TOP2A Overexpression as a Prognostic Biomarker in High-Grade Meningioma: An Integrated Single-Cell and Bulk Transcriptomic Study

Abstract

While prior single-cell studies have identified proliferative neoplastic subpopulations, the prognostic and therapeutic implications of TOP2A focal copy-number status have not been defined. This study aimed to delineate the cellular architecture of high-grade meningioma and to evaluate the clinical and prognostic significance of TOP2A expression together with its focal copy-number status through integrated single-cell and bulk transcriptomic profiling. Single-cell RNA sequencing (scRNA-seq) was integrated with bulk RNA sequencing (bulk RNA-seq) to resolve the cellular landscape of high-grade meningioma in an exploratory cohort, followed by functional subcluster identification, differential expression analysis, and survival analyses. TOP2A was prioritized for multi-level validation: mRNA overexpression was confirmed in an independent bulk cohort, protein overexpression by immunohistochemistry (IHC), and focal gene copy-number status by fluorescence in situ hybridization (FISH). Kaplan–Meier survival analysis was performed to evaluate patient prognosis. Correlations between continuous variables were assessed using Spearman’s rank correlation coefficient. scRNA-seq of an exploratory high-grade cohort revealed a cell-cycle proliferation cluster characterized by high TOP2A expression. In a 160-sample bulk RNA-seq cohort, TOP2A was overexpressed in high-grade and recurrent tumors, and elevated TOP2A mRNA was significantly associated with shorter progression-free survival (PFS). IHC on 154 specimens confirmed TOP2A protein overexpression, and FISH on 27 specimens demonstrated focal TOP2A copy-number gain enriched in high-grade cases. Copy-number gain was concordant with TOP2A mRNA levels. Although TOP2A mRNA and protein overexpression were each associated with shorter PFS, the limited size of the FISH subset precluded an independent survival analysis by copy-number status. This study identifies TOP2A mRNA and protein overexpression as a prognostic biomarker in high-grade meningioma, and shows that focal TOP2A copy-number gain is enriched in high-grade tumors and concordant with TOP2A expression. By integrating transcriptional overexpression with copy-number gain, our findings identify TOP2A as a candidate prognostic biomarker warranting prospective evaluation in high-grade meningioma.