Algorithm-based assessment of T-cell dysfunction and exclusion to forecast ICB sensitivity in pediatric brain ependymoma

Pediatric brain ependymomas are brain tumors difficult to cure despite the advancements in surgery and radiotherapy. Immunotherapies, specifically immune checkpoint blockades (ICB), are traditionally recognized to have a limited efficacy against cold microenvironment as the ones of ependymomas. By employing the Tumor Immune Dysfunction and Exclusion (TIDE) scoring system, this study tries to predict the responsiveness to ICB across molecular subgroups, recurrent/primary presentation and hot vs. cold subtypes. Four GEO datasets from NCBI public library were selected for this study. In total, 150 RNA-bulk sequences of pediatric ependymomas were analyzed (PF-A = 125, ZFTA-RELA = 23, YAP1 = 2). The TIDE algorithm was applied to quantify cytotoxic T-cell infiltration, dysfunction, and exclusion, estimating ICB response probabilities. Group differences were calculated with Kruskal–Wallis and Fisher’s exact tests (p < 0.05). 60% of ependymomas were predicted ICB responders. ZFTA-RELA tumors showed significantly lower TIDE scores than PF-A (–0.099 ± 0.263 vs. 0.060 ± 0.316; p = 0.008) and a higher response rate (78.3% vs. 56.0%; p = 0.063). RELA-fusion tumors exhibited reduced T-cell dysfunction (–0.235 ± 0.221 vs. − 0.098 ± 0.152; p < 0.001). Recurrent tumors demonstrated lower TIDE scores (–0.070 ± 0.328 vs. 0.081 ± 0.296; p < 0.001) and greater predicted response (75.6% vs. 52.4%; p = 0.011). Responders overall had lower TIDE, dysfunction, and exclusion values (all p < 0.01). Pediatric ependymomas are not uniformly immune-silent. ZFTA-RELA and recurrent tumors exhibit a “primed but suppressed” immune phenotype, where the immune machinery is present but functionally restrained, suggesting greater susceptibility to ICB, whereas PF-A tumors remain immune-excluded and may require microenvironmental modulation to achieve immunotherapy benefit.

• Publication year

  2025

• Venue

  Journal of Neuro-Oncology

• Publication date

  2025-12-19

• Fields of study

  Medicine

• Identifiers
  DOI 10.1007/s11060-025-05384-4PMID 41417285PMCID 12717181
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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