500 Single-Nucleus RNA Sequencing Reveals Mechanism for Multiple Recurrent Meningiomas

INTRODUCTION: Patients diagnosed with multiple recurrent meningiomas (MRMs) have worsened long-term neurological morbidity, compared to patients diagnosed with solitary meningiomas. However, the pathophysiology of these tumors is not clear. METHODS: We analyzed single-nucleus RNA-sequencing data from 10X Genomics using Seurat v5. The cells were annotated by a cluster-based approach. Sample integration was done using CCA to minimize batch effects. Differential gene expression (DGE) was calculated through pseudo-bulk analysis of cell types using DESeq2 and the likelihood ratio test (LRT). Gene set enrichment analyses (GSEA) were conducted through clusterProfiler for gene ontology (GO). Receptor-ligand pair interactions were approximated using CellChat. All analyses were processed in RStudio. Significance was denoted as p < 0.05. RESULTS: Our institution collected 4 primary samples that did not recur (control primary), 4 primary samples that later recurred (MRM primary), and 8 recurrent samples (MRM recurrence). Integration allowed for broad cell type classification, with separation of the tumor cells from the cycling cells. The tumor cells were isolated and compared across the three molecular groups. Analysis shows that the MRM primary and MRM recurrence tumor cells have a similar gene expression profile, compared to control primary tumor cells. GO shows upregulation of pathways related to angiogenesis, DNA repair, and neural migration, while heterochromatin regulatory pathways are suppressed. Signaling pathways unique to the MRM tumor cells include incoming signals from cycling cells through the HGF and SEMA4 pathways. Conversely, MRM primary tumor cells activate immune cells through the PROS pathway. CONCLUSIONS: MRM tumors have a greater ability to promote pro-tumorigenic pathways and migration with assistance from cycling cells and by supporting the tumor microenvironment. Further studies are needed to elucidate the precise mechanisms for recurrence in meningiomas.