Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex

Cell. 2023 Aug 17;186(17):3726-3743.e24. doi: 10.1016/j.cell.2023.06.009. Epub 2023 Jul 12.


Elucidating the cellular organization of the cerebral cortex is critical for understanding brain structure and function. Using large-scale single-nucleus RNA sequencing and spatial transcriptomic analysis of 143 macaque cortical regions, we obtained a comprehensive atlas of 264 transcriptome-defined cortical cell types and mapped their spatial distribution across the entire cortex. We characterized the cortical layer and region preferences of glutamatergic, GABAergic, and non-neuronal cell types, as well as regional differences in cell-type composition and neighborhood complexity. Notably, we discovered a relationship between the regional distribution of various cell types and the region's hierarchical level in the visual and somatosensory systems. Cross-species comparison of transcriptomic data from human, macaque, and mouse cortices further revealed primate-specific cell types that are enriched in layer 4, with their marker genes expressed in a region-dependent manner. Our data provide a cellular and molecular basis for understanding the evolution, development, aging, and pathogenesis of the primate brain.

Keywords: cell-type organization; hierarchy; macaque cortex; single-cell; spatial transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cerebral Cortex* / cytology
  • Cerebral Cortex* / metabolism
  • Humans
  • Macaca* / metabolism
  • Mice
  • Single-Cell Analysis*
  • Transcriptome* / genetics