Transcriptional profiling of sequentially generated septal neuron fates

Abstract

The septum is a ventral forebrain structure known to regulate innate behaviors. During embryonic development, septal neurons are produced in multiple proliferative areas from neural progenitors following transcriptional programs that are still largely unknown. Here, we use a combination of single cell RNA sequencing, histology and genetic models to address how septal neuron diversity is established during neurogenesis. We find that the transcriptional profiles of septal progenitors change along neurogenesis, coinciding with the generation of distinct neuron types. We characterize the septal eminence, an anatomically distinct and transient proliferative zone composed of progenitors with distinctive molecular profiles, proliferative capacity and fate potential compared to the rostral septal progenitor zone. We show that Nkx2.1-expressing septal eminence progenitors give rise to neurons belonging to at least three morphological classes, born in temporal cohorts that are distributed across different septal nuclei in a sequential fountain-like pattern. Our study provides insight into the molecular programs that control the sequential production of different neuronal types in the septum, a structure with important roles in regulating mood and motivation.

A developmental atlas of the mouse brain by single-cell mass cytometry

“…While the cell populations we identified by protein-based measurements show general agreement with those previously identified by scRNA-seq [9][10][11][13][14][15]49,16,50,[17][18][19][20][21][22][23][24][51][52][53][54][55]25 , the magnitude of discrepancies between specific protein-mRNA pairs was unexpected, and demonstrates the value of protein measurements to characterize and quantify functional cell states. The wide variety of relationships we observed between mRNA and protein abundance likely arises from a combination of many factors, such as varying rates of mRNA processing and degradation, as well as varying rates of protein translation, maturation, trafficking, and degradation, all of which can differ between specific protein-mRNA pairs, across cell types, and across developmental stages within a single cell type.…”

“…Using this neural mass cytometry approach, we identified and quantified 85 molecularly distinct cell populations across embryonic and postnatal development in the telencephalon, diencephalon, mesencephalon, and rhombencephalon. These cell populations generally show complementary overlap with those previously identified by scRNA-seq studies [9][10][11][13][14][15]49,16,50,[17][18][19][20][21][22][23][24][51][52][53][54][55]25 , although our time-course comparison reveals that mRNA transcript levels do not accurately predict protein abundance during early brain development. Application of URD pseudotime analysis 56 to map cell differentiation captured classical excitatory and inhibitory neuronal trajectories, and revealed two distinct cell-lineage hierarchies for producing embryonic OPCs.…”

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

“…Based on the molecular signature and regional specificity of each subclass, the Subpallium GABAergic division (subclasses 36-62, total 565 clusters) was divided into four classes that are likely related to their distinct developmental origins 66, 67 ( Figure 2b,g ): CGE GABA (containing cortical/pallial GABAergic neurons derived from the caudal ganglionic eminence), MGE GABA (containing cortical/pallial GABAergic neurons derived from the medial ganglionic eminence), CNU GABA (containing striatal/pallidal GABAergic neurons derived from the lateral ganglionic eminence, LGE, as well as from MGE and the embryonic preoptic area), and LSX GABA (containing lateral septum GABAergic neurons derived from the embryonic septum 68 ).…”

A developmentally defined population of neurons in the lateral septum controls responses to aversive stimuli

“…In corresponding coronal sections, the area of the septum was reduced in both male and female mutant mice, particularly in posterior regions ( Figures 1F ; S1D,E ). Since there was no decrease in the overall density of septal cells (identified by immunofluorescence for Zic-family proteins 10 ; Figure S1C ), this size reduction likely implies that the loss of Nkx2.1 -lineage cells is not compensated by any other cell lineages. Nkx2.1 -lineage cells in the septum comprise both neurons and astrocytes 10,18 ; to determine that the cell ablation phenotype is specific to neurons, we performed immunofluorescence staining for the astrocyte marker SOX9 ( Figure S1F ), and found no difference in astrocyte density between WT and cKO samples, either in the LS or in the MS, where the majority of Nkx2.1 -lineage astrocytes reside 7,10,18 ( Figure S1G ).…”

“…In the MGE/PoA, expression of Prdm16 is confined to progenitors, where it controls their proliferative capacity 15 . In the developing septum, Prdm16 expression is sustained in postmitotic neurons 10,41 , potentially reflecting a specific need for this gene in the survival of septal neurons. The Nkx2.1 -lineage in the LS is largely derived from the septal eminence, which produces sequential cohorts of neurons with diverse morphologies and anatomical locations over the neurogenic period 10 .…”