U.S. Department of Health and Human ServicesHHS National Institutes of HealthNIH National Center for Advancing Translational SciencesNCATS

Single-cell RNA-Seq of hPSC-derived Neural Cell Types Reveals Early Glia-specific Differentiation Trajectories

Posted on September 29th, 2022 by Hannah Baskir

Poster presented at ISSCR 2022 by Vukasin Jovanovic. The poster is entitled: Single-cell RNA-Seq of hPSC-derived Neural Cell Types Reveals Early Glia-specific Differentiation Trajectories.

Authors (underlined, presenting): Vukasin M. Jovanovic, Jaroslav Slamecka, Marissa Hirst, David Gailbraith, Chaitali Sen, Carlos A. Tristan, Pinar Ormanoglu, Ilyas Singeç

Download the full-size poster here


During brain development, radial glia cells (RGCs) generate neurons first followed by astrogliogenesis, a process known as the “gliogenic switch” of neural lineage progression. While neurogenesis has been extensively characterized, the underlying molecular mechanisms whereby RGCs differentiate into astrocytes remain elusive. Here, we performed single-cell mRNA sequencing (scRNA-seq) of astrocytes derived from human pluripotent stem cells (hPSC) by using a new highly efficient approach that achieves direct RGC-to-astrocyte conversion in the absence of neurogenesis (Jovanovic et al., 2021). The single-cell transcriptome of these directly differentiated astrocytes was then compared to commercially obtained astrocytes and cortical glutamatergic neurons (FUJIFILM CDI). Altogether, we profiled the transcriptomes of 12,771 cells and unbiased clustering identified 11 transcriptionally distinct cell clusters. After data integration with single-cell transcriptomes of the developing human cortex, as expected, cluster signatures corresponded to 3 broad categories: radial glia, astrocytes, and cortical neurons. To better understand cell type-specific molecular identities, we performed slingshot analysis and identified three different trajectories mapping transition of RGCs into two branches representing astrocytes and one “teleporting” RGCs (in the absence of neurogenesis transitional states were not detected) to excitatory neurons. To correlate gene expression variation to each of the cell types in pseudotime, we performed trajectory-based differential expression analysis (trade-Seq) and identified new gene expression modules that characterize the differentiation of RGCs directly into astroglia at the expense of neurogenesis.