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  • Transcriptomic Dissection of Pediatric Brain Tumors: Unraveling the Glial-Stem vs. Neuronal Dichotomy in Ependymoma and Medulloblastoma

  • Arada Sarkisian,1 Hamed Shafaroodi,2,*
    1. Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
    2. Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences


  • Introduction: Ependymoma and medulloblastoma are two of the most prevalent pediatric brain malignancies. Despite their distinct cellular origins, they frequently present with overlapping clinical and radiological features, making an accurate differential diagnosis a formidable clinical challenge. Because precise classification directly dictates therapeutic strategy and patient prognosis, elucidating the distinct molecular landscapes that drive their divergent tumorigenesis is paramount.
  • Methods: We retrieved gene expression datasets from the GEO database (GSE74195). Differentially expressed genes (DEGs) were identified using GEO2R, applying strict thresholds of adjusted P-value < 0.05 and absolute log2 fold change (|logFC|) >= 2. Functional enrichment analysis was conducted using Enrichr across Gene Ontology (GO), KEGG, and Reactome databases. Protein-protein interaction (PPI) networks were constructed using STRING, and hub genes were prioritized based on node degree centrality.
  • Results: Our analysis revealed a profound transcriptomic dichotomy. A total of 92 upregulated and 49 downregulated genes were identified in Ependymoma compared to Medulloblastoma. The upregulated gene network (exclusive to Ependymoma) was strongly enriched in Extracellular Matrix (ECM) organization, Gliosis, PI3K-Akt signaling, and Glial cell differentiation. The top 10 hub genes in this network were CD44, SOX2, GFAP, ANXA1, VIM, LGALS3, SOX9, S100B, ANXA2, and CCND1. In stark contrast, the downregulated network (characteristic of Medulloblastoma) was significantly enriched in Neuron differentiation, Synaptic signaling, and Nervous system development. Its top 10 hub genes were SNAP25, NEUROD1, SYT4, CHGB, CHGA, STMN2, GABRG2, EOMES, MYT1L, and DCX.
  • Conclusion: This study unveils a fundamental molecular divergence: Ependymoma exhibits a robust glial/stem-like and ECM-remodeling phenotype (centered on the CD44/SOX2/GFAP axis), whereas medulloblastoma retains a distinct neuronal/synaptic differentiation program. Given the morphological similarities that often complicate their diagnosis, these identified hub genes and pathways offer a promising molecular framework. We hope that future research will leverage these concepts to better understand tumorigenesis and improve the differential diagnosis of these two cancers, ultimately paving the way for the design of more precise and targeted therapeutic interventions.
  • Keywords: Ependymoma, Medulloblastoma, Transcriptomics, Neuronal Differentiation, Differential Diagnosis

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