Immune deconvolution and temporal mapping identifies stromal targets and developmental intervals for abrogating murine low-grade optic glioma formation

Leveraging RNA sequencing deconvolution, single cell RNA sequencing and protein-based analyses of Nf1OPG, we define the stromal cell composition during mouse Nf1-OPG evolution, as well as in human pediatric low-grade gliomas (LGGs). We show that T cells and microglia are the main non-neoplastic immune cell populations in both murine and human LGGs. Overall design: For single cell RNA sequencing, the optic nerves of 8 male 12 week-old Nf1OPG mice were pooled. Mice were perfused using D-PBS with calcium, magnesium, glucose, pyruvate (ThermoFisher), and the adult brain dissociation kit (Miltenyi Biotec 130-107-677) was used to prepare single cell suspensions. Single-cell barcoding, cDNA amplification and Gene Expression Library Construction were then performed using Chromium Single Cell 3' Reagent Kits v3, and10x Genomics® was used for sequencing. Nf1-OPG scRNAseq data were analyzed in Partek Flow using CPM normalization and graph-based clustering with the Louvain clustering algorithm.