Summary: The study of the origin and development of cerebellar tumors has been hampered by the complexity and heterogeneity of cerebellar cells that change over the course of development. We used single-cell transcriptomics to study >60,000 cells from the developing murine cerebellum, and show that different molecular subgroups of childhood cerebellar tumors mirror the transcription of cells from distinct, temporally restricted cerebellar lineages. Sonic Hedgehog medulloblastoma transcriptionally mirrors the granule cell hierarchy as expected, whereas Group3 MB resemble Nestin+ve stem cells, Group 4 MB resemble unipolar brush cells, and PFA/PFB ependymoma and cerebellar pilocytic astrocytoma resemble the pre-natal gliogenic progenitor cells. Furthermore, single-cell transcriptomics of human childhood cerebellar tumors demonstrates that many bulk tumors contain a mixed population of cells with divergent differentiation. Our data highlight cerebellar tumors as a disorder of early brain development, and provide a proximate explanation for the peak incidence of cerebellar tumors in early childhood.

Author Contributions S.J. and C.L.K. designed and coordinated analysis of single-cell data. S.J. and A.B.-C. performed the majority of the scRNA-seq analyses and visualizations. J.M. and G.B. contributed to the CNA analysis. Y.H. contributed to the algorithm for marker gene discovery. F.M.G.C., M.C., A.B.-C. and S.J. analyzed transcription factor activity in the scRNA-seq data. N.D.J., S.H. and S.J. contributed to the analysis of the bulk RNA-seq data and the data availability submission. M.V. contributed to timed mating and tissue isolation in developing mouse embryos. D.F., M.V. and L.K.D. and contributed to primary tissue isolation, preparation and production of scRNA-seq libraries. B.K. performed all experiments in cellular models. L.G., S.J., W.T.F. and K.K.M. contributed to literature review and cell cluster annotations. L.G. provided expert advice on identification of developing pre-cerebellar populations. M.K.M. and L.G.M. contributed to the clinical annotation of tumor samples. P.-E.L. and G.T. provided bulk adult human brain RNA-seq samples. M.R., B.P. and A.A. provided human fetal brain samples.