Single-cell transcriptomic landscape of nucleated cells in umbilical cord blood

  1. Yi Zhao
  2. Xiao Li
  3. Weihua Zhao
  4. Jingwan Wang
  5. Jiawei Yu
  6. Ziyun Wan
  7. Kai Gao
  8. Gang Yi
  9. Xie Wang
  10. Bingbing Fan
  11. Qinkai Wu
  12. Bangwei Chen
  13. Feng Xie
  14. Jinghua Wu
  15. Wei Zhang
  16. Fang Chen
  17. Huanming Yang
  18. Jian Wang
  19. Xun Xu
  20. Bin Li
  21. Shiping Liu
  22. Yong Hou
  23. Xiao Liu

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Abstract

Background

For both pediatric and adult patients, umbilical cord blood (UCB) transplant is a therapeutic option for a variety of hematologic diseases, such as blood cancers, myeloproliferative disorders, genetic diseases, and metabolic disorders. However, the level of cellular heterogeneity and diversity of nucleated cells in UCB has not yet been assessed in an unbiased and systemic fashion. In the present study, nucleated cells from UCB were subjected to single-cell RNA sequencing to simultaneously profile the gene expression signatures of thousands of cells, generating a rich resource for further functional studies. Here, we report the transcriptomes of 17,637 UCB cells, covering 12 major cell types, many of which can be further divided into distinct subpopulations.

Results

Pseudotemporal ordering of nucleated red blood cells identifies wave-like activation and suppression of transcription regulators, leading to a polarized cellular state, which may reflect nucleated red blood cell maturation. Progenitor cells in UCB also comprise 2 subpopulations with activation of divergent transcription programs, leading to specific cell fate commitment. Detailed profiling of cytotoxic cell populations unveiled granzymes B and K signatures in natural killer and natural killer T-cell types in UCB.

Conclusions

Taken together, our data form a comprehensive single-cell transcriptomic landscape that reveals previously unrecognized cell types, pathways, and mechanisms of gene expression regulation. These data may contribute to the efficacy and outcome of UCB transplant, broadening the scope of research and clinical innovations.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giz047

    Yi Zhao 1BGI-Shenzhen, Shenzhen 518083, China3School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiao Li 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJingwan Wang 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZiyun Wan 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKai Gao 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGang Yi 4Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXie Wang 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJinghua Wu 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBingbing Fan 2Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, Guangdong Province, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWei Zhang 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFang Chen 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuanming Yang 1BGI-Shenzhen, Shenzhen 518083, China5James D. Watson Institute of Genome Sciences, Hangzhou 310058, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJian Wang 1BGI-Shenzhen, Shenzhen 518083, China5James D. Watson Institute of Genome Sciences, Hangzhou 310058, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXun Xu 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBin Li 1BGI-Shenzhen, Shenzhen 518083, China4Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShiping Liu 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWeihua Zhao 2Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, Guangdong Province, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYong Flou 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiao Liu 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz047 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101675 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101676 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101677

  2. Version published to 10.1093/gigascience/giz047
  3. Version published to 10.1101/346106v1 on bioRxiv