Spatial transcriptomics and single-nucleus RNA sequencing reveal a transcriptomic atlas of adult human spinal cord
- Department of Anesthesiology, West China Hospital, Sichuan University, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, China
- Department of Anesthesiology, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), China
- Department of Intensive Care Unit, Affiliated Hospital of Zunyi Medical University, China
- Department of Orthopedic Surgery, Affiliated Hospital of Zunyi Medical University, China
- Department of Anesthesiology, Affiliated Hospital of Zunyi Medical University, China
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, China
Figures
Figure 1 with 1 supplement
Identification of human spinal cell types from spatial transcriptomics.
(A) Overview of the experimental workflow for spatial transcriptomics. (B) UMAP plot showing 17 cell types in the spinal cord. Dots, individual spots; colors, cell types. (C) Representative image …
Figure 1—figure supplement 1
Uniform manifold approximation and projection (UMAP) plot showing the contribution of each donor to spinal cluster formation by spatial transcriptomics.
Figure 2 with 1 supplement
Identification of spinal cell types using single-nucleus RNA-seq.
(A) Overview of the experimental workflow for single-nucleus RNA-seq. (B) UMAP plot showing eight major cell types. Dots, individual cells; colors, cell types. (C) Dot plot showing the expression of …
Figure 2—figure supplement 1
The characteristics of eight cell types in the human spinal cord by single-nucleus RNA-seq.
(A, B) Heatmap (A) and violin plot (B) showing the expression of selected marker genes across all eight cell types in the spinal cord by single-nucleus RNA-seq. (C) UMAP plot showing the …
Figure 3 with 6 supplements
Identification of neuronal subtypes in the human spinal cord.
(A) UMAP plot showing 21 neuronal clusters. Dots, individual cells; colors, neuronal clusters. (B) Dot plot showing the expression of selected marker genes across all 21 neuronal clusters. (C) UMAP …
Figure 3—figure supplement 1
The gene expression features in 21 neuronal subtypes of human spinal cord.
(A) Heatmap showing the expression of the top three most differentially expressed genes across different human spinal neuronal clusters.(B) Dot plot showing the expression of the top three most …
Figure 3—figure supplement 2
GO term analysis for four functional subpopulations in human spinal cord.
(A–D) Summarized GO terms among the top genes in excitatory (A), inhibitory (B), motor (C), and mixed excitatory and inhibitory (D) clusters of the human spinal cord. GO, Gene Ontology.
Figure 3—figure supplement 3
The spatial spot showing the distribution pattern of 21 neuronal clusters in the human spinal cord.
The color scale represents the probable percentage of single-nucleus RNA-seq data that mapped to spatial spots. For a specific spot, the sum of the probable percentage of C0-C20 was defined as 1.
Figure 3—figure supplement 4
The spatial distribution patterns of neuronal clusters in different spinal subregions of each donor.
(A–F) Gene set variation analysis (GSVA) showing the spatial distribution patterns of neuronal clusters in different subregions of coronal sections from the lumber spinal cord of each human donor. …
Figure 3—figure supplement 5
UMAP plot showing the expression of representative marker genes in human spinal neuronal clusters.
UMAP, uniform manifold approximation and projection.
Figure 3—figure supplement 6
Immunofluorescence results of CCK, SST, and FOXP2.
(A) Representative section showing the spatial distribution of CCK in the human spinal cord. (B) Representative immunofluorescence images of CCK in human spinal neurons. (C, D) Representative …
Figure 4 with 3 supplements
Human–mouse cell-type homology.
(A) UMAP plot showing the coclustering of mouse and human neurons. Dots, individual cells. Colors, species. (B) UMAP plot showing the distribution of putative homologous neuronal clusters of humans …
Figure 4—figure supplement 1
Expression of top 20 most differentially expressed genes in the functional subtypes of human and mouse spinal cord.
(A, B) Dot plot showing the expression of the top 20 most differentially expressed genes between excitatory, inhibitory, and cholinergic clusters of the spinal cord in humans (A) and mice (B).
Figure 4—figure supplement 2
Expression of classic ion channels and transcription factors in human and mouse spinal neuronal clusters.
(A, B) Dot plot (A) and heatmap (B) showing the expression of classic ion channels in human spinal neuronal clusters. (C, D) Dot plot (C) and heatmap (D) showing the expression of classic ion …
Figure 4—figure supplement 3
Expression of selected marker genes in human spinal neuronal clusters.
(A–L) UMAP plot showing the broad (A–I) or low (J–L) expression of selected marker genes in human spinal neuronal clusters. UMAP, uniform manifold approximation and projection.
Figure 5
Sex differences in gene expression in human spinal neuronal types.
(A) UMAP plot showing barcodes in all spinal neuronal clusters from males and females. Dots, individual cells. Colors, sexes. (B) Volcano plot showing DEGs of all spinal neurons between males and …
Figure 6 with 1 supplement
Identification of human DRG cell types from spatial transcriptomics.
(A) Overview of the experimental workflow for spatial transcriptomics in human DRG. (B) UMAP plot showing 16 cell types in the spinal cord. Dots, individual spots; colors, cell types. (C) Dot plot …
Figure 6—figure supplement 1
UMAP plot showing the contribution of each donor to cluster formation in the DRG by spatial transcriptomics.
UMAP, uniform manifold approximation and projection; DRG, dorsal root ganglia.
Figure 7 with 4 supplements
Identification of neuronal subtypes in human DRG.
(A) UMAP plot showing 13 neuronal clusters of human DRG neurons. Dots, individual spots; colors, neuronal clusters. (B) UMAP plot showing the expression of representative marker genes. (C) Putative …
Figure 7—figure supplement 1
The gene expression features in 13 neuronal subtypes of human DRG.
(A) UMAP plot showing 13 types of human DRG neurons.Dots, individual spots; colors, cell types. (B) Dot plot showing the expression of representative marker genes across all DRG neuronal subtypes. (C…
Figure 7—figure supplement 2
Expression of the top 3 most differentially expressed genes across human DRG neuronal subclusters.
(A, B) Dot plot (A) and heatmap (B) showing the expression of the top three most differentially expressed genes across human DRG neuronal subclusters. DRG, dorsal root ganglia.
Figure 7—figure supplement 3
Expression of classical marker genes in human and mouse DRG neuronal clusters.
(A, B) Heatmap showing the expression of classical marker genes in human (A) and mouse (B) DRG neuronal clusters. DRG, dorsal root ganglia.
Figure 7—figure supplement 4
Expression of IL4R, IL31RA, and IL13RA1 in human and mouse DRG neuronal clusters.
(A, B) Dot plot showing the expression of IL4R, IL31RA, and IL13RA1 in human (A) and mouse (B) DRG neuronal clusters. (C, D) Heatmap showing the expression of IL4R, IL31RA, and IL13RA1 in human (C) …
Figure 8
Ligand‒receptor interactions between the human DRG and spinal cord.
(A) Putative ligand‒receptor interactions of neuronal clusters between the human DRG and spinal cord. The thickness of connecting lines is proportional to the number of total ligand‒receptor …
Additional files
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MDAR checklist
- https://cdn.elifesciences.org/articles/92046/elife-92046-mdarchecklist1-v1.docx
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Supplementary file 1
The expression profiles of each neuronal cluster of the human spinal cord.
- https://cdn.elifesciences.org/articles/92046/elife-92046-supp1-v1.xlsx
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Supplementary file 2
The expression profiles of each neuronal cluster of the mouse spinal cord.
- https://cdn.elifesciences.org/articles/92046/elife-92046-supp2-v1.xlsx
