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

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Yidi Sun
Ying Lei
Chao Li
Sha Liao
Juan Meng
Yiqin Bai
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
Zhao Li
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 Tan
Jianfeng Liu
Mingyuan Zheng
Shengkang Li
Yaling Huang
Yan Hong
Zirui Huang
Min Li
Mengmeng Jin
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
Jing Wang
Jiao Fang
Yun Lin
Qing Xie
Jie He
Huatai Xu
Wei Huang
Jan Mulder
Huanming Yang
Yangang Sun
Mathias Uhlen
Muming Poo
Jian Wang
Jianhua Yao
Wu Wei
Yuxiang Li
Zhiming Shen
Longqi Liu
Zhiyong Liu
Xun Xu
Chengyu Li

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.

Originalsprog	Engelsk
Tidsskrift	Cell
Vol/bind	186
Udgave nummer	17
Sider (fra-til)	3726-3743.e24
Antal sider	43
ISSN	0092-8674
DOI	https://doi.org/10.1016/j.cell.2023.06.009
Status	Udgivet - 2023

Bibliografisk note

Funding Information:
The project was supported by National Science and Technology Innovation 2030 Major Program ( STI2030-2021ZD0200100 ), Shanghai Municipal Science and Technology Major Project ( 2018SHZDZX05 ), National Key R&D Program of China ( 2022YEF0203200 ), Strategic Priority Research Program of CAS ( XDB32010100 and XDA27010400 ), Lingang Laboratory ( LG202105-01-01 , LG202104-02 , LG202104-02-02 , LG202104-02-03 , LG202104-02-04 , and LG202104-02-06 ), Shanghai Municipal of Science and Technology Project ( 21015800100 ), International Partnership Program of Chinese Academy of Sciences ( 153D31KYSB20170059 ), Scientific Instrument Developing Project of CAS ( YJKYYQ20190052 ), Scientific Instrument Developing Project of NNSFC ( 31827803 ), National Natural Science Foundation of China ( 31900466 and 32161133024 ), and Shenzhen Basic Research Project for Excellent Young Scholars ( 2020251518 ). This work is part of the “SpatioTemporal Omics Consortium” (STOC) paper package. A list of STOC members is available at: http://sto-consortium.org . We would like to thank Xiaodong Lu for his help in figure improvement and Hanbo Chen for his contribution to image registration.

Publisher Copyright:
© 2023 The Author(s)

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