Abstract B14: Pinpointing the origins of pediatric brain tumors using single-cell transcriptomic analysis
Authors: Jessa Selin , Blanchet-Cohen Alexis , Krug Brian , Vladoiu Maria C. , Coutelier Marie , Faury Damien , Poreau Brice , De Jay Nicolas , Farmer W. Todd , Hu Yixing , Hébert Steven , Monlong Jean , Murai Keith K. , McConechy Melissa , Bourque Guillaume , Ragoussis Jiannis , Garzia Livia , Taylor Michael D. , Jabado Nada , Kleinman Claudia L. 
Published: August 2020

Abstract
Childhood tumors of the central nervous system are deadly diseases, and for many tumor types outcome has not improved over the last three decades. Current evidence supports a model in which genetic alterations drive changes in neurodevelopmental gene expression programs, leading to oncogenesis postnatally. We hypothesize that there are specific cellular states during normal brain development that are vulnerable targets for oncogenic mutations. However, comprehensive developmental data for many brain regions relevant to pediatric brain tumors (PBT) are lacking. Here, we leverage single-cell RNA-sequencing to generate a reference transcriptome atlas of the developing brain in two regions where PBT commonly arise, the forebrain and the pons. We profile &gt;65,000 cells from healthy embryonic and neonatal mouse and human specimens, and characterize cellular diversity, dynamics related to differentiation, and transcription factor regulatory activity. We use a novel strategy to project bulk RNA-seq profiles for a cohort of 200 PBT onto these cell types. We show that this projection stratifies tumors by type, and for several PBT subtypes, we identify their closest transcriptional match among the cell populations of the normal developing brain. WNT-subtype medulloblastoma matches the lower rhombic-lip derived mossy fiber neuron lineage. In embryonal tumors with multilayered rosettes, we identify prenatal neurogenic radial glial cells as candidate cells of origin, while Group 2a/b atypical teratoid/rhabdoid tumors originate outside the neuro-ectoderm. Finally, single-cell profiling of patient tumor samples shows that these tumors mimic the transcriptional programs of their corresponding normal lineages and contain a mixture of cells with varying degrees of differentiation. We identify impaired differentiation of specific neural progenitors as a common oncogenic mechanism underlying PBT, and further demonstrate that this differentiation blockade may be reversible. Our findings thus provide a rational framework to guide future modeling and therapeutics. More broadly, we assemble a high-resolution developmental dataset, a valuable resource for the study of neuroscience and many brain pathologies.
Citation Format: Selin Jessa, Alexis Blanchet-Cohen, Brian Krug, Maria C. Vladoiu, Marie Coutelier, Damien Faury, Brice Poreau, Nicolas De Jay, W. Todd Farmer, Yixing Hu, Steven Hébert, Jean Monlong, Keith K. Murai, Melissa McConechy, Guillaume Bourque, Jiannis Ragoussis, Livia Garzia, Michael D. Taylor, Nada Jabado, Claudia L. Kleinman. Pinpointing the origins of pediatric brain tumors using single-cell transcriptomic analysis [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B14.