We identify three main states of mesenchymal GBM cells with distinct genetic and environmental associations: (1) a MES state that expresses a hypoxia program and is associated with NF1 deletion, macrophage abundance, an increased macrophage to microglia ratio, and M2 activated macrophages; (2) a MES state that expresses astrocytic genes and is associated with T cell abundance and cytotoxicity; and (3) an intermediate state which may represent their parental state. Here, NF1 is linked to glioblastoma.