Molecular and anatomical atlases from progenitors to adult neurons in the mouse spinal cord

The developing spinal cord has long been a classic model for understanding neurodevelopmental mechanisms yet linking developmental cell types to their adult counterparts has proved elusive. Developmental transcription factors are required for the differentiation and specification of cell types during embryogenesis and are expressed in discrete domains in the developing spinal cord. Yet in the adult, expression of these developmental transcription factors is lost, making it difficult to connect embryonic progenitor domains to their adult cell types and function. We will address this gap in knowledge by tracking developmental lineages over time using genetic lineage tracing of molecularly-defined progenitor domains and assaying the changes in transcription, epigenome, and anatomical distribution. Comprehensive understanding of the developmental lineages will reveal true structural and functional complexity of spinal cord circuits that are not reflected in single-cell transcriptomics of adult tissue. While we will profile the entire spinal cord, we will focus our analyses on the developing dorsal progenitor domains that give rise to adult cell types involved in somatosensory-motor integration.
The goal of this proposal is to generate three types of mouse atlases. In Aim 1, we will generate a molecular signature atlas that catalogs the transcriptional and epigenomic changes of the developing spinal cord using the 10x Genomics Multiome platform. We will profile these molecular signatures at three major time points across the lifetime of the animal and along the rostral-caudal axis. In Aim 2, we will generate an anatomical phenotype developmental atlas to understand the spatial distribution of the molecular signatures using standard histological techniques and a multiplexed spatial transcriptomics platform, MERSCOPE. We will unambiguously link adult cell types to their developmental progenitors using five CRE-recombinase mouse lines that together isolate the progenitor domains of the developing spinal cord. We will also define the molecular signatures of discrete spinal projection neurons. In Aim 3, we will create a molecular lineage 3-dimensional atlas of all five CRE-lineages at the same three major time points using whole tissue clearing and light sheet microscopy.
Altogether, these three atlases will provide an invaluable resource for the spinal cord and somatosensory neuroscience community. Comprehensive cell profiling of the spinal cord will catalog spinal cell types in native states that can be compared to injured or diseased states. It will also serve as a reference for the cell type profiling of the spinal cord in other species. Furthermore, by adding on a layer of developmental lineage, we will answer long standing questions about the development of the spinal cord. Understanding this developmental relationship will provide insight into whether a particular adult cell type is constrained by its developmental lineage, how discrete progenitor domains generate the diversity of cell types in the adult spinal cord and lay the necessary foundation for cell-type regeneration and engineering efforts for spinal cord tissue.