Transcriptomic encoding of sensorimotor transformation in the midbrain
- National Institute of Biological Sciences, China
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, China
- University of Chinese Academy of Sciences, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), China
- Beijing Institute for Brain Disorders, Capital Medical University, China
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, China
- Chinese Institute for Brain Research, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, China
Figures
Figure 1 with 2 supplements
Identification and characterization of cell types and spatial heterogeneity of mouse superior colliculus (SC) neurons.
(A) Unbiased clustering of single-nucleus RNA-sequencing (snRNA-seq) data of mouse SC cells. Each dot represents an individual cell. The cells were grouped into 26 clusters, and the cell types were …
Figure 1—figure supplement 1
Quality of single-nucleus RNA-sequencing (snRNA-seq) metrics and the spatial distribution of neurons.
(A) Number of genes (nGene) and number of unique molecular identifiers (nUMI) of each cluster. (B) t-Distributed stochastic neighbor embedding (t-SNE) plot of the two replicates of single-nucleus …
Figure 1—figure supplement 2
Comparison of neuronal subtypes and spatial mapping results.
(A) t-Distributed stochastic neighbor embedding (t-SNE) plot displaying the distribution of excitatory neurons and inhibitor neurons from Zeisel’s study. (B) t-SNE plots showing the diversity of …
Figure 2 with 2 supplements
Projection-based analyses of single-cell gene expression profiles.
(A) Schematic diagram showing injection of AAV mixture into the superior colliculus (SC) of vGlut2-IRES-Cre mice for sparse labeling of glutamatergic SC neuron projections. (B) Two reconstructed …
Figure 2—figure supplement 1
Electrophysiological properties and the expression of differentially expressed genes (DEGs) between lateral posterior thalamic nucleus (LPTN)- and zona incerta (ZI)-projecting superior colliculus (SC) neurons.
(A) Schematic diagram showing current-clamp whole-cell recording from LPTN- or ZI-projecting SC neurons labeled with EGFP. (B, C) Quantitative analyses of resting membrane potential (B) and firing …
Figure 2—video 1
3D reconstruction of layer-specific neuron projection patterns from SC to downstream brain regions by in vivo sparse-labeling strategy and M-CRITIC, related to Figure 2B–C.
Figure 3 with 3 supplements
Synaptic inactivation of Cbln2+ and Pitx2+ superior colliculus (SC) neurons.
(A) Sample coronal section showing the restricted distribution of EGFP-expressing neurons in the optic nerve (Op) layer of the SC in Cbln2-IRES-Cre mice. (B) Sample micrographs showing the …
Figure 3—figure supplement 1
Generation of Cbln2-IRES-Cre mice to test the function of Cbln2+ and Pitx2+ superior colliculus (SC) neurons.
(A) Heatmap showing the computed layer specificity score of 10 differentially expressed genes (DEGs) of lateral posterior thalamic nucleus (LPTN)-projecting and zona incerta (ZI)-projecting neurons. …
Figure 3—video 1
An example video showing that synaptic inactivation of Cbln2+ SC neurons by TeNT impaired visually-evoked freezing responses.
Related to Figure 3D.
Figure 3—video 2
An example video showing that synaptic inactivation of Pitx2+ SC neurons by TeNT impaired prey capture behavior in the arena.
Related to Figure 3K.
Figure 4 with 1 supplement
Sensory responses of Cbln2+ and Pitx2+ superior colliculus (SC) neurons.
(A, B) Sample micrographs showing the optical fiber tracks above GCaMP7-positive SC neurons in Cbln2-IRES-Cre (A) and Pitx2-Cre (B) mice. (C) Schematic diagram of the experimental configuration …
Figure 4—figure supplement 1
Sensory response properties of Cbln2+ and Pitx2+ superior colliculus (SC) neurons.
(A) Distribution of receptive field centers (red spots) of recorded Cbln2+ SC neurons in five Cbln2-IRES-Cre mice in the meridian plot of the mouse retina on the tangent screen. The coordinate …
Figure 5 with 1 supplement
Retrograde tracing of Cbln2+ and Pitx2+ superior colliculus (SC) neurons using rabies virus (RV).
(A) Series of schematic diagrams showing the strategy for monosynaptic retrograde tracing of Cbln2+ and Pitx2+ SC neurons using a combination of AAV and RV. Left, AAV helpers and RV used for …
Figure 5—figure supplement 1
Rabies virus (RV) tracing of Cbln2+ and Pitx2+ superior colliculus (SC) neurons.
(A, B) Example micrographs showing the expression of EGFP (green) and DsRed (red) in the Cbln2+ and Pitx2+ neurons in the SC of Cbln2-IRES-Cre (A) and Pitx2-Cre mice (B), respectively. Note the …
Figure 6
Efferent projections of Cbln2+ and Pitx2+ superior colliculus (SC) neurons are segregated.
