Outcome-associated factors in a molecularly defined cohort of central neurocytoma

Abstract

Central neurocytomas (CN) are intraventricular brain tumors predominantly occurring in young adults. Although prognosis is usually favorable, tumor recurrence is common, particularly following subtotal resection (STR). Currently, the risk of progression is evaluated using atypical features and an elevated Ki67 proliferation index. However, these markers lack consistent definitions, raising the need for objective criteria. Genome-wide DNA methylation profiles were examined in 136 tumors histologically classified as CN. Clinical/histopathological characteristics were assessed in 93/90 cases, and whole-exome sequencing was conducted in 12 cases. Clinical and molecular characteristics were integrated into a survival model to predict progression-free survival (PFS). A diagnosis of CN was epigenetically confirmed in 125 of 136 cases (92%). No DNA methylation subgroups were identified, but global DNA hypomethylation emerged as a hallmark feature of CN associated with higher recurrence risk. Risk stratification based on histological features of atypia and Ki67 proliferation index was not reproducible across neuropathologists. Hypomethylation at the FGFR3 locus, accompanied by increased FGFR3 protein expression, was observed in 97% of cases. Gross total resection was associated with significantly improved PFS compared to STR, while patients undergoing STR receiving radiotherapy had a better outcome (p = 0.0001). Younger patients were identified as having a higher risk of recurrence (p = 0.026). Patient age and treatment strategy were key factors associated with survival outcomes in this cohort. These findings underscore the importance of closer follow-up for younger patients and radiotherapy for STR cases. Furthermore, FGFR3 represents a hallmark feature and potential therapeutic target, warranting further investigation.

Keywords: DNA methylation profiling; FGFR3; Neurocytoma; Progression-free survival; Radiotherapy.

Fig. 1

Study cohort selection of the central neurocytoma based on DNA methylation analysis. A The DNA methylation profiles of 134 patients with the histopathological diagnosis of CN and two gliomas were analyzed using the Heidelberg Brain Tumor Classifier v12.8 to exclude misdiagnoses. Six cases fell into other methylation classes, and 5 did not yield a sufficient classifier score (< 0.9). B The median age at diagnosis of the remaining cases was 29 years (n = 123, NA n = 3). The sex distribution was equal. C In the t-distributed stochastic neighbor embedding (t-SNE) representation, 111 primary and 22 recurrent CNs, including six matched pairs, formed a distinct group separate from other methylation classes of the reference data set from Capper et al. 2018. Cases that have been excluded based on the brain tumor classifier result (red outlines) mapped mostly to other groups, except for one case (#3), which had a prediction score < 0.9 and localized adjacent to the CN group (for consistency excluded from further analyses)

Fig. 2

Adjuvant radiotherapy is assocatiated with lower recurrence risk in subtotally resected patients. A-B Gross total resection (GTR; p = 0.047) and adjuvant radiation therapy (aRT, p = 0.019) are significantly associated with better outcome in CN patients. C-D However, the advantage of adjuvant radiation was limited to patients with a subtotal resection (STR group, p = 0.0001), with no significant effect on PFS for GTR patients (p = 0.37)

Fig. 3

FGFR3 gene body hypomethylation and FGFR3 overexpression are characteristic for CN. A Clustering the methylation values of the FGFR3 locus of primary tumors and control tissue from Capper et al. 2018 revealed severe hypomethylation at the gene body as a distinct feature of CN. However, individual FGFR3 CpG sites, especially three sites denoted as CN specific in a previous study by Lee et al. 2024 showed high variance. FGFR3 methylation levels did not correspond to FGFR3 staining intensity. B-C FGFR3 staining intensity ranged from strong in 30/71 (42%) cases to intermediate in 41/71 (58%) cases. D FGFR3 immunohistochemistry often demonstrated a gradient effect with stronger staining intensity at the periphery with progressively weaker staining towards the center due to a fixation artifact. E Kaplan-Meier estimates did not show a significant PFS difference between cases with strong (+ +) and intermediate (+) staining intensity. F FGFR3 demethylation was consistent across primary and recurrent samples and did not show any association with sample material, the development of a recurrence, or age

Fig. 4

Lower DNA methylation and younger age predict recurrence. A Definition of risk groups based on recurrence and observation time. B-C The high-risk group was characterized by a significantly younger mean age and young age increases progression risk (P.H. – proportional hazard). Dashed lines indicate PFS probability bounds at the study’s endpoint. D-E Mean methylation was significantly decreased across the genome in the high-risk group, and low DNA methylation is a predictor for progression. F From a non-interventionist perspective, we first model PFS using mean methylation, age, EOR, and aRT. G Followingly, we remove mean methylation as it is not a significant predictor and observe no drastic change in the estimation of coefficients. H Visualization of the reduced model in a nomogram with an example calculation