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The trans-omics landscape of COVID-19

Author

Listed:
  • Peng Wu

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology
    Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Dongsheng Chen

    (BGI-Shenzhen)

  • Wencheng Ding

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology
    Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Ping Wu

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology
    Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Hongyan Hou

    (Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Yong Bai

    (BGI-Shenzhen)

  • Yuwen Zhou

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Kezhen Li

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology
    Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Shunian Xiang

    (BGI-Shenzhen)

  • Panhong Liu

    (BGI-Shenzhen)

  • Jia Ju

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Ensong Guo

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology
    Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Jia Liu

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology
    Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Bin Yang

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology
    Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Junpeng Fan

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology)

  • Liang He

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology)

  • Ziyong Sun

    (Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Ling Feng

    (Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology)

  • Jian Wang

    (Union Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Tangchun Wu

    (Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology)

  • Hao Wang

    (Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology)

  • Jin Cheng

    (Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang)

  • Hui Xing

    (Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang)

  • Yifan Meng

    (State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center)

  • Yongsheng Li

    (Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University)

  • Yuanliang Zhang

    (BGI-Shenzhen)

  • Hongbo Luo

    (BGI-Shenzhen
    BGI-Guizhou, BGI-Shenzhen)

  • Gang Xie

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Xianmei Lan

    (BGI-Shenzhen)

  • Ye Tao

    (BGI-Shenzhen)

  • Jiafeng Li

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Hao Yuan

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Kang Huang

    (BGI-Shenzhen)

  • Wan Sun

    (BGI-Shenzhen)

  • Xiaobo Qian

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Zhichao Li

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Mingxi Huang

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Peiwen Ding

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Haoyu Wang

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Jiaying Qiu

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Feiyue Wang

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Shiyou Wang

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Jiacheng Zhu

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Xiangning Ding

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Chaochao Chai

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Langchao Liang

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Xiaoling Wang

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Lihua Luo

    (BGI-Shenzhen
    BGI Education Center, University of Chinese Academy of Sciences)

  • Yuzhe Sun

    (BGI-Shenzhen)

  • Ying Yang

    (BGI-Shenzhen)

  • Zhenkun Zhuang

    (BGI-Shenzhen
    School of Biology and Biological Engineering, South China University of Technology)

  • Tao Li

    (BGI-Shenzhen)

  • Lei Tian

    (BGI-Shenzhen)

  • Shaoqiao Zhang

    (BGI-Hubei, BGI-Shenzhen)

  • Linnan Zhu

    (BGI-Shenzhen)

  • Ashley Chang

    (BGI-Shenzhen)

  • Lei Chen

    (College of Veterinary Medicine, Yangzhou University)

  • Yiquan Wu

    (HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health)

  • Xiaoyan Ma

    (University of Cambridge)

  • Fang Chen

    (BGI-Shenzhen)

  • Yan Ren

    (BGI-Shenzhen)

  • Xun Xu

    (BGI-Shenzhen
    Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen)

  • Siqi Liu

    (BGI-Shenzhen)

  • Jian Wang

    (BGI-Shenzhen
    James D. Watson Institute of Genome Science)

  • Huanming Yang

    (BGI-Shenzhen
    James D. Watson Institute of Genome Science)

  • Lin Wang

    (Union Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Chaoyang Sun

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology
    Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Ding Ma

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology
    Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

  • Xin Jin

    (BGI-Shenzhen
    School of Medicine, South China University of Technology, Guangzhou
    Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen)

  • Gang Chen

    (Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology
    Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology)

Abstract

The outbreak of coronavirus disease 2019 (COVID-19) is a global health emergency. Various omics results have been reported for COVID-19, but the molecular hallmarks of COVID-19, especially in those patients without comorbidities, have not been fully investigated. Here we collect blood samples from 231 COVID-19 patients, prefiltered to exclude those with selected comorbidities, yet with symptoms ranging from asymptomatic to critically ill. Using integrative analysis of genomic, transcriptomic, proteomic, metabolomic and lipidomic profiles, we report a trans-omics landscape for COVID-19. Our analyses find neutrophils heterogeneity between asymptomatic and critically ill patients. Meanwhile, neutrophils over-activation, arginine depletion and tryptophan metabolites accumulation correlate with T cell dysfunction in critical patients. Our multi-omics data and characterization of peripheral blood from COVID-19 patients may thus help provide clues regarding pathophysiology of and potential therapeutic strategies for COVID-19.

Suggested Citation

  • Peng Wu & Dongsheng Chen & Wencheng Ding & Ping Wu & Hongyan Hou & Yong Bai & Yuwen Zhou & Kezhen Li & Shunian Xiang & Panhong Liu & Jia Ju & Ensong Guo & Jia Liu & Bin Yang & Junpeng Fan & Liang He &, 2021. "The trans-omics landscape of COVID-19," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-24482-1
    DOI: 10.1038/s41467-021-24482-1
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    Citations

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    Cited by:

    1. Yafeng Li & Jessica S. Hook & Qing Ding & Xue Xiao & Stephen S. Chung & Marcel Mettlen & Lin Xu & Jessica G. Moreland & Michalis Agathocleous, 2023. "Neutrophil metabolomics in severe COVID-19 reveal GAPDH as a suppressor of neutrophil extracellular trap formation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Samuel Druzak & Elizabeth Iffrig & Blaine R. Roberts & Tiantian Zhang & Kirby S. Fibben & Yumiko Sakurai & Hans P. Verkerke & Christina A. Rostad & Ann Chahroudi & Frank Schneider & Andrew Kam Ho Wong, 2023. "Multiplatform analyses reveal distinct drivers of systemic pathogenesis in adult versus pediatric severe acute COVID-19," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    3. Zhiqiang Pang & Lei Xu & Charles Viau & Yao Lu & Reza Salavati & Niladri Basu & Jianguo Xia, 2024. "MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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