Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex
Ao Chen(BGI Group (China)), Yidi Sun(Center for Excellence in Brain Science and Intelligence Technology), Yidi Sun(BGI Group (China)), Ying Lei(BGI Group (China)), Chao Li(BGI Group (China)), Chao Li(Center for Excellence in Brain Science and Intelligence Technology), Sha Liao(BGI Group (China)), Juan Meng(Shanghai Institute of Nutrition and Health), Yiqin Bai(BGI Group (China)), Zhen Liu(BGI Group (China)), Zhen Liu(Shanghai Institute of Nutrition and Health), Zhifeng Liang(Center for Excellence in Brain Science and Intelligence Technology), Zhiyong Zhu(BGI Group (China)), Nini Yuan(BGI Group (China)), Hao Yang(BGI Group (China)), Zihan Wu(BGI Group (China)), Feng Lin(BGI Group (China)), Kexin Wang(BGI Group (China)), Mei Li(BGI Group (China)), Shuzhen Zhang(BGI Group (China)), Meisong Yang(BGI Group (China)), Tianyi Fei(BGI Group (China)), Zhenkun Zhuang(BGI Group (China)), Yiming Huang(BGI Group (China)), Yong Zhang(BGI Group (China)), Yuanfang Xu(BGI Group (China)), Luman Cui(BGI Group (China)), Ruiyi Zhang(BGI Group (China)), Lei Han(BGI Group (China)), Xing Sun(BGI Group (China)), Bichao Chen(BGI Group (China)), Wenjiao Li(BGI Group (China)), Baoqian Huangfu(BGI Group (China)), Kailong Ma(BGI Group (China)), Jianyun Ma(Shanghai Institute of Nutrition and Health), Li Zhao(BGI Group (China)), Yikun Lin(BGI Group (China)), He Wang(Center for Excellence in Brain Science and Intelligence Technology), Yanqing Zhong(Center for Excellence in Brain Science and Intelligence Technology), Huifang Zhang(BGI Group (China)), Qian Yu(BGI Group (China)), Yaqian Wang(BGI Group (China)), Xing Liu(BGI Group (China)), Jian Peng(BGI Group (China)), Chuanyu Liu(BGI Group (China)), Wei Chen(BGI Group (China)), Wentao Pan(Tencent (China)), Yingjie An(Center for Excellence in Brain Science and Intelligence Technology), Shihui Xia(Center for Excellence in Brain Science and Intelligence Technology), Yanbing Lu(BGI Group (China)), Mingli Wang(BGI Group (China)), Xinxiang Song(BGI Group (China)), Shuai Liu(BGI Group (China)), Zhifeng Wang(BGI Group (China)), Chun Gong(Center for Excellence in Brain Science and Intelligence Technology), Xin Huang(BGI Group (China)), Yue Yuan(BGI Group (China)), Yun Zhao(Center for Excellence in Brain Science and Intelligence Technology), Qinwen Chai(Center for Excellence in Brain Science and Intelligence Technology), Xing Haw Marvin Tan(BGI Group (China)), Jianfeng Liu(BGI Group (China)), Mingyuan Zheng(BGI Group (China)), Shengkang Li(BGI Group (China)), Yaling Huang(BGI Group (China)), Hong Yan(BGI Group (China)), Zirui Huang(BGI Group (China)), Min Li(BGI Group (China)), Mengmeng Jin(Center for Excellence in Brain Science and Intelligence Technology), Yan Li(BGI Group (China)), Yan Li(BGI Group (China)), Hui Zhang(BGI Group (China)), Suhong Sun(Center for Excellence in Brain Science and Intelligence Technology), Li Gao(BGI Group (China)), Yinqi Bai(BGI Group (China)), Mengnan Cheng(BGI Group (China)), Guohai Hu(Center for Excellence in Brain Science and Intelligence Technology), Shiping Liu(BGI Group (China)), Bo Wang(Center for Excellence in Brain Science and Intelligence Technology), Bin Xiang(Shanghai Institute of Nutrition and Health), Shuting Li(BGI Group (China)), Huanhuan Li(BGI Group (China)), Mengni Chen(BGI Group (China)), Shiwen Wang(BGI Group (China)), Minglong Li(BGI Group (China)), Weibin Liu(BGI Group (China)), Xin Liu(BGI Group (China)), Qian Zhao(BGI Group (China)), Michael Lisby(BGI Group (China)), Jing Wang(BGI Group (China)), Fang Jiao(Center for Excellence in Brain Science and Intelligence Technology), Yun Lin(BGI Group (China)), Qing Xie(BGI Group (China)), Zhen Liu(Science for Life Laboratory), Zhen Liu(BGI Group (China)), Jie He(Center for Excellence in Brain Science and Intelligence Technology), Huatai Xu(Science for Life Laboratory), Wei Huang(Center for Excellence in Brain Science and Intelligence Technology), Jan Mulder(BGI Group (China)), Huanming Yang(BGI Group (China)), Yan-Gang Sun(Shanghai Institute of Nutrition and Health), Yan-Gang Sun(BGI Group (China)), Mathias Uhlén(Center for Excellence in Brain Science and Intelligence Technology), Mu‐ming Poo(BGI Group (China)), Jian Wang(BGI Group (China)), Jianhua Yao(BGI Group (China)), Wei Wu(Shanghai Institute of Nutrition and Health), Yuxiang Li(BGI Group (China)), Yuxiang Li(BGI Group (China)), Zhiming Shen(Center for Excellence in Brain Science and Intelligence Technology), Longqi Liu(BGI Group (China)), Zhiyong Liu(Shanghai Institute of Nutrition and Health), Zhiyong Liu(Shanghai Institute of Nutrition and Health), Xun Xu(BGI Group (China)), Chengyu Li(Center for Excellence in Brain Science and Intelligence Technology), Chengyu Li(Center for Excellence in Brain Science and Intelligence Technology)
Cited by 197Open Access
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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