Single-cell transcriptomics of the early developing mouse cerebral cortex disentangles the spatial and temporal components of neuronal fate acquisition

Abstract

In the developing cerebral cortex, how progenitors that seemingly display limited diversity end up in producing a vast array of neurons remains a puzzling question. The prevailing model that recently emerged suggests that temporal maturation of these progenitors is a key driver in the diversification of the neuronal output. However, temporal constrains are unlikely to account for all diversity across cortical regions, especially in the ventral and lateral domains where neuronal types significantly differ from their dorsal neocortical counterparts born at the same time. In this study, we implemented single-cell RNAseq to sample the diversity of progenitors and neurons along the dorso-ventral axis of the early developing pallium. We first identified neuronal types, mapped them on the tissue and performed genetic tracing to determine their origin. By characterising progenitor diversity, we disentangled the gene expression modules underlying temporal vs spatial regulations of neuronal specification. Finally, we reconstructed the developmental trajectories followed by ventral and dorsal pallial neurons to identify gene waves specific of each lineage. Our data suggest a model by which discrete neuronal fate acquisition from a continuous gradient of progenitors results from the superimposition of spatial information and temporal maturation.

Transcriptional heterogeneity of ventricular zone cells in the ganglionic eminences of the mouse forebrain

“…Several initial studies performed bulk RNA-sequencing on the embryonic ventral forebrain, but these studies were not able to differentiate molecular characteristics between progenitor domains (Tucker et al, 2008;Zechel et al, 2014). More recent studies performed comprehensive scRNAseq experiments on the developing neocortex, but they did not focus on the ventral telencephalon or interneuron development (Di Bella et al, 2021;Loo et al, 2019;Moreau et al, 2021;Telley et al, 2019;Telley et al, 2016). scRNAseq studies that targeted GEs found that initial signatures of mature interneuron (IN) subtypes appear in postmitotic precursors whereas very little transcriptional diversity was detected in VZ and SVZ progenitors (Chen et al, 2017;Mayer et al, 2018;Mi et al, 2018).…”

Bidirectional interaction between Protocadherin 8 and transcription factor Dbx1 regulates cerebral cortex development

“…Thus, suggesting of possible synergic role of Dbx1 and Pcdh8 in cell identity determination. Indeed, Pcdh8 KD in Dbx1 EE cells reversed induction of Nr4a2 expression supporting that Pcdh8 is in part responsible for Nr4a2 expression and SPlike phenotype of Dbx1-derived lineages (Arai et al, 2019;Moreau et al, 2021). Moreover, further analysis showed the action of Pcdh8 KD on downregulation (Dbx1 EE + Pcdh8 KD) and upregulation (Pcdh8 EE) of Dbx1, thus pointing to Pcdh8 as a post-transcripitional modulator of Dbx1 expression.…”

“…To better appreciate the possible implication of such candidates downstream of Dbx1 we used scRNAseq. We first used a previously generated dataset sampling cell diversity around the pallialsubpallial boundary (PSB) at E12.5 (Moreau et al, 2021). We found Cdh2, Pcdh9 and Pcdh19 broadly expressed, with no specific enrichment (https://apps.institutimagine.org/mouse_pall ium/).…”

“…Since Dbx1 expression is initiated in APs of the VP but strongly increases upon transition to the basal progenitor (BP) state, we compared the temporal dynamics of both genes. We used a previously reconstructed differentiation trajectory in which cells of the VP lineage are aligned along a pseudotime axis corresponding to their differentiation state, from AP to neuron (Moreau et al 2021). We found that Pcdh8 and Dbx1 are expressed sequentially in the VP lineage, with Pcdh8 peaking in APs, followed by Dbx1 in BPs (Figure 2E).…”

“…A Shiny App to explore scRNAseq data from the mouse septum is available at: https://apps.institutimagine.org/mouse_septum/. Additionally, the Shiny App that allows making the pseudotime reconstructions of the ventral pallium (Moreau et al, 2021) is available at: https://apps.institutimagine.org/mouse_pallium/.…”