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Construction of a human cell landscape at single-cell level

Author

Listed:
  • Xiaoping Han

    (Zhejiang University School of Medicine
    Zhejiang University School of Medicine)

  • Ziming Zhou

    (Zhejiang University School of Medicine)

  • Lijiang Fei

    (Zhejiang University School of Medicine)

  • Huiyu Sun

    (Zhejiang University School of Medicine)

  • Renying Wang

    (Zhejiang University School of Medicine)

  • Yao Chen

    (Zhejiang University School of Medicine)

  • Haide Chen

    (Zhejiang University School of Medicine
    Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine)

  • Jingjing Wang

    (Zhejiang University School of Medicine
    Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine)

  • Huanna Tang

    (Zhejiang University School of Medicine)

  • Wenhao Ge

    (Zhejiang University School of Medicine)

  • Yincong Zhou

    (Zhejiang University)

  • Fang Ye

    (Zhejiang University School of Medicine)

  • Mengmeng Jiang

    (Zhejiang University School of Medicine)

  • Junqing Wu

    (Zhejiang University School of Medicine)

  • Yanyu Xiao

    (Zhejiang University School of Medicine)

  • Xiaoning Jia

    (Zhejiang University School of Medicine)

  • Tingyue Zhang

    (Zhejiang University School of Medicine)

  • Xiaojie Ma

    (Zhejiang University)

  • Qi Zhang

    (Zhejiang University School of Medicine)

  • Xueli Bai

    (Zhejiang University School of Medicine)

  • Shujing Lai

    (Zhejiang University School of Medicine)

  • Chengxuan Yu

    (Zhejiang University School of Medicine)

  • Lijun Zhu

    (Zhejiang University School of Medicine)

  • Rui Lin

    (Hangzhou Repugene Technology)

  • Yuchi Gao

    (Annoroad Gene Technology)

  • Min Wang

    (Veritas Genetics Asia)

  • Yiqing Wu

    (Zhejiang University School of Medicine)

  • Jianming Zhang

    (Zhejiang University School of Medicine)

  • Renya Zhan

    (Zhejiang University School of Medicine)

  • Saiyong Zhu

    (Zhejiang University)

  • Hailan Hu

    (Zhejiang University School of Medicine)

  • Changchun Wang

    (Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital)

  • Ming Chen

    (Zhejiang University)

  • He Huang

    (Zhejiang University School of Medicine
    Zhejiang University
    Zhejiang University)

  • Tingbo Liang

    (Zhejiang University School of Medicine)

  • Jianghua Chen

    (Zhejiang University School of Medicine)

  • Weilin Wang

    (Zhejiang University School of Medicine)

  • Dan Zhang

    (Zhejiang University School of Medicine)

  • Guoji Guo

    (Zhejiang University School of Medicine
    Zhejiang University School of Medicine
    Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine
    Zhejiang University)

Abstract

Single-cell analysis is a valuable tool for dissecting cellular heterogeneity in complex systems1. However, a comprehensive single-cell atlas has not been achieved for humans. Here we use single-cell mRNA sequencing to determine the cell-type composition of all major human organs and construct a scheme for the human cell landscape (HCL). We have uncovered a single-cell hierarchy for many tissues that have not been well characterized. We established a ‘single-cell HCL analysis’ pipeline that helps to define human cell identity. Finally, we performed a single-cell comparative analysis of landscapes from human and mouse to identify conserved genetic networks. We found that stem and progenitor cells exhibit strong transcriptomic stochasticity, whereas differentiated cells are more distinct. Our results provide a useful resource for the study of human biology.

Suggested Citation

  • Xiaoping Han & Ziming Zhou & Lijiang Fei & Huiyu Sun & Renying Wang & Yao Chen & Haide Chen & Jingjing Wang & Huanna Tang & Wenhao Ge & Yincong Zhou & Fang Ye & Mengmeng Jiang & Junqing Wu & Yanyu Xia, 2020. "Construction of a human cell landscape at single-cell level," Nature, Nature, vol. 581(7808), pages 303-309, May.
    • Handle: RePEc:nat:nature:v:581:y:2020:i:7808:d:10.1038_s41586-020-2157-4
    DOI: 10.1038/s41586-020-2157-4
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    Citations

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    Cited by:

