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Han L, Wei X, Liu C, Volpe G, Zhuang Z, Zou X, Wang Z, Pan T, Yuan Y, Zhang X, Fan P, Guo P, Lai Y, Lei Y, Liu X, Yu F, Shangguan S, Lai G, Deng Q, Liu Y, Wu L, Shi Q, Yu H, Huang Y, Cheng M, Xu J, Liu Y, Wang M, Wang C, Zhang Y, Xie D, Yang Y, Yu Y, Zheng H, Wei Y, Huang F, Lei J, Huang W, Zhu Z, Lu H, Wang B, Wei X, Chen F, Yang T, Du W, Chen J, Xu S, An J, Ward C, Wang Z, Pei Z, Wong CW, Liu X, Zhang H, Liu M, Qin B, Schambach A, Isern J, Feng L, Liu Y, Guo X, Liu Z, Sun Q, Maxwell PH, Barker N, Muñoz-Cánoves P, Gu Y, Mulder J, Uhlen M, Tan T, Liu S, Yang H, Wang J, Hou Y, Xu X, Esteban MA, Liu L. Cell transcriptomic atlas of the non-human primate Macaca fascicularis. Nature 2022; 604:723-731. [PMID: 35418686 DOI: 10.1038/s41586-022-04587-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 02/23/2022] [Indexed: 12/22/2022]
Abstract
Studying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell-cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs.
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Affiliation(s)
- Lei Han
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Xiaoyu Wei
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chuanyu Liu
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Giacomo Volpe
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Zhenkun Zhuang
- BGI-Shenzhen, Shenzhen, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xuanxuan Zou
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhifeng Wang
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China
| | - Taotao Pan
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China
| | - Yue Yuan
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Zhang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Peng Fan
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Pengcheng Guo
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Lei
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Xingyuan Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Feng Yu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Shuncheng Shangguan
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
| | - Guangyao Lai
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
| | - Qiuting Deng
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ya Liu
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China
| | - Liang Wu
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Quan Shi
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hao Yu
- BGI-Shenzhen, Shenzhen, China
| | - Yunting Huang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Mengnan Cheng
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiangshan Xu
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Chunqing Wang
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanhang Zhang
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Duo Xie
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yunzhi Yang
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yeya Yu
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Huiwen Zheng
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yanrong Wei
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Fubaoqian Huang
- BGI-Shenzhen, Shenzhen, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Junjie Lei
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Waidong Huang
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhiyong Zhu
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Bo Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xiaofeng Wei
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Fengzhen Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Tao Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Wensi Du
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jing Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Shibo Xu
- Institute for Stem Cells and Neural Regeneration, School of Pharmacy, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Juan An
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Science and Technology of China, Hefei, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zongren Wang
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhong Pei
- Department of Neurology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | - Xiaolei Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Huafeng Zhang
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingyuan Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Baoming Qin
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Division of Hematology/Oncology, Harvard Medical School, MA, Boston, USA
| | - Joan Isern
- Spanish National Center for Cardiovascular Research (CNIC), Madrid, Spain
| | - Liqiang Feng
- State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yan Liu
- Institute for Stem Cells and Neural Regeneration, School of Pharmacy, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xiangyu Guo
- Jinan University, Guangzhou, China.,Hubei Topgene Biotechnology Co., Ltd, Wuhan, China
| | - Zhen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nick Barker
- A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Pura Muñoz-Cánoves
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), ICREA and CIBERNED, Barcelona, Spain
| | - Ying Gu
- BGI-Shenzhen, Shenzhen, China
| | - Jan Mulder
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Mathias Uhlen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Tao Tan
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Shiping Liu
- BGI-Shenzhen, Shenzhen, China.,BGI-Beijing, Beijing, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, China. .,BGI-Beijing, Beijing, China. .,Shenzhen Bay Laboratory, Shenzhen, China. .,BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China. .,BGI-Beijing, Beijing, China. .,BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
| | - Miguel A Esteban
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China. .,Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. .,Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen, China. .,BGI-Beijing, Beijing, China. .,Shenzhen Bay Laboratory, Shenzhen, China. .,BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.
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