Abstract
Neurofibromatosis type 1 (NF-1) is the most common cancer predisposition syndrome in which 15-20% of affected individuals develop glioma. Large scale DNA and RNA bulk profiling showed the high molecular complexity of NF-1 glioma with the tumor cellular ecosystem constituted by multiple malignant clones and heterogenous immune microenvironment. However, the composition and function of infiltrating cells was mostly hidden in the bulk tumor mass, and the extended granularity of NF-1 glioma immune microenvironment remained still unexplored. Here, to address this challenge, we collected glioma samples from 53 NF-1 patients including 27 high-grade and 26 low-grade tumors, and we analyzed their gene expression at the highest resolution through single nuclei RNA sequencing. A total of 288,372 single cells have been classified by integrating multiple computational approaches (including genomic copy number inference, gene signature enrichment, pathway-based deconvolution and integrative non-negative matrix factorization). The non-tumor cell compartment (124,082 cells, 43%) has been dissected for the deep characterization of each cell type that populate the microenvironment of NF-1 glioma. We unraveled the complexity of the immune infiltration and identified different subpopulations exhibiting specific immune functions within myeloid and lymphoid components. Different glioma niches have been revealed by comparing the relative composition of the immune microenvironment across the tumors. Recruitment and activation of cytotoxic CD8+ T cells and natural killers by an active crosstalk with dendritic and pro-inflammatory myeloid cells defined an immune-supportive phenotype that can mediate a potential anti-tumor response in low-grade NF-1 glioma. Regulatory T cell infiltration and effector T cell exhaustion, instead, induced immune suppression in another tumor niche. Conversely, the complete absence of lymphocytes characterized a large set of cold tumors, mostly high-grade glioma. The elucidation of the complex immune interplay in the different tumor niches provides novel insights for the application of immunotherapies in NF-1 glioma patients.