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Pediatric ependymoma in the molecular era: real-world experience with diagnostic correlation and long-term clinical
Katerina Trkova1,2,3, Ales Vicha4,5,6, David Sumerauer4,5,6
1Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University Prague and Motol and Homolka University Hospital, V Uvalu 84, Prague, Czech Republic. katerina.trkova@fnmotol.cz.
Purpose:
Real-world longitudinal data documenting the diagnostic impact of DNA methylation array (MA) profiling in pediatric ependymoma remain sparse. We report a single-center retrospective analysis evaluating MA-driven reclassification, molecular subgroup distribution, and long-term survival outcomes in a national pediatric referral cohort.
Methods:
Sixty-three pediatric patients with a histological ependymoma diagnosis treated at Motol and Homolka University Hospital (2010-2025) were included. DNA methylation profiling, RNA sequencing, copy number variation and t-SNE analysis were performed. Survival was estimated by the Kaplan-Meier method.
Results:
MA confirmed ependymoma in 48 patients (76.2%) and reclassified 15 (23.8%) as non-ependymoma entities, including newly described tumor types. The reclassification rate was 36.1% in the pre-2019 cohort versus 7.4% post-2019. Posterior fossa group A (PFA) ependymoma was the predominant subgroup (n = 26). Ten-year overall survival (OS) was 69.6% and event-free survival (EFS) 47.7%. Gross total resection was the only factor significantly associated with improved survival (OS 75% vs. 40%, p = 0.017). Chromosome 1q gain, identified exclusively in PFA patients, was associated with a high relapse rate despite standard therapy.
Conclusion:
MA-driven reclassification affected nearly one quarter of patients, with substantially higher rates in the pre-molecular era, confirming that integrated molecular diagnosis is indispensable in all pediatric CNS tumors referred with a histological diagnosis of ependymoma.
Insights
DNA methylation array profiling significantly reclassified pediatric ependymoma cases, impacting diagnosis and treatment. Integrated molecular diagnosis is crucial for accurate pediatric central nervous system tumor classification.
Area of Science:
- Pediatric neuro-oncology
- Molecular diagnostics
- Cancer genomics
Background:
- Pediatric ependymoma diagnosis relies on histology, but molecular profiling offers deeper insights.
- Limited real-world data exists on the diagnostic impact of DNA methylation array (MA) profiling in pediatric ependymoma.
- This study addresses the need for longitudinal data on MA's role in diagnosis and outcomes.
Purpose of the Study:
- To evaluate the diagnostic impact of DNA methylation array (MA) profiling in pediatric ependymoma.
- To assess MA-driven reclassification rates and molecular subgroup distribution.
- To analyze long-term survival outcomes in a national pediatric referral cohort.
Main Methods:
- Retrospective analysis of 63 pediatric patients with histological ependymoma.
- Utilized DNA methylation profiling, RNA sequencing, and copy number variation analysis.
- Kaplan-Meier method estimated overall survival (OS) and event-free survival (EFS).
Main Results:
- MA reclassified 23.8% of cases, with higher rates pre-2019 (36.1%) vs. post-2019 (7.4%).
- Posterior fossa group A (PFA) ependymoma was the most common subgroup (n=26).
- Ten-year OS was 69.6%, EFS was 47.7%. Gross total resection significantly improved survival (p=0.017). Chromosome 1q gain in PFA patients correlated with high relapse rates.
Conclusions:
- DNA methylation array profiling is essential for accurate diagnosis of pediatric ependymoma, reclassifying nearly a quarter of cases.
- Integrated molecular diagnosis is indispensable for pediatric central nervous system tumors with initial ependymoma histology.
- Molecular subtyping and identifying genetic alterations like 1q gain are critical for prognostic assessment and treatment stratification.
