Local Tumor Microenvironment Niches Correlate with Survival and Immunotherapy Response in Human Glioblastoma

Background: Glioblastoma (GBM) is an aggressive form of primary brain cancer. Recent efforts to characterize GBM using single-cell or spatial transcriptomics have revealed tremendous intra-tumoral heterogeneity among malignant cells and across different tumor areas. However, most studies have focused on malignant cells, and the spatial and cellular heterogeneity of the tumor microenvironment (TME) remains poorly understood. Consequently, it is unclear how TME compositions and organizations influence clinical outcomes for patients. Results: Spatial transcriptomics on 25 tumors, integrated with single-cell RNA sequencing and histological analyses, enabled the estimation of cellular composition within the TME across 46,000 spots (55-m wide). This analysis identified spatial associations between mesenchymal-like cancer cells and monocyte-derived macrophages and revealed six unique niches (N1-N6) characterized by distinct cellular composition and biological pathway activations. Deconvolution of large-scale bulk RNA-seq datasets using a spatial transcriptomics reference revealed that tumor niche composition significantly associated with patient survival and response to immunotherapy. Specifically, the N1 niche, characterized by the enrichment of mesenchymal-like cancer cells and monocyte-derived macrophages alongside hypoxic signature, was associated with lower overall survival. In contrast, the N5 niche, characterized by the enrichment of oligodendrocyte progenitor-like cancer cells and microglia-derived tumor-associated macrophages, was associated with longer patients survival. Analysis of data from patients treated with immunotherapy identified that niches N1 and N3, characterized by mixed mesenchymal-like and astrocyte-like cells, were associated with poor response to anti-PD-1 immune checkpoint inhibitors. Conclusions: Our results demonstrate that GBM exhibits significant spatial heterogeneity within the TMEs, comprising distinct niche classes, and that the specific niche compositions are associated with overall survival and immunotherapy responsiveness. Our results suggest incorporation of TME niche categories as biomarkers for risk stratification and therapeutic decisions for GBM patients.