Clinicopathological and molecular characterization of a case classified by DNA‑methylation profiling as "CNS embryonal tumor with BRD4-LEUTX fusion"

Abstract

Central Nervous System (CNS) embryonal tumors represent a heterogeneous group of highly aggressive tumors occurring preferentially in children but also described in adolescents and adults. In 2021, the CNS World Health Organization (WHO) classification drastically changed the diagnosis of the other CNS embryonal tumors including new histo-molecular tumor types. Here, we report a pediatric case of a novel tumor type among the other CNS embryonal tumors classified within the methylation class "CNS Embryonal Tumor with BRD4-LEUTX Fusion". The patient was a 4-year girl with no previous history of disease. For a few weeks, she suffered from headaches, vomiting and mild fever associated with increasing asthenia and loss of weight leading to a global deterioration of health. MRI brain examination revealed a large, grossly well-circumscribed tumoral mass lesion located in the left parietal lobe, contralateral hydrocephalus and midline shift. Microscopic examination showed a highly cellular tumor with a polymorphic aspect. The majority of the tumor harbored neuroectodermal features composed of small cells with scant cytoplasm and hyperchromatic nuclei associated with small "medulloblastoma-like" cells characterized by syncytial arrangement and focally a streaming pattern. Tumor cells were diffusely positive for Synaptophysin, CD56, INI1 and SMARCA4 associated with negativity for GFAP, OLIG-2, EMA, BCOR, LIN28A and MIC-2. Additional IHC features included p53 protein expression in more than 10% of the tumor's cells and very interestingly, loss of H3K27me3 expression. The Heidelberg DNA-methylation classifier classified this case as "CNS Embryonal Tumor with BRD4:LEUTX Fusion". RNA-sequencing analyses confirmed the BRD4 (exon 13)-LEUTX (exon 2) fusion with no other molecular alterations found by DNA sequencing. Our case report confirmed that a new subgroup of CNS embryonal tumor with high aggressive potential, loss of H3K27me3 protein expression, BRDA4-LEUTX fusion, named "Embryonal CNS tumor with BRD4-LEUTX fusion", has to be considered into the new CNS WHO classification.

Keywords: BRD4; Brain tumor; CNS embryonal tumor; DNA methylation; H3K27me3 protein expression; LEUTX.

Fig. 1

Radiological features. Pre-operative brain MRI a–f Images revealed a grossly well-marginated tumor mass lesion of approximately 8 × 9 cm located in the left parietal lobe. The lesion exerted severe mass effect on the ipsilateral lateral ventricle and adjacent brain parenchyma, resulting in contralateral active hydrocephalus (*in a and c) and midline shift. There was only mild peritumoral vasogenic edema. Signal intensity was strikingly heterogenous on all sequences suggesting the presence of core calcifications, necrosis and hemorrhage. The peripheral solid tumoral components displayed significant T2 prolongation (△ in a) and restricted diffusion on DW-images b, e and corresponding ADC map (△ in c), indicating high cellularity. ASL perfusion d demonstrated markedly increased CBF. Smaller size metastatic intraventricular (arrows in a–e), leptomeningeal (arrow in f) and parenchymal (bold arrows in e) lesions were present both supra-and infra-tentorially. The left parietal lobar lesion displayed faint, heterogenous contrast enhancement, whereas the right temporal lobe lesion enhanced avidly. The metastatic intraventricular deposits did not show any contrast uptake. Follow-up brain (g, h) and spinal cord (i) MRI: post contrast coronal T1-weighted (h) and sagittal T1-weighted (i) images of the brain and spinal cord, four weeks after diagnosis, demonstrated marked interval tumoral increase in size and progression of subependymal and leptomeningeal dissemination (arrows). Surrounding vasogenic edema was also increased (*in g). DW: diffusion-weighted; ADC, apparent diffusion coefficient; ASL, arterial spin labeling; CBF, cerebral blood flow

Fig. 2

Histopathological features. a The tumor was highly cellular, composed of small cells with scant cytoplasm and hyperchromatic nuclei (HE, magnification 400×). b, c Intratumoral desmoplasia with focally tumoral cells disposed in a streaming pattern (HE, magnification 200×). d Tumoral geographical necrosis (HE, magnification 100×). e: Microvascular endothelial proliferation (HE, magnification 100×). f Intratumoral hemorrhage (HE, magnification 100×). g Calcifications (HE, magnification 200×). h Presence of numerous “bizarre cells” with high nuclear pleomorphism (HE, magnification 200×). i Reticulin stain highlighted intense desmoplasia (HE, magnification 200×). HE, Hematoxylin–eosin

Fig. 3

Immunohistochemical features. a Diffuse Synaptophysin immunopositivity (magnification 400×). b Diffuse CD56 immunopositivity (magnification 400×). c Intense nuclear immunopositivity of p53 protein in more than 10% of the tumoral cells (magnification 400×). d Loss of Filamine-A expression in tumoral cells with immunopositivity in endothelial cells (magnification 400×). e Loss of H3K27me3 expression in tumoral cells with immunopositivity in endothelial cells (magnification 400×). f High KI-67 proliferation index with some hotspot of more than 50% of immunopositivity in tumoral cells (magnification 200×)

Fig. 4

Copy Number Variation (CNV) profile. DNA methylation profiling analyses by the Heidelberg Classifier V12.5 provided CNV profile of the case revealing gain of chromosome 1p and loss of chromosome 6q, provided by https://www.molecularneuropathology.org