Abstract BACKGROUND Most meningiomas are benign, slow-growing tumors. However, CNS WHO grades 2 and 3 meningiomas display significantly higher aggressiveness and poorer prognosis. Recent investigations into the molecular biology of meningiomas have greatly increased our understanding of these tumors. Furthermore, emergent spatial transcriptomic sequencing methods now provide an unprecedented opportunity to study molecular mechanisms of tumor development within a spatial context and on a single-cell level. This study aims to uncover specific microenvironmental features, cell-cell interactions and transcriptional regulatory mechanisms present in different molecular classes and subclones of meningiomas. MATERIAL AND METHODS We employed single-nuclei RNA sequencing and spatial transcriptomic profiling on a matching set of meningiomas (n=22). We developed a method based on non-negative matrix factorization (NMF) to analyze intra-tumor heterogeneity from both single-cell and spatial transcriptional profiles across samples. Trajectory analysis was performed to screen for expression signatures selectively up-regulated around specific morphological features of the tumors. We clustered cells into types of niches based on compositions of their spatial neighborhoods. RESULTS We annotated cell types in the tumor microenvironment (TME), and identified cellular states of meningioma tumor cells in single-cell and spatial transcriptomic data. Tumors of different subclasses display drastic differences in spatial cell state compositions, suggesting distinct modes of microenvironmental organization. We identified conserved patterns of tumor-TME cell state colocalization and interaction. Benign NF2-mutant meningiomas are characterized by extensive infiltration of myeloid cells which trigger a series of immune and stress response pathways in neighboring tumor cells. Among more malignant tumors, a decrease of immune cell populations is coupled with a marked shift in the TME toward tumor-supportive phenotypes. Moreover, we observed reduced tumor-infiltrative capabilities among tumor-associated myeloid cells and the formation of compartmentalized spatial niches of interacting tumor cells. Additionally, various tumor transcriptional signatures related to extracellular matrix remodeling, fibroblastic markers, and meningothelial signatures were mapped to distinct morphological structures across samples. CONCLUSION Our results reveal that the meningioma TME is heterogenous at the cell state level, with tumor cells and normal cells forming niches that have varying functions in tumor pathophysiology and characterize molecular classes of meningiomas. A series of corresponding RNA markers and spatial signatures were identified, which could potentially be used to increase precision in diagnosis and stratification of meningiomas.
Tang et al. (Wed,) studied this question.