VGLL fusions define a new class of intraparenchymal central nervous system schwannoma

Abstract

Background: Intracerebral schwannomas are rare tumors resembling their peripheral nerve sheath counterparts but localized in the central nervous system (CNS). They are not classified as a separate tumor type in the 2021 World Health Organization classification. This study aimed to compile and characterize these rare neoplasms morphologically and molecularly.

Methods: We analyzed 20 tumor samples by histology, RNA next-generation sequencing, DNA-methylation profiling, copy number analyses, and single-nucleus RNA sequencing (snRNA-seq). Clinical data, including age, sex, and disease progression, were collected. Magnetic resonance imaging (MRI) series were included when available.

Results: All cases with tissue available for histology review (n = 13) were morphologically consistent with intracerebral schwannoma, but differed in their extent of glial fibrillary acidic protein staining. All (n = 20) shared DNA-methylation profiles distinct from other CNS tumors, as well as from Vestigial-like family (VGLL)-altered peripheral nerve sheath tumors. Most cases (n = 14/17) harbored fusions of either Vestigial-like family member 3 (VGLL3) or Vestigial-like Family member 1 (VGLL1) (CHD7::VGLL3 [n = 9/17] and EWSR1::VGLL1 [n = 5/17]). In 2 cases, the presence of a VGLL3 fusion was also confirmed by copy number analyses (n = 2/17). MRI (n = 4) showed well-defined, nodular tumors with strong, homogeneous enhancement and no diffusion restriction. Tumors were located throughout the neuroaxis (supratentorial [n = 15], infratentorial [n = 4], and spinal [n = 1]). snRNA-seq of a VGLL1-fused tumor indicated VGLL1 upregulation in 28.6% of tumor cells (n = 1). During a median follow-up of 1.8 years (range 3 months-9 years), none of the tumors recurred (n = 10).

Conclusions: We identify and define a new benign tumor class, designated VGLL-altered intraparenchymal CNS schwannomas. These tumors feature VGLL alterations and a specific DNA-methylation profile, with schwannoma-like histopathology and CNS localization, akin to previously classified intracerebral schwannomas.

Keywords: VGLL; gliofibroma; glioma; schwannoma; tumor.

Figure 1.

Overview of case 10 highlights nodular growth and varying cell density (A). Areas of varying cell density, resembling Antoni A and Antoni B patterns; H&E, 50× (B). Circumscribed, well-demarcated growth from CNS tissue, H&E, 100× (C). Focal hemosiderin deposits were present in many tumors (D). Depiction of rhythmic growth pattern with palisading of tumor cells; H&E, 200× (E). Fibrotic anucleate zones; H&E, 100× (F). Mineralization could be found in some tumors; H&E, 100× (G). Vascular proliferations were observed in single cases (H). One case demonstrated neuroblastoma-like cell-dense areas (I). All tumors at least focally showed dense fiber network, reticulin silver stain (J). Rosenthal fibers were seen in the surrounding CNS tissue but also in the margin of tumor nodules (K). Tumor samples were evaluated for morphological features and immunohistochemical marker expression. Qualitative and semiquantitative results are summarized (L). All tumor samples expressed GFAP, MAP2C, and S100 in varying degrees; 100× (M–O). The majority of tumors showed weak and focal CD34 expression, 200× (P). OLIG2 protein is absent in the vast majority of tumor cells. Here it highlights the nuclei of cells in the surrounding reactive CNS tissue; 200× (Q).

Figure 2.

tSNE representation of the tumor set in the context of selected reference methylation classes (A). PXA = pleomorphic xanthoastrocytoma; SEGA = subependymal giant cell astrocytoma; DIA/DIG = diffuse infantile astrocytoma/ganglioglioma; CHGL = chordoid glioma of the third ventricle; RGNT = rosette-forming glioneuronal tumor; DLGNT = diffuse leptomeningeal glioneuronal tumor; MPNST = malignant peripheral nerve sheath tumor; MYB/MYBL1 = diffuse astrocytoma, MYB- or MYBL1-altered (A). Two main fusion types were detected in the tumor set, CHD7::VGLL3 (B) and EWSR1::VGLL1 (C). Most cases did not show signs of fusion breakpoints in the copy number profile (CNP); examples for CNP-negative cases of CHD7::VGLL3 fusion (case 2) and EWSR1::VGLL1 fusion (case 11). Only cases 1 and 3 showed detectable breakpoints in CHD7 and VGLL3 by manual inspection (D).

Figure 3.

Representative pre-surgery MRI in ceT1w sequences of four cases with corresponding H&E. The nodular, well-defined growth is already visible on imaging and shows histomorphological correlate (A–C). The intense rim-like contrast enhancement in case 15 could be due to extensive vascular proliferations seen in the H&E-stained section of the tumor sample (D).

Figure 4.

Overview of the results of the single-nucleus RNA sequencing of case 11. UMAP clustering showed a homogeneously composed tumor cell population constituting 57.8% of the total cells, with a small fraction (4.2%) of cycling tumor cells, 5.3% astrocytes, 2.5% endothelial cells, and 34.5% immune cells (A). Depiction of well-demarcated nodular growth of tumor vs. non-tumor tissue; H&E, 200× (B and C). Immunohistochemical staining of GFAP and MAP2c in tumor and non-tumor tissue of this case, each 200× (D and E). RNA expression levels of immunohistochemical markers used in this series correlate well with the light microscopy appearance of the sample. In addition, upregulation of VGLL1 was detected in the tumor cells in contrast to non-tumor cell types. No elevated RNA levels of EWSR1 were observed (G). VGLL tumor cells showed little similarity to normal CNS cell types of the embryonal human brain, but, in this analysis, demonstrate the highest resemblance with peripheral Schwann cells (F).

Figure 5.

Detailed anatomical location of the 20 VGLL-fused intraparenchymal CNS schwannomas with proportions of detected fusion types in supratentorial, infratentorial, and spinal cases (A). Overall proportion and case numbers of detected fusion types in this case series (B). We observed a slight male predominance (C). Age distribution among patients (D). No relapse of disease was reported for the patients in this series (D). Parts of the figure were created with BioRender.com.