(A) Schematic diagram showing the strategy to map the efferent projections of Cbln2+ and Pitx2+ SC neurons. (B) Example coronal sections of Cbln2-IRES-Cre and Pitx2-Cre mice showing the distribution …
Figure 7
Anterograde and retrograde mapping of Cbln2+ superior colliculus (SC)-lateral posterior thalamic nucleus (LPTN) and Pitx2+ SC-zona incerta (ZI) pathways.
(A) Sample micrographs showing the distribution of EGFP-positive axons in the LPLR and LPMR (collectively the LPTN) of Cbln2-IRES-Cre (left) and Pitx2-Cre (right) mice. (B) Quantitative analysis of …
Figure 8 with 3 supplements
Activation of the Cbln2+ superior colliculus (SC)-lateral posterior thalamic nucleus (LPTN) and Pitx2+ SC-zona incerta (ZI) pathways.
(A) Sample micrographs showing the expression of ChR2-mCherry in the Cbln2+ SC neurons of Cbln2-IRES-Cre mice (left) and the optical fiber track above the ChR2-mCherry+ axons in the LPTN (right). (B)…
Figure 8—figure supplement 1
Activation of Cbln2+ superior colliculus (SC)-lateral posterior thalamic nucleus (LPTN) pathway and Pitx2+ SC-zona incerta (ZI) pathway.
(A) Schematic diagram showing whole-cell recording from ChR2-mCherry+ SC neurons in the acute brain slice. (B, C) Example traces of phase-locked spiking activity evoked by light-pulse train (1 ms, 5 …
Figure 8—video 1
An example video showing that light stimulation of ChR2-mCherry+ axon terminals of Cbln2+ SC neurons in the LPTN induced freezing response in mice.
Related to Figure 8B–C.
Figure 8—video 2
An example video showing light stimulation of ChR2-mCherry+ axon terminals of Pitx2+ SC neurons in the ZI promoted predatory hunting behavior in mice, related to Figure 8F–G.
Author response image 1
Quality control metrices and spatial distribution of Ex-2.
(A) Violin plots showing the number of detected genes (nGene) and unique molecular identifiers (uUMI) of each cell types identified in the SC. (B) Scatter plot displaying the correlation between …
Author response image 2
Comparison of mapping results for SC.
(A) tSNE displaying the spatial distribution of excitatory neuron subtypes from Zeisel’s study. (B) Heatmap showing the layer specificity for each subtype computed by SPACED.
Author response image 3
Impact of the number of selected genes on mapping results of SPACED.
(A) Scatter plot showing the relation between number of selected genes and the number of assigned clusters. (B) Heatmap showing the computed layer specificity for each excitatory neuron subtype with …
Author response image 4
Mapping cortical pyramidal neurons to spatial locations.
(A) UMAP showing the distribution of cortical pyramidal neuron subtypes (left) and their probable locations (right). (B) Heatmap showing the layer specificity of each subtype revealed by SPACED.
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Mus musculus) | Pitx2-Cre mice | Mutant Mouse Resource Center | Cat# 000126-UCD, RRID:MMRRC_000126-UCD | |
| Strain, strain background (Mus musculus) | vGlut2-IRES-Cre mice | JAX Mice | Cat# JAX:028863, RRID:IMSR_JAX:028863 | |
| Strain, strain background (Mus musculus) | Cbln2-IRES-Cre mice | NIBS | NA | |
| Genetic reagent (virus) | AAV-EF1α-DIO-EGFP-2A-TeNT | Thomas Südhof Lab at Stanford University | NA | |
| Genetic reagent (virus) | pAAV-EF1α-DIO-ChR2-mCherry | Addgene | RRID:Addgene_20297 | |
| Genetic reagent (virus) | AAV-EF1α-DIO-jGCaMP7s | Addgene | RRID:Addgene_104463 | |
| Genetic reagent (virus) | AAV2-retro-hSyn-DIO-EGFP | TaiTool | NA | |
| Genetic reagent (virus) | AAV2/9-hSyn-DIO-EGFP-2A-TeNT | TaiTool | NA | |
| Genetic reagent (virus) | AAV2/9-hSyn-DIO-EGFP | TaiTool | NA | |
| Genetic reagent (virus) | AAV2/9-hSyn-DIO-ChR2-mCherry | TaiTool | NA | |
| Genetic reagent (virus) | AAV2/9-hSyn-DIO-mCherry | TaiTool | NA | |
| Genetic reagent (virus) | AAV2/9-hSyn-DIO-jGCaMP7s | TaiTool | NA | |
| Genetic reagent (virus) | AAV2/9-EF1α-DIO-EGFP-2A-TVA | BrainVTA | NA | |
| Genetic reagent (virus) | AAV2/9-EF1α-DIO-RV-G | BrainVTA | NA | |
| Genetic reagent (virus) | RV-EnvA-ΔG-DsRed | BrainVTA | NA | |
| Antibody | Rabbit polyclonal anti-EGFP | Abcam | Cat# ab290, RRID:AB_303395 | |
