Article | Published:

Tracing haematopoietic stem cell formation at single-cell resolution

Nature volume 533, pages 487492 (26 May 2016) | Download Citation

Abstract

Haematopoietic stem cells (HSCs) are derived early from embryonic precursors, such as haemogenic endothelial cells and pre-haematopoietic stem cells (pre-HSCs), the molecular identity of which still remains elusive. Here we use potent surface markers to capture the nascent pre-HSCs at high purity, as rigorously validated by single-cell-initiated serial transplantation. Then we apply single-cell RNA sequencing to analyse endothelial cells, CD45 and CD45+ pre-HSCs in the aorta–gonad–mesonephros region, and HSCs in fetal liver. Pre-HSCs show unique features in transcriptional machinery, arterial signature, metabolism state, signalling pathway, and transcription factor network. Functionally, activation of mechanistic targets of rapamycin (mTOR) is shown to be indispensable for the emergence of HSCs but not haematopoietic progenitors. Transcriptome data-based functional analysis reveals remarkable heterogeneity in cell-cycle status of pre-HSCs. Finally, the core molecular signature of pre-HSCs is identified. Collectively, our work paves the way for dissection of complex molecular mechanisms regulating stepwise generation of HSCs in vivo, informing future efforts to engineer HSCs for clinical applications.

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Primary accessions

Gene Expression Omnibus

Data deposits

All of the single-cell and ten-cell RNA-seq data have been deposited in Gene Expression Omnibus under accession numbers GSE67120 and GSE66954.

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Acknowledgements

We thank H. Wu, J. Zheng, and H. Guo for discussion, and S. Hou and L. Zhang for technique support. This work was supported by the Chinese National Key Program on Basic Research (2011CB964800, 2012CB966904, 2012CB966704, 2012CB966604), the National Natural Science Foundation of China (31425012, 31371185, 81400076, 31322037, 81561138005, 81421002, 81561138003, 81370596, 91439128), National Key Program on Stem Cell and Translational Research (SQ2016ZY05002341), and a SKLEH-Pilot Research Grant (ZK12-04 and ZK13-04).

Author information

Author notes

    • Fan Zhou
    • , Xianlong Li
    • , Weili Wang
    • , Ping Zhu
    • , Jie Zhou
    •  & Wenyan He

    These authors contributed equally to this work.

Affiliations

  1. State Key Laboratory of Proteomics, Translational Medicine Center of Stem Cells, 307-Ivy Translational Medicine Center, Laboratory of Oncology, Affiliated Hospital, Academy of Military Medical Sciences, Beijing 100071, China.

    • Fan Zhou
    • , Jie Zhou
    • , Wenyan He
    • , Meng Ding
    • , Fuyin Xiong
    • , Xiaona Zheng
    • , Zhuan Li
    • , Yanli Ni
    •  & Bing Liu
  2. Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China

    • Xianlong Li
    • , Ping Zhu
    • , Lu Wen
    •  & Fuchou Tang
  3. State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences, Tianjin 300020, China

    • Weili Wang
    • , Xiaohuan Mu
    • , Tao Cheng
    • , Weiping Yuan
    •  & Bing Liu
  4. Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China

    • Ping Zhu
    •  & Fuchou Tang
  5. Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China

    • Lu Wen
    •  & Fuchou Tang
  6. Collaborative Innovation Center for Cancer Medicine, National Institute of Biological Sciences, Tianjin 300020, China

    • Tao Cheng
  7. State Key Laboratory of Proteomics, Genetic Laboratory of Development and Diseases, Institute of Biotechnology, Beijing 100071, China

    • Yu Lan
  8. Center for Molecular and Translational Medicine (CMTM), Beijing 100101, China

    • Fuchou Tang
  9. Institute of Hematology, Medical College of Jinan University, Guangzhou 510632, China

    • Bing Liu

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Contributions

B.L., F.T., and W.Y. designed the study. F.Z. performed the pre-HSC-related experiments with help from Z.L. and X.Z.; W.W. and W.H. performed the HSC transplantation and HPC assay of Rictor mutant embryos with help from X.M.; Y.N. performed the flow cytometry with help from F.Z.; X.L. performed the single-cell RNA-sequencing; and P.Z. and J.Z. performed the bioinformatics analysis with help from F.X., M.D., and L.W. B.L., F.T., W.Y., and Y.L. wrote the manuscript with support from T.C.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Weiping Yuan or Fuchou Tang or Bing Liu.

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DOI

https://doi.org/10.1038/nature17997

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