Single-nucleus transcriptomics identifies cell cycle and synaptic pathway dysregulation during OPC-to-glioma progression.

Gliomas are characterized by poor survival rate and limited options for treatment. Based on the transcriptional enrichment for oligodendrocyte progenitor cell (OPC) transcripts, the proneural glioma is thought to arise from transformation of OPCs. Here, we injected mutant BB-p53n OPCs (with Trp53 deletion and PDGF-BB overexpression) into recipient mice and performed single-nucleus RNA sequencing (snRNA-seq) of the injected cells and of brain tissue at early and late time points after injection, coincident with neuroimaging detection of tumoral masses. Analysis of tumor-bearing brain samples, identified a cluster that was not detected in the normal brain, but was enriched for OPC markers (Olig2), cell cycle genes (Myc) and glioma markers (Top2a, Sox2), which we named "OPC-like." The clusters with "OPC-like" signature, were also the ones with greater genomic distribution of inferred copy number variations (inferCNVs) and high proliferative rate, and were therefore denoted as "tumors." The inferCNV genomic load was higher in late-stage samples compared to early ones, indicative of progressive genomic instability. Immunohistochemical analysis validated the high proliferative rate and widespread expression of the "OPC-like" markers TOP2A and SOX2. Pseudotime analysis of cycling cells identified a trajectory of decreasing cell cycle checkpoint regulation and increasing synaptic signaling from early to late timepoints. Thus, the early timepoints were characterized by the emergence of highly proliferative cell clusters with a unique "OPC-like" transcriptional signature and inferCNVs, and the late timepoints were characterized by further genomic spreading of inferCNVs, loss of cell cycle checkpoints and transcriptional changes consistent with increased neuron-glioma interactions.