| Antibody | Polycolonal anti-mCherry | Abcam | Cat# ab167453, RRID:AB_2571870; Cat# ab205402, RRID:AB_2722769 | |
| Sequence-based reagent | M-Cbln2-cre-upF | Tsingke Biological Technology, China | Primer | 5’-GGTACCTACTGTGTATCGCCAG-3’ |
| Sequence-based reagent | CRE-AS | Tsingke Biological Technology, China | Primer | 5’-CTGTTTCACTATCCAGGTTACG-3’ |
| Sequence-based reagent | CRE-S | Tsingke Biological Technology, China | Primer | 5’-TACTGACGGTGGGAGAATG-3’ |
| Sequence-based reagent | M-Cbln2-ires-cre-doR | Tsingke Biological Technology, China | Primer | 5’-GTTTGAAGCTGCACTGAGAGAG-3’ |
| Chemical compound, drug | D-AP5/CNQX | Tocris | Cat# 0106 / 0190 | |
| Chemical compound, drug | Picrotoxin/TTX | Tocris | Cat# 1128 / 1078 | |
| Chemical compound, drug | 4-AP | Sigma | Cat# 275875 | |
| Chemical compound, drug | DAPI | Sigma | Cat# D8417 | |
| Software, algorithm | GraphPad Prism 9.0.0 | GraphPad, 2015 | https://www.graphpad.com/scientific-software/prism/ | |
| Software, algorithm | Cell ranger 3.0.2 | Zheng et al., 2017 | http://10xgenomics.com | |
| Software, algorithm | R version 3.6.1 | R Development Core Team, 2020 | https://www.r-project.org | |
| Software, algorithm | Seurat 3.1.0 | Stuart et al., 2019 | https://satijalab.org/seurat/ | |
| Software, algorithm | Scrublet 0.2.1 | Wolock et al., 2019 | https://github.com/swolock/scrublet | |
| Software, algorithm | batchelor 1.0.1 | Haghverdi et al., 2018 | https://github.com/MarioniLab/MNN2017/ | |
| Software, algorithm | pheatmap 1.0.12 | Kolde, 2019 | https://github.com/raivokolde/pheatmap | |
| Software, algorithm | rgl 0.100.54 | Adler and Murdoch, 2020 | https://github.com/dmurdoch/rgl | |
| Software, algorithm | metascape | Zhou et al., 2019 | https://metascape.org/gp/index.html#/main/step1 | |
| Software, algorithm | Image J v1.48h3 | Schneider et al., 2012 | https://imagej.nih.gov/ij/ | |
| Software, algorithm | MATLAB 2019b | MATLAB, 2018 | https://www.mathworks.com | |
| Software, algorithm | Brainrender 2.0 | Claudi et al., 2020 | https://github.com/brainglobe/brainrender |
Additional files
-
Supplementary file 1
Sample information for high-throughput single-nucleus RNA-sequencing (snRNA-seq) of nucleus from superior colliculus (SC) and top 50 differentially expressed genes among nine major cell types in SC, related to Figure 1A.
- https://cdn.elifesciences.org/articles/69825/elife-69825-supp1-v2.xlsx
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Supplementary file 2
Differentially expressed genes among 9 excitatory neuron subtypes and 10 inhibitory neuron subtypes, related to Figure 1C–D.
- https://cdn.elifesciences.org/articles/69825/elife-69825-supp2-v2.xlsx
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Supplementary file 3
Sample information for patch-seq of neurons from superior colliculus (SC), related to Figure 2H.
- https://cdn.elifesciences.org/articles/69825/elife-69825-supp3-v2.xlsx
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Supplementary file 4
Differentially expressed genes between zona incerta (ZI)- and lateral posterior thalamic nucleus (LPTN)-projecting neurons in superior colliculus (SC), related to Figure 2I.
- https://cdn.elifesciences.org/articles/69825/elife-69825-supp4-v2.xlsx
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Supplementary file 5
Differentially expressed genes between excitatory neuron subtype Ex-3 and Ex-6, and between Ex-1 and Ex-4, related to Figure 2L–M, respectively.
- https://cdn.elifesciences.org/articles/69825/elife-69825-supp5-v2.xlsx
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Supplementary file 6
Summary of all experimental designs.
- https://cdn.elifesciences.org/articles/69825/elife-69825-supp6-v2.xlsx
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Supplementary file 7
Summary of cell-counting strategies.
- https://cdn.elifesciences.org/articles/69825/elife-69825-supp7-v2.xlsx
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Supplementary file 8
Summary of statistical analyses.
- https://cdn.elifesciences.org/articles/69825/elife-69825-supp8-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/69825/elife-69825-transrepform-v2.docx
