Single-cell analyses and machine learning define hematopoietic progenitor and HSC-like cells derived from human PSCs

Blood, vol. 136, pp. 2893–2904

Abstract

Hematopoietic stem and progenitor cells (HSPCs) develop in distinct waves at various anatomical sites during embryonic development. The in vitro differentiation of human pluripotent stem cells (hPSCs) recapitulates some of these processes; however, it has proven difficult to generate functional hematopoietic stem cells (HSCs). To define the dynamics and heterogeneity of HSPCs that can be generated in vitro from hPSCs, we explored single-cell RNA sequencing (scRNAseq) in combination with single-cell protein expression analysis. Bioinformatics analyses and functional validation defined the transcriptomes of naïve progenitors and erythroid-, megakaryocyte-, and leukocyte-committed progenitors, and we identified CD44, CD326, ICAM2/CD9, and CD18, respectively, as markers of these progenitors. Using an artificial neural network that we trained on scRNAseq derived from human fetal liver, we identified a wide range of hPSC-derived HSPCs phenotypes, including a small group classified as HSCs. This transient HSC-like population decreased as differentiation proceeded, and was completely missing in the data set that had been generated using cells selected on the basis of CD43 expression. By comparing the single-cell transcriptome of in vitro-generated HSC-like cells with those generated within the fetal liver, we identified transcription factors and molecular pathways that can be explored in the future to improve the in vitro production of HSCs.

Authors 14

1. Patrick S. Stumpf Aachen Joint Research Center for Computational Biomedicine

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Joint Research Center for Computational Biomedicine, Uniklinik Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen, Aachen, Germany;

2. Prakash Ramachandran

   Centre for Inflammation Research · University of Edinburgh

   Affiliation as printed

   Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom;

3. Sara Tamagno

   MRC Centre for Regenerative Medicine · University of Edinburgh

   Affiliation as printed

   Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom;

4. Ann C. Babtie

   Imperial College London

   Affiliation as printed

   Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, United Kingdom; and

5. Martha Lopez‐Yrigoyen

   MRC Centre for Regenerative Medicine · University of Edinburgh

   Affiliation as printed

   Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom;

6. A. Helen Taylor

   MRC Centre for Regenerative Medicine · University of Edinburgh

   Affiliation as printed

   Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom;

7. Jennifer Easterbrook

   MRC Centre for Regenerative Medicine · University of Edinburgh

   Affiliation as printed

   Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom;

8. Beth E. P. Henderson

   Centre for Inflammation Research · University of Edinburgh

   Affiliation as printed

   Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom;

9. Richard A Axton

   MRC Centre for Regenerative Medicine · University of Edinburgh

   Affiliation as printed

   Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom;

10. Neil Cowan Henderson

    Centre for Inflammation Research · University of Edinburgh

    Affiliation as printed

    Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom;

11. Alexander Medvinsky

    MRC Centre for Regenerative Medicine · University of Edinburgh

    Affiliation as printed

    Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom;

12. Katrin Ottersbach

    MRC Centre for Regenerative Medicine · University of Edinburgh

    Affiliation as printed

    Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom;

13. Nicola Romanò

    University of Edinburgh

    Affiliation as printed

    Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom

14. Lesley M. Forrester

    MRC Centre for Regenerative Medicine · University of Edinburgh

    Affiliation as printed

    Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom;