Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

Abstract

The mammalian brain contains many specialized cells that develop from a thin sheet of neuroepithelial progenitor cells. Single-cell transcriptomics revealed hundreds of molecularly diverse cell types in the nervous system, but the lineage relationships between mature cell types and progenitor cells are not well understood. Here we show in vivo barcoding of early progenitors to simultaneously profile cell phenotypes and clonal relations in the mouse brain using single-cell and spatial transcriptomics. By reconstructing thousands of clones, we discovered fate-restricted progenitor cells in the mouse hippocampal neuroepithelium and show that microglia are derived from few primitive myeloid precursors that massively expand to generate widely dispersed progeny. We combined spatial transcriptomics with clonal barcoding and disentangled migration patterns of clonally related cells in densely labeled tissue sections. Our approach enables high-throughput dense reconstruction of cell phenotypes and clonal relations at the single-cell and tissue level in individual animals and provides an integrated approach for understanding tissue architecture.

Microglial colonisation of the developing brain is facilitated by clonal expansion of highly proliferative progenitors and follows an allometric scaling

“…Our findings indicate that some individual microglia undergo mass expansion as evidenced by the clouds of sparse-labelled microglia at P30. This finding is in line with a recent study where in vivo barcoding was used to track clonal expansion of various cell types, including microglia, within the embryonic brain (Ratz et al, 2022). In line with our findings, this study showed that expanded microglial progenitors span anatomical niches in an almost continuum (Ratz et al, 2022).…”

“…This finding is in line with a recent study where in vivo barcoding was used to track clonal expansion of various cell types, including microglia, within the embryonic brain (Ratz et al, 2022). In line with our findings, this study showed that expanded microglial progenitors span anatomical niches in an almost continuum (Ratz et al, 2022). Here we examined the changes in the spatial distribution of sparsely labelled microglia, which were highly clustered during embryonic development in comparison to adulthood, when the labelled microglia were more randomly distributed with a lower NND in line with the formation of the mosaic similar to the trends observed in the total PU.1 + population.…”

Cerebral Organoids as an Experimental Platform for Human Neurogenomics

“…Timelapse microscopy studies conducted in cerebral organoids have demonstrated that the characteristic behaviors of radial glia subtypes are recapitulated in organoids [ 95 , 96 ], as well as their capacity to differentiate via direct and indirect neurogenesis [ 97 ]. In addition to timelapse microscopy, technologies that enable multiplexed tracking of cell lineage at high-throughput using single cell transcriptomics can be applied to cerebral organoids [ 98 , 99 ] and primary tissue [ 79 , 100 , 101 ]. Examining mechanisms underlying human brain development using brain organoids will critically depend on rigorous benchmarking of the differentiation trajectories of neural progenitor cells.…”

Scalable and model-free detection of spatial patterns and colocalization

“…Spatial omics technologies map out organizational structures of cells along with their genomics, transcriptomics, proteomics and epigenomics profiles, providing powerful tools for deciphering mechanisms of functional and spatial arrangements in normal development and disease pathology (Larsson et al 2021;Longo et al 2021;Marx 2021;Deng et al 2022;Dhainaut et al 2022;Ratz et al 2022;Zhao et al 2022). The collection of available approaches provides a wide spectrum of throughput and spatial resolution.…”