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Hao S, Zhu X, Huang Z, Yang Q, Liu H, Wu Y, Zhan Y, Dong Y, Li C, Wang H, Haasdijk E, Wu Z, Li S, Yan H, Zhu L, Guo S, Wang Z, Ye A, Lin Y, Cui L, Tan X, Liu H, Wang M, Chen J, Zhong Y, Du W, Wang G, Lai T, Cao M, Yang T, Xu Y, Li L, Yu Q, Zhuang Z, Xia Y, Lei Y, An Y, Cheng M, Zhao Y, Han L, Yuan Y, Song X, Song Y, Gu L, Liu C, Lin X, Wang R, Wang Z, Wang Y, Li S, Li H, Song J, Chen M, Zhou W, Yuan N, Sun S, Wang S, Chen Y, Zheng M, Fang J, Zhang R, Zhang S, Chai Q, Liu J, Wei W, He J, Zhou H, Sun Y, Liu Z, Liu C, Yao J, Liang Z, Xu X, Poo M, Li C, De Zeeuw CI, Shen Z, Liu Z, Liu L, Liu S, Sun Y, Liu C. Cross-species single-cell spatial transcriptomic atlases of the cerebellar cortex. Science 2024; 385:eado3927. [PMID: 39325889 DOI: 10.1126/science.ado3927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 08/14/2024] [Indexed: 09/28/2024]
Abstract
The molecular and cellular organization of the primate cerebellum remains poorly characterized. We obtained single-cell spatial transcriptomic atlases of macaque, marmoset, and mouse cerebella and identified primate-specific cell subtypes, including Purkinje cells and molecular-layer interneurons, that show different expression of the glutamate ionotropic receptor Delta type subunit 2 (GRID2) gene. Distinct gene expression profiles were found in anterior, posterior, and vestibular regions in all species, whereas region-selective gene expression was predominantly observed in the granular layer of primates and in the Purkinje layer of mice. Gene expression gradients in the cerebellar cortex matched well with functional connectivity gradients revealed with awake functional magnetic resonance imaging, with more lobule-specific differences between primates and mice than between two primate species. These comprehensive atlases and comparative analyses provide the basis for understanding cerebellar evolution and function.
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Affiliation(s)
| | - Xiaojia Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhi Huang
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Qianqian Yang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hean Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yan Wu
- BGI Research, Hangzhou 310030, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yafeng Zhan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu Dong
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- Lingang Laboratory, Shanghai 200031, China
| | - Chao Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - He Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Elize Haasdijk
- Department of Neuroscience, Erasmus MC, 3015 GE Rotterdam, Netherlands
- Netherlands Institute for Neuroscience, Royal Academy of Arts and Sciences, 1105 BA Amsterdam, Netherlands
| | - Zihan Wu
- Tencent AI Lab, Shenzhen 518057, China
| | - Shenglong Li
- BGI Research, Hangzhou 310030, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Haotian Yan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lijing Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | | | - Zefang Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aojun Ye
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Luman Cui
- BGI Research, Shenzhen 518083, China
| | - Xing Tan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | | | - Mingli Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- Lingang Laboratory, Shanghai 200031, China
| | - Jing Chen
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Yanqing Zhong
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wensi Du
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Guangling Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Tingting Lai
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Mengdi Cao
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Yuanfang Xu
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ling Li
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Qian Yu
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | | | - Ying Xia
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ying Lei
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yingjie An
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mengnan Cheng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yun Zhao
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lei Han
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yue Yuan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xinxiang Song
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yumo Song
- BGI Research, Shenzhen 518083, China
| | - Liqin Gu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Chang Liu
- BGI Research, Shenzhen 518083, China
| | | | - Ruiqi Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | | | - Yang Wang
- BGI Research, Shenzhen 518083, China
| | - Shenyu Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Huanhuan Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jingjing Song
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mengni Chen
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wanqiu Zhou
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Nini Yuan
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Suhong Sun
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shiwen Wang
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu Chen
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mingyuan Zheng
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jiao Fang
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ruiyi Zhang
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shuzhen Zhang
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qinwen Chai
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jiabing Liu
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wu Wei
- Lingang Laboratory, Shanghai 200031, China
| | - Jie He
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haibo Zhou
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangang Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanyu Liu
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China
| | | | - Zhifeng Liang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xun Xu
- BGI Research, Hangzhou 310030, China
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China
| | - Muming Poo
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China
| | - Chengyu Li
- Lingang Laboratory, Shanghai 200031, China
| | - Chris I De Zeeuw
- Department of Neuroscience, Erasmus MC, 3015 GE Rotterdam, Netherlands
- Netherlands Institute for Neuroscience, Royal Academy of Arts and Sciences, 1105 BA Amsterdam, Netherlands
| | - Zhiming Shen
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China
| | - Zhiyong Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longqi Liu
- BGI Research, Hangzhou 310030, China
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China
| | - Shiping Liu
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cirong Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, 200031, China
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