Identity and nature of neural stem cells in the adult human subventricular zone

Abstract

The existence of neural stem cells (NSCs) in adult human brain neurogenic regions remains unresolved. To address this, we created a cell atlas of the adult human subventricular zone (SVZ) derived from fresh neurosurgical samples using single-cell transcriptomics. We discovered 2 adult radial glia (RG)-like populations, aRG1 and aRG2. aRG1 shared features with fetal early RG (eRG) and aRG2 were transcriptomically similar to fetal outer RG (oRG). We also captured early neuronal and oligodendrocytic NSC states. We found that the biological programs driven by their transcriptomes support their roles as early lineage NSCs. Finally, we show that these NSCs have the potential to transition between states and along lineage trajectories. These data reveal that multipotent NSCs reside in the adult human SVZ.

Keywords: Cell biology; Molecular biology; Omics; Transcriptomics.

Graphical abstract

Figure 1

Adult human subventricular zone cell atlas (A) Schematic diagram illustrating the sources and brain regions of adult human SVZ neurosurgical samples. Samples were derived from patients with ages ranging from 38 to 72 years old. Eight samples were derived from females and 7 from males. The marks on the right panels show the 15 subventricular zone sample sites. (B) t-distributed stochastic neighbor embedding visualization (tSNE) of adult SVZ cells colored by cell types. NSC—neural stem cell, NK—natural killer, RBC—red blood cell. (C) Heatmap of top 100 genes expressed in each SVZ cell type. (D) Localization of cell types within normotypic autopsy SVZs using cell-type-specific protein markers. Scale bar, 100mm. (E) Expression of indicated genes in all SVZ cell type clusters visualized on tSNE.

Figure 2

Neural stem cell diversity within the adult subventricular zone (A) Schematic diagram illustrating sources of samples from adult human SVZ regions and fetal brains, and uniform manifold approximation and projection (UMAP) visualization of the merged progenitor cells selected from the adult SVZ NSC-like cluster and the fetal datasets colored by original cell annotations. (B) UMAP visualization of the merged progenitor cells selected from the adult SVZ NSC-like cluster and fetal datasets by clusters. Bar graph shows the dataset source of the cells contributing to each cluster. (C) Dot plot of the top 10 genes expressed in each of the 4 NSC clusters compared to all SVZ clusters. (D) Dot plot of the top 10 genes expressed in each of the 4 NSC clusters compared to NSC clusters. Ribosomal genes are not shown (see STAR Methods). Redundant genes are shown only once. (E) Expression of curated known gene markers of RG, NSCs, neuronal progenitors and oligodendrocyte progenitors. (F) Transcriptome size of adult NSC-like and fetal brain cells. Confidence interval = 95%. (G) Ribosomal gene content of adult NSC-like and fetal brain cells. Confidence interval = 95%. (H) Cell cycle phase scores calculated based on expression of G2M and S markers. (I) Summary of gene set enrichment analysis using curated human brain cell types published single-cell RNA-seq datasets. Dendrogram shows unsupervised hierarchical clustering of the data. Color bar indicates normalized enrichment score. Red and blue colors represent significant enrichment or down-regulation (FDR < 0.0001), respectively, yellow indicates no significant result. (J) Localization of aRG1, aRG2, npNSCs, and opNSCs within normotypic autopsy SVZs using cell type-specific protein markers. Scale bar, 50μm.

Figure 3

Enriched neural stem cell biological programs Biological program analysis performed for aRG1, npNSCs, aRG2, and opNSCs, using a maximum of the top 500 differentially expressed genes. Unique pathways/process are boxed and colored according to their state. Shared pathways/processes are boxed white.

Figure 4

Subventricular zone cellular interactions Dot plot showing the ligand-receptor interactions from all niche cell types to NSCs. Scale bar is the mean expression of the ligand-receptor pair. Dot size is the mean of percentage of expressed cells for each cell type pair. MM∗∗—Macrophage and Microglia, Oligo∗∗—Oligodendrocyte, UN1—unidentified.

Figure 5

Neural stem cell transition capacity (A) Cluster-based velocity analysis (PAGA, see STAR Methods) for adult and fetal brain cell types. Numbers are transition confidence ranging from 0 to 100. (B) Summary schematic showing cell transitions with confidences greater than 10. a—adult, astro—astrocyte. APC—astrocyte progenitor cell, OPC—oligodendrocyte progenitor cell, EN—excitatory neuron, IPC—intermediate progenitor cell, RG—radial glia, SVZ—subventricular zone.