Comprehensive single-cell atlas of the developing mouse brain

PROJECT SUMMARY
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.

Grant Number: 5U01MH130962-04
NIH Institute/Center: NIH
Principal Investigator: Paola Arlotta