Macaque Cortex Cell Organization via Single-Cell Study
Summary
In the present investigation, scientists employed an innovative, expansive spatial transcriptomics technique known as stereo-seq, in addition to devising a protocol for the creation of centimeter-scale cerebral sections derived from primates. Through an extensive single-nucleus RNA sequencing and spatial transcriptomic examination of 143 macaque cortical regions, the researchers established an exhaustive atlas encompassing 264 transcriptome-defined cortical cellular classifications, subsequently delineating their three-dimensional spatial arrangement throughout the cortex. A methodical evaluation of these cellular varieties and their molecular signatures within the cortex and designated regions facilitated the discovery of interconnections between cellular composition and the stratified organization inherent to visual and somatosensory modalities. Furthermore, comparative analysis across species unveiled cellular distinctions exclusive to the primate lineage.
Fig.1 Graphical abstract. (Chen, 2023)
Research Criteria
In this scholarly endeavor, the underlying conceptual premise revolves around the utilization of single-cell spatial transcriptomic scrutiny to elucidate the cellular and molecular orchestration within the macaque cortex. The article's objective encompasses the identification and cartographic representation of the myriad cell types disseminated throughout the entire cortex, while concurrently investigating the correlation between cellular composition, intricacy, cortical stratification, and evolutionary development. Additionally, the article engages in comparative transcriptomic assessments involving human, macaque, and murine cortices to reveal cell types and genes that are distinctive to the primate lineage.
Fig.2 Experimental design. (Chen, 2023)
Sample Type
Macaque cortex
Result—Types of Cells in the Macaque Cortex according to Their Transcriptomic Taxonomy
In the snRNA-seq analysis, cortical tissues from two cynomolgus monkey brains were utilized, resulting in the acquisition of 646,393 and 846,847 cells per monkey, respectively. Following integration and transcriptome profiling of single cells, dimensionality reduction and clustering analysis facilitated the identification of 264 cell clusters across 143 cortical regions, encompassing nine conventional lobes. The clustering results demonstrated reproducibility, as confirmed by Jaccard similarity and random forest analyses. Subsequently, a three-level taxonomy tree was constructed, categorizing cell types into three major classes—glutamatergic, GABAergic, and non-neuronal cells—along with their respective subclasses. The glutamatergic neuron subclasses correlated significantly with projection-property-inferred subclasses, while GABAergic neuron subclasses were annotated by prominent marker genes. Non-neuronal subclasses included astrocytes, oligodendrocyte precursor cells, oligodendrocytes, microglia, endothelial cells, and vascular leptomeningeal cells. This comprehensive cell-type taxonomy of the macaque cerebral cortex was achieved through snRNA-seq analysis combined with spatial transcriptome information.
Fig.3 Macaque cortex transcriptomic cell-type taxonomy. (Chen, 2023)
Result—Different Cell Types' Spatial Distribution in the Macaque Cortex
Researchers utilized stereo-seq technology to capture mRNAs from brain sections of adult male cynomolgus monkeys, precisely contacting a large silicon chip structured with regular 2D arrays of DNA nanoballs. The team innovated a section-flattening technique post-cryo-sectioning to ensure smooth surface contact between the brain sections and the stereo-seq chips. These samples were subjected to stereo-seq analysis, with an AI-assisted automatic segmentation method employed for single-cell identification, yielding a high-reliability rate. The researchers registered and annotated spatially resolved single cells, identifying cell types for tens of millions of cortical cells. This resulted in the creation of molecularly defined, 3D cell-type maps of the cortex, exhibiting high consistency across sections and biological replicates. Further examination of these maps revealed distinct cell-type compositions in each cortical region, with higher neighborhood complexity in deeper layers. This suggests that differential local circuits could originate from distinct local cell compositions, demonstrating neighborhood-composition specificity across different layers and regions.
Fig.4 Single-cell spatial transcriptome map of the macaque cortex. (Chen, 2023)
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Reference
- Chen. A.; et al. Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex. Cell. 2023, S0092-8674(23): 00679-7.
