Temporal and Pseudotemporal Dissection of the Cerebellar Developmental Program at Single-Cell Resolution
Carter R1, Bihannic L2, Rosencrance C3, Phoenix T2, Natarajan S1, Easton J3, Northcott P2 and Gawad C1,3
1Departments of Oncology, 2Developmental Neurobiology, and 3Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
The mammalian cerebellum is involved in sensory-motor coordination and higher-order cognitive processes. Its well-characterized circuitry and limited number of abundant cell types makes it an ideal region to study brain development using single-cell genomics. To perform a genome-wide unbiased survey of factors that carefully coordinate cerebellar precursor proliferation, migration, and differentiation, we profiled the transcriptomes of over 40,000 single murine cells from the developing cerebellum at 13 time points from embryonic day 10 through post-natal day 10. After performing quality control analyses and normalization, we are able to create two-dimensional representations that faithfully recapitulate what is known about cerebellar development.We are also able to identify distinct groups of cells using dynamic tree cut after hierarchical clustering, which revealed new members of transcription factor, epigenetic modifier, and secreted protein gene modules that are expressed in distinct cell types as the cerebellum develops.By isolating the two major lineages and performing pseudotemporal ordering, we are also able to perform even higher resolution ordering of the cerebellar developmental gene expression program.Finally, we have identified specific cell types that have large changes in expression that may represent cell fate commitment of the two major mature cerebellar cell lineages and have isolated factors that have the largest changes in expression in those cell types.Together, our study provides high-resolution ordering and dissection of cerebellar development that will serve as a foundation for understanding how aberrations to that tightly regulated program results in human disease.