A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, United States
- Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, United States
- Howard Hughes Medical Institute and Computational and Systems Biology Program, Sloan Kettering Institute, United States
Figures
Figure 1 with 2 supplements
Construction of a single-cell RNA expression atlas during mouse cranial neural tube closure.
(A) Images of mouse embryos spanning the stages of cranial neural tube closure. Bars, 100 µm. (B) Schematics of cranial tissues collected for scRNA-sequencing (dashed boxes, left) and neural tube closure in the midbrain (right) at the indicated stages. The heart was removed at later stages. (C, D) UMAP projections of all cranial cell populations analyzed colored by cell type (C) or embryonic stage (D). (E) UMAP projections of cranial neural plate cells colored by embryonic stage. (F–I) UMAP projections of cranial neural plate cells colored by normalized expression of genes primarily associated with the forebrain (Otx2), midbrain and rhombomere 1 (En1), hindbrain (Gbx2), and ventral midline (Shh). (J) UMAP projection of cranial neural plate cells colored by neural plate region.
Figure 1—figure supplement 1
Assignment of cell identities in the mouse cranial region.
(A) Dot plot showing the normalized expression of a subset of markers used for cell type determination. (B) UMAP projection of all cranial cells analyzed (39,463 cells), colored by PhenoGraph cluster. Assigned cell types are listed on the right. (C) Distribution of cell cycle stages in the dataset.
Figure 1—figure supplement 2
Assignment of cell identities in the mouse cranial neural plate.
(A) Dot plot showing the normalized expression of a subset of markers used to assign cells to different neural plate regions. (B) UMAP projection of cranial neural plate cells (17,695 cells) reclustered in the absence of other cell types, colored by PhenoGraph cluster. Assigned neural plate regions are listed on the right. (C) UMAP projections of cranial neural plate cells colored by normalized gene expression. Markers for radial glial cells (Gfap) and immature neurons (Neurod1, Dcx) were not detected in the cranial neural plate at these stages, suggesting that cells are pre-neurogenic, although weak expression of neuronal cytoskeletal components (Nefl, Tubb3/Tuj1, Mapt) was observed.
Figure 2 with 3 supplements
Temporal changes in gene expression reveal shared and region-specific transcriptional trajectories.
(A–C) Cells from the forebrain (A), midbrain/r1 (B), and hindbrain (C) at progressive stages of neural plate development, plotted relative to the time-correlated diffusion component 0 (DC0) in each region. (D–F) Normalized expression of E-cadherin (Cdh1) and N-cadherin (Cdh2) plotted relative to the normalized time-correlated diffusion component (DC0) in each region. (G) E-cadherin protein (magenta) is lost from cell-cell junctions and N-cadherin protein (green) accumulates at cell-cell junctions between E7.75 and E8.5 in the mouse cranial neural plate. (H) UMAP projections of cranial neural plate cells colored by normalized gene expression, showing examples of genes that are downregulated or upregulated throughout the cranial neural plate (left) and genes that are specifically upregulated in the forebrain, midbrain/r1, or hindbrain. Bars, 100 μm (left panels in G), 20 μm (middle and right panels in G).
Figure 2—figure supplement 1
Analysis of gene expression trends in the developing forebrain, midbrain/r1, and hindbrain.
(A–F) UMAP projections of neural plate cells separated by region based on known markers of anterior-posterior identity. Cells are colored by embryo stage (A–C) or by their value along the top diffusion component (DC0) for each region (D–F). Higher DC0 values correlate with later time points. (G–I) Gene expression profiles were clustered by differential expression along DC0 and the average normalized expression (solid blue line)+/-1 standard deviation (dotted blue lines) and the expression of all individual genes in each cluster (gray lines) are shown.
Figure 2—figure supplement 2
Examples of genes that are temporally regulated throughout the cranial neural plate.
(A–C) UMAP projections of cranial neural plate cells colored by normalized gene expression. Genes that display globally decreasing expression (A), globally increasing expression (B), or increasing expression in a subset of domains (C) are shown.
