Non-supratentorial YAP1- fused ependymomas: report of two cases

Ependymoma is a heterogeneous group of central nervous system tumors [1]. Over the past decade, molecular profiling advancements have enabled the classification of ependymomas into at least ten subtypes, based on anatomical sites (supratentorial, posterior fossa, and spinal cord) and molecular alterations [2]. Supratentorial ependymomas (ST-EPNs) are primarily characterized by two types of fusion variations involving the zinc finger translocation-associated gene (ZFTA) and Yes1-Associated Transcriptional regulator (YAP1) [2]. ZFTA fusion occurs in approximately 66–84% of pediatric ST-EPNs and generally indicates a poor prognosis. In contrast, YAP1 fusion is relatively rare (6–7% of pediatric cases) and usually suggests a more indolent biological behavior. Recently, it has been noted that ZFTA- or YAP1-fusion-positive ependymomas can also occur in the posterior fossa (PF) or spinal cord (SP) [1, 3]. Here, we report two cases of non-supratentorial YAP1-fused ependymomas (one cerebellar and one intramedullary) and comprehensively investigate their histopathological and molecular characteristics, as well as prognosis, to provide detailed insights into these rare cases.

Case #1: An 18-month-old boy had been walking unsteadily for one month and experienced persistent vomiting for four days. Cranial magnetic resonance imaging (MRI) revealed a lesion in the cerebellum with contrast enhancement (Fig. 1A). Histopathological examination showed conventional histology of ependymoma (WHO grade 3) with high cellularity, perivascular pseudorosettes, abundant mitotic activity, microvascular proliferation and necrosis (Fig. 1B). Some tumor areas demonstrated a dense proliferation of spindle cells with mesenchymal differentiation. Spindle cells have moderate atypia and rare mitotic figures. (Figure 1C and D). The reticulin histochemistry showed widespread background collagen and pericellular reticulin. Case #2: A 51-year-old woman lost temperature sensation below her right rib twenty years ago, but she did not exhibit any obvious physical or limb activity disorders at that time. She received traditional Chinese medicine and local rehabilitation treatment, which led to a gradual subsiding of her loss of temperature sensation. While she developed bilateral numbness in the upper extremities nineteen days ago. Spine MRI revealed an intramedullary space-occupying lesion at the C7 to T1 level (Fig. 1I). Histopathological examination revealed a moderately cellularity, well-circumscribed proliferation with ependymal differentiation (WHO grade 2) (Fig. 1J). The nuclei were round to ovoid with prominent nucleoli. The cytoplasm was granular and eosinophilic, along with numerous hyaline degenerations of the vessel walls (Fig. 1K and L). Mitotic figures were infrequent, and no necrosis or microvascular proliferation was observed.

Fig. 1

In case #1, MRI on the T1 sequence shows a mass in the cerebellum with contrast enhancement (A). H&E staining shows an anaplastic ependymal features with necrosis (B), prominent proliferation of spindle cells (C) and mesenchymal differentiation (D). GFAP is diffusely positive in the tumor cells (E). EMA is expressed with a diffuse paranuclear dot-like immunoexpression (F). Olig2 is negative (G). Ki-67 labeling index is high (30%) (H). In case #2: T1-weighted MRI of the spine shows an intramedullary space-occupying lesion at the level of C7 to T1 with contrast enhancement (I). H&E staining shows ependymal features, moderately cellularity (J), abundant granular eosinophilic cytoplasm (K), and numerous hyaline degenerations of the vessel walls (L). GFAP is positive (M). EMA is expressed with a paranuclear dot-like immunoexpression (N). Olig2 is negative (O). Ki-67 labeling index is low (2%) (P)

