Unraveling the miRNA-EMT-stemness interplay in fusion-positive supratentorial ependymomas: Identifying therapeutic vulnerabilities.

BACKGROUND: Supratentorial ependymomas frequently harbor ZFTA-RELA (ZRfus) gene fusions that initiate oncogenic transcriptional programs; however, the downstream post-transcriptional regulatory mechanisms remain poorly understood. This study aimed to elucidate the contribution of microRNAs (miRNAs) to the aggressive phenotype characteristic of ZRfus + tumors.

METHODS: Small RNA sequencing was performed on fusion-positive (ZRfus+) and fusion-negative (ZRfus-) supratentorial ependymomas, followed by integrative bioinformatic analyses. Differentially expressed miRNAs and their predicted mRNA targets were validated using quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC). Associations with clinical outcomes were evaluated through progression-free survival (PFS) analysis.

RESULTS: Distinct miRNA expression profiles discriminated ZRfus+ from ZRfus- tumors. ZRfus + tumors demonstrated significant upregulation of hsa-miR-138-5p and downregulation of hsa-miR-135b-5p and hsa-miR-216a-3p. Target prediction and pathway enrichment analyses identified TERT, YAP1, RELA, and TP53 as key dysregulated network nodes. Functionally, ZRfus+ tumors exhibited enhanced epithelial-mesenchymal transition (EMT) and stemness signatures, marked by upregulation of SNAIL, SLUG, Nestin, and N-Cadherin. Clinically, ZRfus + status correlated with significantly shorter progression-free survival, underscoring its adverse prognostic significance.

CONCLUSIONS: This study delineates a distinct ZR fus-associated miRNA landscape in supratentorial ependymomas, implicates hsa-miR-138-5p as a potential biomarker of oncogenic signaling and EMT activation, and reveals mechanistic links between fusion-driven transcriptional dysregulation and tumor aggressiveness. These findings lay the groundwork for miRNA-based therapeutic strategies in high-risk pediatric ependymoma subtypes.

IMPORTANCE OF THE STUDY: Supratentorial ependymomas with ZFTA-RELA fusions represent a highly aggressive pediatric brain tumor subtype, yet the post-transcriptional mechanisms driving their malignancy remain unclear. This study fills a critical gap by systematically profiling miRNA expression in fusion-positive and fusion-negative supratentorial ependymomas, revealing a distinct fusion-associated miRNA signature. The identification of hsa-miR-138-5p upregulation and hsa-miR-135b-5p/hsa-miR-216a-3p downregulation, converging on key oncogenic nodes such as TERT, YAP1, RELA, and TP53, provides novel mechanistic insight into how fusion-driven miRNA dysregulation enhances epithelial-mesenchymal transition and stemness. The findings suggest that miRNA-fusion interactions play an important role in tumor aggressiveness and highlight hsa-miR-138-5p as a potential biomarker for disease progression. Clinically, the work advances understanding of fusion-driven ependymoma biology and lays the foundation for developing miRNA-based diagnostic and therapeutic strategies targeting molecular mechanisms of tumor progression.