Figure 2—figure supplement 3
Examples of genes that are upregulated in the forebrain, midbrain/r1, or hindbrain.
(A–C) UMAP projections of cranial neural plate cells colored by normalized gene expression. Genes that display increasing expression in the future forebrain (A), midbrain/r1 (B), or hindbrain (C) are shown.
Figure 3 with 2 supplements
Region-specific patterns of gene expression along the anterior-posterior axis.
(A) UMAP projections of cranial neural plate cells from E8.5–9.0 embryos colored by their value along the anterior-posterior-correlated diffusion component (DC0) (left) or by the normalized expression of markers primarily associated with the forebrain (Otx2), midbrain/r1 (En1), and hindbrain (Gbx2). (B, C) Line plot (B) and heatmap (C) showing the normalized expression of known markers of anterior-posterior identity relative to DC0. DC0 correctly orders forebrain, midbrain/r1, and hindbrain markers relative to their known positions along the anterior-posterior axis. (D) Heatmap showing the normalized expression of 483 genes with high information content relative to DC0. Gene expression profiles are grouped into 11 clusters based on similarities in expression along DC0. Examples of genes in each cluster are listed on the right. (E, F) Schematics showing the predicted expression of example transcriptional regulators along the anterior-posterior axis. Anterior (A), posterior (P). (G) Heatmaps showing the normalized expression of example transcriptional regulators relative to DC0. Heatmaps show one gene per row, one cell per column, with the cells in each row ordered by their value along DC0. Colored bars (right) show the cluster identity relative to DC0. Cells assigned to the forebrain, midbrain/r1, or hindbrain are indicated at the top of each heatmap.
Figure 3—figure supplement 1
Diffusion component analysis of E8.5–9.0 neural plate cells.
UMAP projections of neural plate cells from E8.5-E 9.0 embryos colored by the value along the indicated diffusion component. Red indicates higher DC values and blue indicates lower DC values. The top 10 diffusion components calculated for the dataset are shown.
Figure 3—figure supplement 2
Clustering analysis reveals distinct patterns of gene expression along DC0 in the E8.5–9.0 cranial neural plate.
(A, B) Gene expression profiles in the E8.5–9.0 neural plate were clustered by differential expression along DC0, which correlates with cell position along the anterior-posterior axis. (A) UMAP projections of E8.5–9.0 neural plate cells colored by the average gene expression for each cluster. Red indicates higher expression and blue indicates lower expression of the genes in each cluster. (B) The average normalized gene expression for each cluster (solid blue line)+/-1 standard deviation (dotted blue lines) and all individual genes in each cluster (gray lines) are shown.
Figure 4 with 1 supplement
Patterned gene expression along the mediolateral axis of the developing midbrain and rhombomere 1.
(A) UMAP projections of cranial neural plate cells from E8.5–9.0 embryos colored by their value along the mediolaterally correlated diffusion component (DC2) (left) or by the normalized expression of markers for the ventral midline (Shh), medial cells (Ptch1), or lateral cells (Pax7). (B, C) Line plot (B) and heatmap (C) showing the normalized expression of known markers of mediolateral cell identity relative to DC2 in the midbrain/r1. DC2 correctly orders midline, medial, and lateral markers relative to their known positions along the mediolateral axis. (D) Heatmap showing the normalized expression of 222 genes with high information content relative to DC2. Gene expression profiles are grouped into seven clusters based on similarities in expression along DC2. Examples of genes in each cluster are listed on the right. Cluster 3 (not shown) displayed divergent UMAP patterns associated with anterior-posterior patterning and was excluded from further analysis. (E) Heatmaps showing the normalized expression of specific transcriptional regulators relative to DC2. (F) Schematics showing the predicted expression of example transcriptional regulators along the mediolateral axis of the midbrain/r1. Heatmaps show one gene per row, one cell per column, with the cells in each row ordered by their value along DC0. Colored bars (right) show the cluster identity relative to DC2. Cells assigned to the midline or midbrain/r1 are indicated at the top of each heatmap.