Immunohistochemistry showed GFAP positivity (Fig. 1E, M) and a diffuse paranuclear dot-like pattern of EMA staining in both cases (Fig. 1F, N). The immunoreactivity test was negative for Olig2 (Fig. 1G, O), p65, L1CAM, H3K27M, and EZHIP. Tumors have retained H3K27me3 and ATRX nuclear expression in both cases. The Ki-67 labeling index was found to be 30% in case #1 and 2% in case #2, respectively (Fig. 1H, P). RNA sequencing revealed that case #1 harbored a YAP1-MAML2 fusion (Fig. 2A), while case #2 had a YAP1-FAM118B fusion (Fig. 2B).YAP1 rearrangements were also identified by fluorescence in situ hybridization (FISH) in both cases (Fig. 2C and D). Additionally, DNA methylation analysis was performed using the Infinium Methylation EPIC 935 K BeadChip array (Illumina, San Diego, USA), based on version 11b4 of the Heidelberg brain tumor classifier. Case #1 clustered with YAP1-positive supratentorial ependymoma (calibrated score: 0.99), and case #2 clustered with spinal cord ependymoma (calibrated score: 0.45) (Fig. 2E). No evidence supported primary ST tumors metastasizing to infratentorial or spinal cord locations. For case #1, The final diagnosis was PF-EPN-YAP1-MAML2 fusion-positive, WHO grade 3. Gross total resection followed by focal radiation therapy was performed. However, the tumor locally recurred after four months. For case #2, The final diagnosis was SP-EPN-YAP1-FAM118B fusion-positive, WHO grade 2. Gross total resection was performed without adjuvant treatment, and the patient remained recurrence-free at the six-month follow-up.

Fig. 2

RNA-NGS shows the YAP1-MAML2 fusion in case #1 (A) and YAP1-FAM118B fusion in case #2 (B). Rearrangement of YAP1 is detected by FISH in case #1 (C) and case #2 (D). DNA methylome profiling and t-SNE analysis (E)

As a rare molecular subtype, YAP1-fused EPNs generally indicate a better prognosis. They primarily occur in the supratentorial regions and predominantly affect females (female-to-male ratio of 2.75), especially children under two years old (median age of 1.4 years) [4]. Although YAP1-fused PF- and SP-EPNs have been reported [1, 5], it remains unclear whether they represent a distinct subset of ependymomas or are closely related to YAP1-fused ST-EPNs. Based on the aforementioned results, we propose that the pathological features and prognosis of YAP1-fused infratentorial ependymomas are not entirely identical to those of YAP1-fused ST-EPNs.

In case #1, the YAP1-MAML2 fusion ependymoma, occurred in a child, was located in the cerebellum and exhibited anaplastic features of ependymoma with mesenchymal differentiation. Although DNA methylation analysis clustered the tumor with ST-EPN-YAP1, which generally suggests an improved prognosis, the tumor recurred four months after gross total resection. In case #2, the tumor with a YAP1-FAM118B fusion in the spinal cord was morphologically classified as a grade 2 ependymoma with granular and eosinophilic cytoplasmic cells and notable hyaline degeneration of the vascular wall. The methylation profiling clustered it with the SP-EPN group, albeit with a calibrated score of only 0.45, indicating that further analysis is required for definitive classification. This case involves a 51-year-old woman with a YAP1 -fused ependymoma, which is extremely rare in the spinal cord. For 20 years, she had lost temperature sensation below the level of her right rib. Because there are no MRI results from this period, we can only infer that the prolonged duration of her symptoms suggests the tumor’s very indolent behavior. We are still actively monitoring the patient’s prognosis.

The YAP1 gene encodes the Yap1 protein, a downstream effector of the Hippo tumor suppressor pathway that regulates transcription through the transcriptional enhanced associate domain (TEAD) [6]. Its fusion partners include MAMLD1, FAM118B, MAML2, TFE3, SS18, and ZFTA [7]. Among these, YAP1-MAMLD1 is the most common fusion in YAP1-fused ST-EPN, while YAP1-MAML2 and YAP1-FAM118B fusions are extremely rare [5, 8,9,10]. In summary, this report provides detailed information on YAP1-fused non-ST-EPNs and suggests that this subtype may differ from conventional YAP1-fused ST-EPNs. Further studies are needed to understand the biological functions of YAP1 fusion in the oncogenic and developmental processes of ependymomas at different anatomical sites.