Mapping Clonal Relationships in Mouse Brain with Single-Cell Analysis
Summary
The intricate mammalian brain comprises a multitude of specialized cells that originate from a delicate layer of neuroepithelial progenitor cells. Although single-cell transcriptomics has elucidated the remarkable molecular diversity of cell types within the nervous system, the lineage relationships connecting mature cell types and progenitor cells remain enigmatic. The authors present an innovative in vivo barcoding methodology for concurrently profiling cellular phenotypes and clonal associations in the mouse brain, harnessing single-cell and spatial transcriptomics. By reconstructing myriad clones, the study identifies fate-restricted progenitor cells within the mouse hippocampal neuroepithelium and establishes that microglia emanate from a limited number of primitive myeloid precursors that undergo massive expansion, generating widely dispersed progeny. Merging spatial transcriptomics with clonal barcoding facilitates disentangling migration patterns of clonally related cells in densely labeled tissue sections. This pioneering approach permits the comprehensive reconstruction of cellular phenotypes and clonal relationships at the single-cell and tissue level within individual specimens, offering an integrated framework for deciphering tissue architecture.
Research Criteria
Single cell and spatial transcriptomics were used to simultaneously profile cell phenotypes and clonal relationships in the mouse brain.
Fig.1 Experimental design. (Michael, 2022)
Sample Type
Cells and tissues from mouse brains.
Result—Molecular Identity of Barcoded Brain Cells
Utilizing the TREX approach, researchers isolated EGFP+ barcoded cells from the cortex, striatum, and hippocampus of 2-week-old murine brains for scRNA-seq analysis. Graph-based clustering revealed 40 molecularly defined cell classes across the brain regions. The comparison of gene expression profiles and cell type composition between barcoded and non-injected samples validated the non-perturbative nature of lentivirus-mediated barcoding, highlighting TREX's utility for progenitor cell barcoding and postnatal profiling.
Fig.2 TREX enables simultaneous profiling of cell phenotype and clonality. (Michael, 2022)
Result—Spatial Profiling of Transcriptomes, Cell Types and Clones
The researchers developed Space-TREX, a method integrating Spatial Transcriptomics (ST) and clonal tracing, enabling in situ expression profiling of barcoded mouse brain sections alongside spatial gene and protein expression. This approach generated datasets containing spatial gene expression patterns, cell types, clones, and neuroanatomical definitions. By aligning brain sections with the Allen Mouse Brain reference atlas, they extracted numerous cloneIDs and evaluated clone dispersion across multiple regions. Space-TREX demonstrated the ability to map clonal barcodes, gene expression, and cell types in situ, offering valuable insights into progenitor cells and their progeny in the developing brain.
Fig.3 Space-TREX enables simultaneous profiling of transcriptomes and clones in situ. (Michael, 2022)
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Reference
- Michael, R.; et al. Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics. Nature Neuroscience. 2022, 25(3): 285-294.