Figure 4—figure supplement 1
Clustering analysis reveals distinct patterns of gene expression along DC2 in the E8.5–9.0 cranial neural plate.
(A, B) Gene expression profiles in the E8.5–9.0 neural plate were clustered by differential expression along DC2, which correlates with cell position along the mediolateral axis. (A) UMAP projections of E8.5–9.0 neural plate cells colored by the average gene expression for each cluster. Red indicates higher expression and blue indicates lower expression of genes in the cluster. (B) The average normalized gene expression for each cluster (solid blue line)+/-1 standard deviation (dotted blue lines) and all individual genes in each cluster (gray lines) are shown. (C–F) Heatmaps (C, E) and line plots (D, F) showing the normalized expression of a subset of transcriptional regulators (C, D) or transmembrane and secreted proteins (E, F) that appear to show graded changes in expression relative to DC2. Heatmaps show one gene per row, one cell per column, with the cells in each row ordered by their value along DC2. Cells assigned to the midline or midbrain/r1 are indicated at the top of each heatmap.
Figure 5 with 2 supplements
Multiscale analysis of spatial gene expression in the mouse cranial neural plate.
(A) Plot of genes by Z-Normalized Moran’s I relative to DC0 and DC2 for all genes expressed in the E8.5–9.0 cranial neural plate. Genes meeting the cutoff for further analysis are colored according to cluster identity at D=10; other genes are shown in gray. (B) Spatially informative genes from (A) replotted by spatial autocorrelation (Moran’s I) along DC0 and DC2, colored by cluster identity at D=10. (C) Dendrogram of spatially informative genes showing gene clusters at different distances corresponding to the average correlation among genes. Left, the number of clusters at each distance (black curve) and the average correlation between expression patterns within clusters (blue curve). Right, dendrogram showing the relationships between clusters, colored by cluster identity at D=10 as in A and B. (D) UMAP projections of E8.5–9.0 neural plate cells colored by normalized gene expression. Examples of genes that mark specific presumptive brain structures (the telencephalon, diencephalon, and rhombomere 1), midline or lateral domains, or subsets of rhombomeres are shown. Brackets and boxes indicate regions of increased gene expression. Spatial cluster identities at a stringency of D=6 (top and middle panels) or D=4 (bottom panels) are indicated.
Figure 5—figure supplement 1
Multiscale clustering analysis reveals spatial patterns of gene expression in the cranial neural plate.
UMAP projections of E8. 5–9.0 neural plate cells colored by the average expression of genes in each spatial cluster. Red indicates higher expression and blue indicates lower expression of the genes in each cluster.
Figure 5—figure supplement 2
Comparison of mediolateral patterning in the cranial neural plate and dorsal-ventral patterning in the spinal cord.
(A) Schematic of gene expression in neural precursors along the dorsal-ventral axis of the spinal cord (Delile et al., 2019). (B) UMAP projections of E8.5–9.0 cranial neural plate cells colored by normalized gene expression, ordered from lateral to medial. Of 29 genes that are spatially patterned in the spinal cord, 9 were not expressed in the midbrain/r1 region. The mediolateral expression of 17 of the remaining 20 genes roughly corresponded to their dorsal-ventral positions in the spinal cord (Arx and Ascl1 are not shown). The other 3 genes were either expressed in patterns that were distinct from their expression in the spinal cord (Lmx1a and Lmx1b) or were not detected in our spatially patterned dataset (Ferd3l). Genes in mediolateral clusters (blue), anterior-posterior clusters (green), or both (orange) are indicated.
Figure 6 with 1 supplement
Patterned expression of secreted and transmembrane proteins in the cranial neural plate.
