Chromatin remodeling-driven stratification and a five-gene RiskScore define proliferative aggressiveness and therapeutic vulnerabilities in neuroblastoma

Background: Neuroblastoma is clinically heterogeneous, and epigenetic dysregulation-particularly chromatin remodeling-may organize aggressive tumor states and inform prognosis and therapeutic opportunities. This study aimed to define chromatin remodeling-associated neuroblastoma subtypes and develop a robust, biologically interpretable prognostic risk score derived from subtype-associated transcriptional changes, with external validation and functional characterization. Methods: A curated chromatin remodeling gene set was analyzed in RNA sequencing (RNA-seq) cohorts. Consensus clustering defined molecular subtypes in GSE62564 (n=498). Differential expression between subtypes [adjusted P value <0.05, |log fold change (FC)| ≥1] were screened by least absolute shrinkage and selection operator (LASSO) Cox regression. Collinearity control and multivariable Cox refinement yielded a five-gene signature. The RiskScore was evaluated by Kaplan-Meier analysis and time-dependent receiver operating characteristic (ROC) in GSE62564 and externally validated in GSE181559 (n=97) and FWR144 (n=144). Pathway analyses, transcription factor (TF) activity inference, and in silico drug sensitivity prediction were performed to support biological interpretation and therapeutic hypotheses. Results: Chromatin remodeling-based clustering stratified patients into prognostically distinct subtypes. The five-gene RiskScore robustly discriminated overall survival (OS) and achieved favorable time-dependent area under the curve (AUC) in the development cohort, remaining prognostic in both external cohorts. High-RiskScore tumors exhibited enhanced cell-cycle and DNA repair-related programs, consistent with a proliferative tumor-intrinsic aggressive phenotype. Drug sensitivity prediction suggested candidate vulnerabilities concordant with these mechanisms. Conclusions: Chromatin remodeling programs define reproducible neuroblastoma subtypes and support a stable five-gene prognostic RiskScore with external validation, linking aggressive biology to mechanistic pathways and therapeutic hypotheses.