oncogene was related to copy number variations (chromothripsis) on Chromosome 22. Given the light microscopic appearance suggestive of ependymal differentiation, ultrastructural studies were performed. Transmission electron microscopy revealed loose arrangement of the cells in the abundant matrix containing dense collagen fibrils (Figure 2C). Even in hypercellular regions corresponding to perivascular pseudorosettes by light microscopy, cell-to-cell contacts/junctions were not observed. Lumina, cilia, and microvilli typical of ependymal differentiation were not present. Unusual neoplasm with glial (?) differentiation, harboring MN1::PATZ1 fusion, NEC. Neuroepithelial tumors PATZ1 fusion-positive (NET-PATZ1) are extremely rare, recently recognized, predominantly pediatric CNS tumors. Histologically, these tumors exhibit hypercellularity, rounded or spindle cell morphologies, variable nuclear shapes and eosinophilic cytoplasm. The mitotic activity is typically moderate and occasionally high. The majority of NET-PATZ1 present with endothelial proliferation and about one-third of them show pronounced necrosis recognized by formation of the perivascular astroblastoma-like pseudorosettes. Despite the range of histopathology, a common DNA methylation signature helps to identify NET-PATZ1 [1]. Chromosomal rearrangements involving PATZ1 are highly specific for NET-PATZ1. The 5′-partner genes in PATZ1 rearranged neoplasms (EWSR1 or MN1), which encode the transcription activation domain in the emerging chimeric oncoprotein, are also present in astroblastoma (MN1::BEND2, less frequently EWSR1::BEND2) and intracranial myxoid mesenchymal tumors with FET-CREB fusions (EWSR1::ATF1, EWSR1::CREB1, or EWSR1::CREM) [1, 2]. In contrast, the 3′-partner genes are disease-specific: BEND2 fusions are found in astroblastoma, whereas PATZ1 fusions act as oncogenic drivers in NET-PATZ1 regardless of the 5′-fusion partner. Identical PATZ1 fusions have been found in individual cases of extracranial spindle and round cell sarcomas, which may show variable coexpression of myogenic and neurogenic markers (S100, SOX10, and GFAP). Although PATZ1-fusion positive CNS and extra-CNS tumors may share common histopathological and immunohistochemical features, the cellular origin of NET-PATZ1 remains uncertain, wavering between glioneuronal and mesenchymal [2]. In our case, ultrastructural investigation revealed the absence of ependymal submicroscopic features and in addition showed tumor cells loosely embedded in a collagenous stroma, more typical of mesenchymal neoplasms, however myogenic immunohistochemical markers were negative. On the basis of the layered diagnostic information complying with WHO CNS5, involving high-throughput molecular technologies apart from the morphological examination, the primary diagnosis of anaplastic ependymoma in the studied clinical case was refined. At the time the integrated diagnosis of this unusual and puzzling case was completed, the patient had commenced radiotherapy in accordance with the primary diagnosis of anaplastic ependymoma. Given the limited information regarding the long-term prognosis of NET-PATZ1 tumors, it was decided to proceed with complete radiotherapy to the total focal dose of 59.4 Gy. Transmission electron microscopy studies were performed on the equipment supported by Nikon Center of Excellence at Belozersky Institute of Physico-Chemical Biology and Lomonosov Moscow State University Development program (PNR 5.13). The study was supported by Foundation for support and development in the field of Pediatric Hematology, Oncology and Immunology "Science for Children." Transmission electron microscopy investigations were supported by Russian Science Foundation grant 21-75-00109. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The Independent Ethics Committee and the Scientific Council of the Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology approved the study. Written voluntary consent to the patient participation in the study was obtained from legal representative. The authors confirm that the data supporting the findings of this study are available within the article. Raw data that support the findings of this study are available from the corresponding author, upon reasonable request (see Box 1).