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03 04, 2021;28 (3): 472-487.e7.

Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis.

Anna Maria Ranzoni, Andrea Tangherloni, Ivan Berest, Simone Giovanni Riva, Brynelle Myers, Paulina M Strzelecka, Jiarui Xu, Elisa Panada, Irina Mohorianu, Judith B Zaugg, Ana Cvejic
Author Information
  1. Anna Maria Ranzoni: University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
  2. Andrea Tangherloni: University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
  3. Ivan Berest: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69115 Heidelberg, Germany.
  4. Simone Giovanni Riva: University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
  5. Brynelle Myers: Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
  6. Paulina M Strzelecka: University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
  7. Jiarui Xu: University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
  8. Elisa Panada: Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
  9. Irina Mohorianu: Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK.
  10. Judith B Zaugg: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69115 Heidelberg, Germany.
  11. Ana Cvejic: University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. Electronic address: as889@cam.ac.uk.
PMID: 33352111 DOI: 10.1016/j.stem.2020.11.015

Abstract

Regulation of hematopoiesis during human development remains poorly defined. Here we applied single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to over 8,000 human immunophenotypic blood cells from fetal liver and bone marrow. We inferred their differentiation trajectory and identified three highly proliferative oligopotent progenitor populations downstream of hematopoietic stem cells (HSCs)/multipotent progenitors (MPPs). Along this trajectory, we observed opposing patterns of chromatin accessibility and differentiation that coincided with dynamic changes in the activity of distinct lineage-specific transcription factors. Integrative analysis of chromatin accessibility and gene expression revealed extensive epigenetic but not transcriptional priming of HSCs/MPPs prior to their lineage commitment. Finally, we refined and functionally validated the sorting strategy for the HSCs/MPPs and achieved around 90% enrichment. Our study provides a useful framework for future investigation of human developmental hematopoiesis in the context of blood pathologies and regenerative medicine.

Keywords

bone marrow fetal hematopoiesis fetal liver hematopoietic stem cells scATAC-seq scRNA-seq

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Grants

  1. MC_PC_17230/Medical Research Council
  2. 677501/European Research Council
  3. MR/M008975/1/Medical Research Council
  4. 203151/Wellcome Trust
  5. MC_PC_12009/Medical Research Council
  6. MR/R006237/1/Medical Research Council

MeSH Term

Cell Lineage
Chromatin Immunoprecipitation Sequencing
Hematopoiesis
Hematopoietic Stem Cells
Humans
RNA-Seq
Single-Cell Analysis
Journal Article Research Support, Non-U.S. Gov't

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