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

Cell 2023

Chen, Ao and Sun, Yidi and Lei, Ying and Li, Chao and Liao, Sha and Meng, Juan and Bai, Yiqin and Liu, Zhen and Liang, Zhifeng and Zhu, Zhiyong and Yuan, Nini and Yang, Hao and Wu, Zihan and Lin, Feng and Wang, Kexin and Li, Mei and Zhang, Shuzhen and Yang, Meisong and Fei, Tianyi and Zhuang, Zhenkun and Huang, Yiming and Zhang, Yong and Xu, Yuanfang and Cui, Luman and Zhang, Ruiyi and Han, Lei and Sun, Xing and Chen, Bichao and Li, Wenjiao and Huangfu, Baoqian and Ma, Kailong and Ma, Jianyun and Li, Zhao and Lin, Yikun and Wang, He and Zhong, Yanqing and Zhang, Huifang and Yu, Qian and Wang, Yaqian and Liu, Xing and Peng, Jian and Liu, Chuanyu and Chen, Wei and Pan, Wentao and An, Yingjie and Xia, Shihui and Lu, Yanbing and Wang, Mingli and Song, Xinxiang and Liu, Shuai and Wang, Zhifeng and Gong, Chun and Huang, Xin and Yuan, Yue and Zhao, Yun and Chai, Qinwen and Tan, Xing and Liu, Jianfeng and Zheng, Mingyuan and Li, Shengkang and Huang, Yaling and Hong, Yan and Huang, Zirui and Li, Min and Jin, Mengmeng and Li, Yan and Zhang, Hui and Sun, Suhong and Gao, Li and Bai, Yinqi and Cheng, Mengnan and Hu, Guohai and Liu, Shiping and Wang, Bo and Xiang, Bin and Li, Shuting and Li, Huanhuan and Chen, Mengni and Wang, Shiwen and Li, Minglong and Liu, Weibin and Liu, Xin and Zhao, Qian and Lisby, Michael and Wang, Jing and Fang, Jiao and Lin, Yun and Xie, Qing and Liu, Zhen and He, Jie and Xu, Huatai and Huang, Wei and Mulder, Jan and Yang, Huanming and Sun, Yangang and Uhlen, Mathias and Poo, Muming and Wang, Jian and Yao, Jianhua and Wei, Wu and Li, Yuxiang and Shen, Zhiming and Liu, Longqi and Liu, Zhiyong and Xu, Xun and Li, Chengyu

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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