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Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients
Xianwen Ren; Wen Wen; Xiaoying Fan; Wenhong Hou; Bin Su; Pengfei Cai; Jiesheng Li; Fei Tang; Fan Zhang; Yu Yang; Jiangping He; Wenji Ma; Jingjing He; Pingping Wang; Qiqi Cao; Fangjin Chen; Yuqing Chen; Xuelian Cheng; Guohong Deng; Wenyu Ding; Yingmei Feng; Rui Gan; Chuang Guo; Shuai He; Chen Jiang; Juanran Liang; Yi-Min Li; Jun Lin; Yun Ling; Haofei Liu; Jianwei Liu; Nianping Liu; Yang Liu; Meng Luo; Qiang Ma; Qibing Song; Wujianan Sun; Gaoxiang Wang; Feng Wang; Ying Wang; Xiaofeng Wen; Qian Wu; Xiaowei Xie; Xinxin Xiong; Xudong Xing; Hao Xu; Chonghai Yin; Dongdong Yu; Kezhuo Yu; Biao Zhang; Tong Zhang; Jincun Zhao; Peidong Zhao; Jianfeng Zhou; Wei Zhou; Sujuan Zhong; Xiaosong Zhong; Shuye Zhang; Lin Zhu; Ping Zhu; Bing Zou; Jiahua Zou; Zengtao Zuo; Fan Bai; Xi Huang; Xiuwu Bian; Penghui Zhou; Qinghua Jiang; Zhiwei Huang; Jin-Xin Bei; Lai Wei; Xindong Liu; Tao Cheng; Xiangpan Li; Fu-Sheng Wang; Hongyang Wang; Bing Su; Kun Qu; Xiaoqun Wang; JieKai Chen; Ronghua Jin; Zemin Zhang.
Affiliation
  • Xianwen Ren; BIOPIC, Peking University
  • Wen Wen; National Center for Liver Cancer Second Military Medical University, Shanghai, China
  • Xiaoying Fan; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China
  • Wenhong Hou; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
  • Bin Su; Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
  • Pengfei Cai; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
  • Jiesheng Li; Beijing Advanced Innovation Center for Genomics (ICG), BIOPIC and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interd
  • Fei Tang; Beijing Advanced Innovation Center for Genomics (ICG), BIOPIC and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interd
  • Fan Zhang; Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China
  • Yu Yang; Beijing Advanced Innovation Center for Genomics (ICG), BIOPIC and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interd
  • Jiangping He; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China
  • Wenji Ma; State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Tec
  • Jingjing He; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, C
  • Pingping Wang; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, China
  • Qiqi Cao; National Center for Liver Cancer Second Military Medical University, Shanghai, China
  • Fangjin Chen; Center for Quantitative Biology, Peking University, Beijing, 100871, China
  • Yuqing Chen; Beijing Advanced Innovation Center for Genomics (ICG), BIOPIC and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interd
  • Xuelian Cheng; State Key Laboratory of Experimental Hematology and National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, C
  • Guohong Deng; Department of Infectious Diseases, Southwest Hospital, Army Medical University, Chongqing, 400038, China
  • Wenyu Ding; State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Tec
  • Yingmei Feng; Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
  • Rui Gan; Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China
  • Chuang Guo; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
  • Shuai He; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, C
  • Chen Jiang; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
  • Juanran Liang; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
  • Yi-Min Li; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff
  • Jun Lin; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
  • Yun Ling; Department of Infectious Disease, Shanghai Public Health Clinical Center, Shanghai, 201052, China
  • Haofei Liu; State Key Laboratory of Experimental Hematology and National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, C
  • Jianwei Liu; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China
  • Nianping Liu; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
  • Yang Liu; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, C
  • Meng Luo; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, China
  • Qiang Ma; State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Tec
  • Qibing Song; Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
  • Wujianan Sun; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
  • Gaoxiang Wang; Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
  • Feng Wang; Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
  • Ying Wang; Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
  • Xiaofeng Wen; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
  • Qian Wu; State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
  • Xiaowei Xie; State Key Laboratory of Experimental Hematology and National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, C
  • Xinxin Xiong; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, C