    1. Han Luo & Xuyang Xia & Li-Bin Huang & Hyunsu An & Minyuan Cao & Gyeong Dae Kim & Hai-Ning Chen & Wei-Han Zhang & Yang Shu & Xiangyu Kong & Zhixiang Ren & Pei-Heng Li & Yang Liu & Huairong Tang & Rongh, 2022. "Pan-cancer single-cell analysis reveals the heterogeneity and plasticity of cancer-associated fibroblasts in the tumor microenvironment," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Jingyang Qian & Hudong Bao & Xin Shao & Yin Fang & Jie Liao & Zhuo Chen & Chengyu Li & Wenbo Guo & Yining Hu & Anyao Li & Yue Yao & Xiaohui Fan & Yiyu Cheng, 2024. "Simulating multiple variability in spatially resolved transcriptomics with scCube," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    3. Jiao Qu & Fa Yang & Tao Zhu & Yingshuo Wang & Wen Fang & Yan Ding & Xue Zhao & Xianjia Qi & Qiangmin Xie & Ming Chen & Qiang Xu & Yicheng Xie & Yang Sun & Dijun Chen, 2022. "A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    4. Mírian Romitti & Adrien Tourneur & Barbara Faria da Fonseca & Gilles Doumont & Pierre Gillotay & Xiao-Hui Liao & Sema Elif Eski & Gaetan Simaeys & Laura Chomette & Helene Lasolle & Olivier Monestier &, 2022. "Transplantable human thyroid organoids generated from embryonic stem cells to rescue hypothyroidism," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    5. Yanyu Xiao & Jingjing Wang & Jiaqi Li & Peijing Zhang & Jingyu Li & Yincong Zhou & Qing Zhou & Ming Chen & Xin Sheng & Zhihong Liu & Xiaoping Han & Guoji Guo, 2023. "An analytical framework for decoding cell type-specific genetic variation of gene regulation," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    6. Ziye Xu & Tianyu Zhang & Hongyu Chen & Yuyi Zhu & Yuexiao Lv & Shunji Zhang & Jiaye Chen & Haide Chen & Lili Yang & Weiqin Jiang & Shengyu Ni & Fangru Lu & Zhaolun Wang & Hao Yang & Ling Dong & Feng C, 2023. "High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    7. Fang Ye & Guodong Zhang & Weigao E. & Haide Chen & Chengxuan Yu & Lei Yang & Yuting Fu & Jiaqi Li & Sulei Fu & Zhongyi Sun & Lijiang Fei & Qile Guo & Jingjing Wang & Yanyu Xiao & Xinru Wang & Peijing , 2022. "Construction of the axolotl cell landscape using combinatorial hybridization sequencing at single-cell resolution," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    8. Yuan Liao & Lifeng Ma & Qile Guo & Weigao E & Xing Fang & Lei Yang & Fanwei Ruan & Jingjing Wang & Peijing Zhang & Zhongyi Sun & Haide Chen & Zhongliang Lin & Xueyi Wang & Xinru Wang & Huiyu Sun & Xiu, 2022. "Cell landscape of larval and adult Xenopus laevis at single-cell resolution," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    9. Joyce B. Kang & Aparna Nathan & Kathryn Weinand & Fan Zhang & Nghia Millard & Laurie Rumker & D. Branch Moody & Ilya Korsunsky & Soumya Raychaudhuri, 2021. "Efficient and precise single-cell reference atlas mapping with Symphony," Nature Communications, Nature, vol. 12(1), pages 1-21, December.
    10. Ajita Shree & Musale Krushna Pavan & Hamim Zafar, 2023. "scDREAMER for atlas-level integration of single-cell datasets using deep generative model paired with adversarial classifier," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    11. Silvia Tiberti & Carlotta Catozzi & Ottavio Croci & Mattia Ballerini & Danilo Cagnina & Chiara Soriani & Caterina Scirgolea & Zheng Gong & Jiatai He & Angeli D. Macandog & Amir Nabinejad & Carina B. N, 2022. "GZMKhigh CD8+ T effector memory cells are associated with CD15high neutrophil abundance in non-metastatic colorectal tumors and predict poor clinical outcome," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    12. Jing Qi & Yang Zhou & Jiao Hua & Liying Zhang & Jialin Bian & Beibei Liu & Zicen Zhao & Shuilin Jin, 2021. "The scRNA-seq Expression Profiling of the Receptor ACE2 and the Cellular Protease TMPRSS2 Reveals Human Organs Susceptible to SARS-CoV-2 Infection," IJERPH, MDPI, vol. 18(1), pages 1-17, January.
    13. Fei Wang & Peiwen Ding & Xue Liang & Xiangning Ding & Camilla Blunk Brandt & Evelina Sjöstedt & Jiacheng Zhu & Saga Bolund & Lijing Zhang & Laura P. M. H. Rooij & Lihua Luo & Yanan Wei & Wandong Zhao , 2022. "Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    14. Md Tauhidul Islam & Jen-Yeu Wang & Hongyi Ren & Xiaomeng Li & Masoud Badiei Khuzani & Shengtian Sang & Lequan Yu & Liyue Shen & Wei Zhao & Lei Xing, 2022. "Leveraging data-driven self-consistency for high-fidelity gene expression recovery," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    15. Xin Li & Bairu Li & Shaobin Gu & Xinyue Pang & Patrick Mason & Jiangfeng Yuan & Jingyu Jia & Jiaju Sun & Chunyan Zhao & Robert Henry, 2024. "Single-cell and spatial RNA sequencing reveal the spatiotemporal trajectories of fruit senescence," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    16. Dongsheng Chen & Jian Sun & Jiacheng Zhu & Xiangning Ding & Tianming Lan & Xiran Wang & Weiying Wu & Zhihua Ou & Linnan Zhu & Peiwen Ding & Haoyu Wang & Lihua Luo & Rong Xiang & Xiaoling Wang & Jiayin, 2021. "Single cell atlas for 11 non-model mammals, reptiles and birds," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    17. Xiaoyu Song & Jiayi Ji & Joseph H. Rothstein & Stacey E. Alexeeff & Lori C. Sakoda & Adriana Sistig & Ninah Achacoso & Eric Jorgenson & Alice S. Whittemore & Robert J. Klein & Laurel A. Habel & Pei Wa, 2023. "MiXcan: a framework for cell-type-aware transcriptome-wide association studies with an application to breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    18. Allen W. Lynch & Myles Brown & Clifford A. Meyer, 2023. "Multi-batch single-cell comparative atlas construction by deep learning disentanglement," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    19. Lei Xiong & Kang Tian & Yuzhe Li & Weixi Ning & Xin Gao & Qiangfeng Cliff Zhang, 2022. "Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space," Nature Communications, Nature, vol. 13(1), pages 1-17, December.

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