(A, B) Heatmaps showing the normalized expression of transmembrane and secreted proteins relative to DC0 (A) or DC2 (B). Heatmaps show one gene per row, one cell per column, with the cells in each row ordered by their value along DC0 or DC2. Colored bars (right) show the cluster identity relative to DC0 or DC2. Cells assigned to the forebrain (FB), midbrain/r1 (MB/r1), hindbrain (HB), or midline are indicated at the top of each heatmap. (C) Schematics showing the predicted expression of example transmembrane and secreted proteins along the anterior-posterior axis. Anterior (A), posterior (P). (D–F) UMAP projections of cranial neural plate cells from E8.5–9.0 embryos colored by the normalized expression of a subset of Wnt ligands (D), Frizzled receptors (E), and Ephrin ligands and Eph receptors (F). Spatial cluster identities at D=10 are indicated.
Figure 6—figure supplement 1
Patterned expression of gene families.
(A–K) UMAP projections of E8.5–9.0 neural plate cells colored according to relative expression of an individual member of the indicated gene family. (A) Wnt ligands, (B) Frizzled receptors, (C) Eph/Ephrin signaling molecules, (D) Fgf ligands, (E) Fgf receptors, (F) Fox transcription factors, (G) Hes transcription factors, (H) Irx transcription factors, (I) Msx transcription factors, (J) Pax transcription factors, and (K) Zic transcription factors. Spatial cluster identities at a stringency of D=10 are shown.
Figure 7
Single-cell RNA sequencing reveals region-specific transcriptional programs activated by SHH signaling.
(A) Maximum-intensity projections of the midbrain and anterior hindbrain regions of the cranial neural plate of 5-somite mouse embryos treated with vehicle control (left) or with 2 µM Smoothened Agonist (SAG) stained for FOXA2 and NKX6-1. SAG-treated embryos display an expanded floor plate region. Bars, 100 μm. (B, C) UMAP projections of 1619 and 1409 cranial neural plate cells from control and SAG-treated embryos at E8.5, respectively, colored by treatment (B) or neural plate domain (C). (D–J) Heatmaps showing the normalized expression of candidate SHH target genes that were upregulated or downregulated throughout the cranial neural plate (D) or in the indicated region(s) (E–J) in SAG-treated embryos. Heatmaps show one gene per row, one cell per column, with the cells in each row grouped by control (green) or SAG treatment (orange), indicated at the top of each heatmap. Genes involved in SHH signaling (red) and genes assigned to medial (purple), lateral (blue), anterior-posterior (green), or other spatial clusters (orange) are indicated. Genes that had a MAST hurdle value >0.24 or<−0.24 and a false discovery rate adjusted p-value of p<0.001 in at least one region were indicated as differentially expressed in all regions in which p<0.001 and the MAST hurdle value was >0.10 or<−0.10.
Additional files
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Supplementary file 1
Cell type and quality control metrics for wild-type and SAG treatment datasets.
The total number of cells post-filtering, the number of cells assigned to each cell type, and quality metrics (median number of UMIs, median number of genes, median percent mitochondrial UMIs, median percent ribosomal UMIs, and mean reads/UMI) are shown for each replicate in the wild-type, SAG treatment, and SAG control datasets.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp1-v1.xlsx
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Supplementary file 2
PhenoGraph clustering of all cranial cells in E7.5–9.0 embryos.
Gene expression for each PhenoGraph cluster in the full cranial cell dataset. The false-discovery rate (FDR) adjusted p-value, MAST hurdle value, and empirical log2 fold change are shown for each gene.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp2-v1.xlsx
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Supplementary file 3
PhenoGraph clustering of cranial neural plate cells in E7.5–9.0 embryos.
Gene expression for each PhenoGraph cluster in the cranial neural plate are shown. The false-discovery rate (FDR) adjusted p-value, MAST hurdle value, and empirical log2 fold change are shown for each gene.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp3-v1.xlsx
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Supplementary file 4
Temporally regulated genes in the forebrain, midbrain/r1, and hindbrain of E7.5–9.0 embryos.
