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

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      Cell
      Elsevier BV
      cell-type organization, hierarchy, macaque cortex, single-cell, spatial transcriptome

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          Abstract

          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.

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          Author and article information

          Journal
          Cell
          Cell
          Elsevier BV
          1097-4172
          0092-8674
          Aug 17 2023
          : 186
          : 17
          Affiliations
          [1 ] BGI-Shenzhen, Shenzhen 518103, China; Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark; BGI Research-Southwest, BGI, Chongqing 401329, China; JFL-BGI STOmics Center, Jinfeng Laboratory, Chongqing 401329, China.
          [2 ] Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China. Electronic address: ydsun@ion.ac.cn.
          [3 ] BGI-Shenzhen, Shenzhen 518103, China; BGI-Hangzhou, Hangzhou 310012, China.
          [4 ] Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
          [5 ] BGI-Shenzhen, Shenzhen 518103, China; BGI Research-Southwest, BGI, Chongqing 401329, China; JFL-BGI STOmics Center, Jinfeng Laboratory, Chongqing 401329, China.
          [6 ] Lingang Laboratory, Shanghai 200031, China.
          [7 ] CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
          [8 ] BGI-Shenzhen, Shenzhen 518103, China.
          [9 ] Tencent AI Lab, Shenzhen 518057, China.
          [10 ] BGI-Shenzhen, Shenzhen 518103, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China.
          [11 ] BGI-Shenzhen, Shenzhen 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.
          [12 ] BGI-Shenzhen, Shenzhen 518103, China; Guangdong Bigdata Engineering Technology Research Center for Life Sciences, Shenzhen 518083, China.
          [13 ] China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.
          [14 ] Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark.
          [15 ] Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China.
          [16 ] Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm 17121, Sweden; Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden.
          [17 ] Tencent AI Lab, Shenzhen 518057, China. Electronic address: jianhuayao@tencent.com.
          [18 ] Lingang Laboratory, Shanghai 200031, China; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China. Electronic address: wuwei@lglab.ac.cn.
          [19 ] BGI-Shenzhen, Shenzhen 518103, China; BGI Research-Wuhan, BGI, Wuhan 430074, China. Electronic address: liyuxiang@genomics.cn.
          [20 ] Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China. Electronic address: zmshen@ion.ac.cn.
          [21 ] BGI-Shenzhen, Shenzhen 518103, China; BGI-Hangzhou, Hangzhou 310012, China. Electronic address: liulongqi@genomics.cn.
          [22 ] Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China. Electronic address: zhiyongliu@ion.ac.cn.
          [23 ] BGI-Shenzhen, Shenzhen 518103, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China. Electronic address: xuxun@genomics.cn.
          [24 ] Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: tonylicy@lglab.ac.cn.
          Article
          S0092-8674(23)00679-7
          10.1016/j.cell.2023.06.009
          37442136
          53b8ba6b-8e54-490e-b031-2a42d5867a7f
          History

          macaque cortex,spatial transcriptome,cell-type organization,hierarchy,single-cell

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