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