  • Xudong Xing; Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, Chi
  • Hao Xu; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
  • Chonghai Yin; State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Tec
  • Dongdong Yu; Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
  • Kezhuo Yu; Beijing Advanced Innovation Center for Genomics (ICG), BIOPIC and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interd
  • Biao Zhang; State Key Laboratory of Experimental Hematology and National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, C
  • Tong Zhang; Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
  • Jincun Zhao; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff
  • Peidong Zhao; Analytical Biosciences Beijing Limited, Beijing, China
  • Jianfeng Zhou; Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
  • Wei Zhou; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China
  • Sujuan Zhong; State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
  • Xiaosong Zhong; Beijing Shijitan Hospital, Capital Medical University, Beijing, China
  • Shuye Zhang; Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai 201508, China
  • Lin Zhu; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
  • Ping Zhu; State Key Laboratory of Experimental Hematology and National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, C
  • Bing Zou; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
  • Jiahua Zou; Cancer Center, Huanggang Hospital of Traditional Chinese Medicine, Huanggang, 438000, China
  • Zengtao Zuo; State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Tec
  • Fan Bai; Beijing Advanced Innovation Center for Genomics (ICG), BIOPIC and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interd
  • Xi Huang; Center for Infection and Immunity, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
  • Xiuwu Bian; Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing 400038, P. R. China
  • Penghui Zhou; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, C
  • Qinghua Jiang; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, China
  • Zhiwei Huang; Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China
  • Jin-Xin Bei; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, C
  • Lai Wei; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
  • Xindong Liu; Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University, Chongqing 400038, P. R. China
  • Tao Cheng; State Key Laboratory of Experimental Hematology and National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, C
  • Xiangpan Li; Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
  • Fu-Sheng Wang; Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, Chi
  • Hongyang Wang; National Center for Liver Cancer Second Military Medical University, Shanghai, China
  • Bing Su; Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
  • Kun Qu; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
  • Xiaoqun Wang; State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Tec
  • JieKai Chen; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
  • Ronghua Jin; Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
  • Zemin Zhang; Beijing Advanced Innovation Center for Genomics (ICG), BIOPIC and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interd
Preprint in En | PREPRINT-BIORXIV | ID: ppbiorxiv-360479
ABSTRACT
Dysfunctional immune response in the COVID-19 patients is a recurrent theme impacting symptoms and mortality, yet the detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 205 COVID-19 patients and controls to create a comprehensive immune landscape. Lymphopenia and active T and B cell responses were found to coexist and associated with age, sex and their interactions with COVID-19. Diverse epithelial and immune cell types were observed to be virus-positive and showed dramatic transcriptomic changes. Elevation of ANXA1 and S100A9 in virus-positive squamous epithelial cells may enable the initiation of neutrophil and macrophage responses via the ANXA1-FPR1 and S100A8/9-TLR4 axes. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis and designing effective therapeutic strategies for COVID-19. HIGHLIGHTSO_LILarge-scale scRNA-seq analysis depicts the immune landscape of COVID-19 C_LIO_LILymphopenia and active T and B cell responses coexist and are shaped by age and sex C_LIO_LISARS-CoV-2 infects diverse epithelial and immune cells, inducing distinct responses C_LIO_LICytokine storms with systemic S100A8/A9 are associated with COVID-19 severity C_LI
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Full text: 1 Collection: 09-preprints Database: PREPRINT-BIORXIV Type of study: Prognostic_studies Language: En Year: 2020 Document type: Preprint
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Full text: 1 Collection: 09-preprints Database: PREPRINT-BIORXIV Type of study: Prognostic_studies Language: En Year: 2020 Document type: Preprint