Comprehensive single-cell atlas of the developing mouse brain

The developing mouse brain is a foundational experimental model for investigation of the origins of cell types in the mammalian brain. Comprehensive knowledge of mouse brain development is critical for comparative studies of neurodevelopmental processes, which are key to understanding the remarkable evolutionary innovations that distinguish humans from other species. In addition, developmental information enables refining cell taxonomy in the adult brain by incorporating knowledge of cell type and lineage origins into adult cell classification. Despite the transformative insights enabled by the recently created molecular atlas of the adult mouse brain, we currently lack a comprehensive census of cell types of the developing mouse brain, and the lineage relationships that link them to their adult counterparts. Here we seek to generate a comprehensive, spatially- and temporally-resolved, cellular-resolution atlas of the whole developing mouse brain, sampled at high resolution through the entire period of embryonic and postnatal brain development (from E8.0 to P28). We will employ three complementary approaches to generate comprehensive multi-omic single-cell profiles: 10x Genomics single-cell RNA-seq (scRNA-seq), 10x Genomics Multiome (simultaneous single-nucleus RNA-seq and ATAC-seq, for combined transcriptomic and epigenomic profiling), and Smart-seq3 (for full-length deep RNA-sequencing). In parallel, we will use the spatially resolved transcriptomic method MERFISH across the same densely-sampled timeline, to identify the spatial distribution of all cell types and dynamic changes in cell states across the entire mouse brain. We will apply computational methods to predict developmental lineage relationships from these spatially and temporally resolved datasets, and experimentally validate lineage relationships through both barcode-based in vivo lineage tracing and by functionally testing candidate molecular effectors using multiplexed in utero CRISPR screening (Perturb-seq). Finally, we will pilot integration of developmental datasets across species, mapping single-cell omics datasets from the developing human and non-human primate brains onto the comprehensive mouse brain developing cell type atlas established here, to create a computational alignment of developmental time that will enable understanding of differential regulation of specific developmental events across species. Overall, this project brings together a team of investigators with extensive, demonstrated expertise in brain development, circuitry, single-cell genomics, and assembly of brain atlases to produce a comprehensive developmental brain cell atlas, intended to serve as a first-of-its-kind foundational resource to the neuroscience community for the study of mechanisms of mammalian brain development and neurodevelopmental disorders. Our proposed project will contribute substantially to the overarching goal of BICAN to generate fundamental knowledge on diverse cell types and their three-dimensional organizational principles in the brain across lifespan and evolution.