Gene correlation scores for the temporally correlated diffusion component (DC0) in each region are shown for the forebrain, midbrain/r1, and hindbrain cranial neural plate populations. The cluster number, Pearson correlation coefficient, and normalized range of expression are shown for each gene.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp4-v1.xlsx
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Supplementary file 5
Diffusion component gene correlations in the E8.5–9.0 cranial neural plate.
Gene correlations with each of the top 10 diffusion components in the E8.5–9.0 cranial neural plate are shown. The false discovery rate (FDR) adjusted p-value and Pearson correlation coefficient for each diffusion component are shown for each gene.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp5-v1.xlsx
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Supplementary file 6
Spatially patterned genes in the E8.5–9.0 cranial neural plate.
All genes detected in cells from wild-type E8.5–9.0 embryos are shown. The results of HotSpot analysis are given, including the Geary’s C spatial autocorrelation coefficient (C, MSD), the z-scored coefficient (Z, MSD), the p-value (Pval, MSD), the false discovery rate adjusted p-value (FDR, MSD), and the normalized range of expression for each gene, in addition to the results of HotSpot analysis for the anterior-posterior (AP) axis-correlated diffusion component (DC0) and the mediolateral (ML) axis-correlated diffusion component (DC2). Cluster identities along the AP axis (DC0), ML axis (DC2), and at various 2D distance (D) values are shown.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp6-v1.xlsx
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Supplementary file 7
Comparison of predicted gene expression patterns to published data.
For genes predicted to be spatially patterned in Supplementary file 6, the predicted expression of genes in anterior-posterior (AP) or mediolateral (ML) clusters was compared with published images in the Mouse Genome Informatics Gene Expression Database. In addition to the information in Supplementary file 6, the predicted and observed expression patterns and whether they agree is reported and a link to available images of wild-type embryos from Theiler stages 12–14 is provided.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp7-v1.xlsx
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Supplementary file 8
Spatially patterned transcriptional regulators in the E8.5–9.0 cranial neural plate.
Spatial (2D) cluster (distance D=10), AP cluster, and ML cluster of transcriptional regulators in the E8.5–9.0 cranial neural plate are shown.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp8-v1.xlsx
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Supplementary file 9
Spatially patterned ligands and receptors in the E8.5–9.0 cranial neural plate.
Spatial (2D) cluster (distance D=10), AP cluster, ML cluster, and NCBI GeneID of genes assigned as ligands or receptors by the indicated source databases are shown.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp9-v1.xlsx
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Supplementary file 10
Differentially expressed genes in SAG-treated and control embryos in the E8.5 cranial neural plate.
Results of MAST differential gene expression analysis in SAG-treated vs, control embryos separated by forebrain, midbrain/r1, and hindbrain regions. The false discovery rate (FDR) adjusted p-value, MAST hurdle value, and empirical log2 fold change value are shown for each gene.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp10-v1.xlsx
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Supplementary file 11
Regional analysis of transcriptional changes upon SAG treatment.
Genes with significant expression changes from Supplementary file 10 (FDR-adjusted p-value P<0.001) grouped by region, including genes deregulated in all cranial neural plate regions (FB-MB-HB), two regions (FB-MB, FB-HB, MB-HB), or single regions (FB, MB, HB). Upregulated genes with a MAST hurdle value >0.24 are highlighted in green. Downregulated genes with a MAST hurdle value <–0.24 are highlighted in red.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp11-v1.xlsx
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Supplementary file 12
Genes used for cell cycle normalization.
Gene ontology (GO) terms associated with the cell cycle and the associated genes used in cell cycle normalization are listed.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp12-v1.xlsx
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Supplementary file 13
Genes used for cell typing.
Genes used to assign cell/tissue type are listed, along with their positive or negative expression in that tissue and any expression overlap in other tissues.
- https://cdn.elifesciences.org/articles/102819/elife-102819-supp13-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/102819/elife-102819-mdarchecklist1-v1.docx
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A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate
eLife 13:RP102819.
https://doi.org/10.7554/eLife.102819.3
