Tracing Cell Lineage

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Summary

In the course of neurogenesis, the embryonic mouse brain's ventricle-lining mitotic progenitor cells engage in terminal cell divisions, engendering an extensive array of postmitotic neurons and glial cells1,2. The association between developmental lineage and cellular diversity continues to be an unresolved matter. The current study employed large-scale progenitor tagging to examine clonal connections and transcriptomic patterns during mouse forebrain maturation. Postnatal clonal divergence and convergence were measured across all primary cell classes, revealing several GABAergic neuron varieties sharing a mutual lineage. The divergence of GABAergic clones transpired during embryogenesis upon cessation of the cell cycle, implying that the initiation of subtype differentiation is contingent upon a lineage-dependent mechanism at the progenitor cell stage.

Research Criteria

The research idea of this article is to use massively parallel tagging of progenitors to track clonal relationships and transcriptomic signatures during mouse forebrain development.

Fig.1 Experimental design. (Bandler, 2021)

Sample Type

Cells from brain

Result—Capture of Gene Expression and Lineages

Researchers have utilized a STICR (scRNA-seq-compatible tracer for identifying clonal relationships) lentiviral lineage barcoding approach to uncover lineage relationships among different cell types within the murine forebrain. By introducing a high-diversity lentiviral library encoding synthetic oligonucleotide sequences (lineage barcodes) into mouse embryos at various developmental stages, mitotic progenitors and their progeny in different forebrain regions were labeled. Using single-cell RNA sequencing (scRNA-seq) on virally infected cells that were FACS-enriched from dissociated postnatal forebrain tissue, researchers analyzed the transcriptomes of 65,700 high-quality cells, enabling them to group cells based on gene expression patterns. Researchers observed that earlier introduction of the lentiviral library resulted in larger multicellular clones. Hierarchical clustering of pairwise correlation between coupling scores revealed structured groups of clonally related cell classes, with notable distinctions between early and late-stage clones, signifying progressive temporal fate specification of progenitors.

Fig.2 Clonal relationships of forebrain cell classes determined via simultaneous capture of transcriptome and lineage barcodes from single cells. (Bandler, 2021)

Result—Clonal Convergence and Divergence

An investigation was conducted by the researchers to explore the clonal relationships between subtypes in finer detail. To achieve this, they annotated 41 clusters based on the expression of marker genes and then mapped them to different regions of the brain. In their study of mice, the researchers aimed to identify if excitatory and inhibitory neurons within the neocortex shared a common progenitor. However, no evidence was found to support this. The researchers also examined whether cell types, which are similar in terms of their transcriptomic profile, have a clonal relationship. Through their study, they discovered examples of both convergence and divergence. For instance, transcriptomically similar astrocyte populations could be generated from dorsal and ventral radial glia. Additionally, the researchers observed clonal divergence in inhibitory neuron clones, which despite having different transcriptomic profiles, exhibited high lineage coupling, connectivity patterns, morphologies, and brain region occupancy. Overall, the findings suggest that a wide variety of GABAergic subtypes can arise from individual progenitors of GABAergic neurons.

Fig.3 Lineage convergence and divergence in the mouse forebrain. (Bandler, 2021)

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Reference

1. Bandler, R.C.; et al. Single-cell delineation of lineage and genetic identity in the mouse brain. Nature. 2022, 601(7893): 404-409.