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The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment

Nature Immunology volume 14, pages 756–763 (2013)Cite this article

Abstract

Understanding how differentiation programs originate from the gene-expression 'landscape' of hematopoietic stem cells (HSCs) is crucial for the development of new clinical therapies. We mapped the transcriptional dynamics underlying the first steps of commitment by tracking transcriptome changes in human HSCs and eight early progenitor populations. We found that transcriptional programs were extensively shared, extended across lineage-potential boundaries and were not strictly lineage affiliated. Elements of stem, lymphoid and myeloid programs were retained in multilymphoid progenitors (MLPs), which reflected a hybrid transcriptional state. By functional single cell analysis, we found that the transcription factors Bcl-11A, Sox4 and TEAD1 (TEF1) governed transcriptional networks in MLPs, which led to B cell specification. Overall, we found that integrated transcriptome approaches can be used to identify previously unknown regulators of multipotency and show additional complexity in lymphoid commitment.

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Figure 1: Transcriptional 'architecture' of the first steps of the human hematopoietic hierarchy.
Figure 2: Six predominant transcriptional programs are associated with commitment of human HSCs.
Figure 3: Complexity of the expression of transcription factors during commitment.
Figure 4: Single-cell shRNA-based silencing screen for transcription factors that determine commitment of MLPs to the lymphoid fate.
Figure 5: Effects of the silencing of BCL11A, BCL6, SOX4 or TEAD1 on B cell commitment in vivo.
Figure 6: Silencing of BCL11A, SOX4 or TEAD1 mediated by shRNA does not affect the proliferation or apoptosis of B cell progenitors but results in lower expression of master regulators of B cell commitment.

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References

  1. Orkin, S.H. & Zon, L.I. Hematopoiesis: an evolving paradigm for stem cell biology. Cell 132, 631–644 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Enver, T., Pera, M., Peterson, C. & Andrews, P.W. Stem cell states, fates, and the rules of attraction. Cell Stem Cell 4, 387–397 (2009).

    CAS  PubMed  Google Scholar 

  3. Zandi, S., Bryder, D. & Sigvardsson, M. Load and lock: the molecular mechanisms of B-lymphocyte commitment. Immunol. Rev. 238, 47–62 (2010).

    CAS  PubMed  Google Scholar 

  4. Nutt, S.L. & Kee, B.L. The transcriptional regulation of B cell lineage commitment. Immunity 26, 715–725 (2007).

    CAS  PubMed  Google Scholar 

  5. Georgopoulos, K. Haematopoietic cell-fate decisions, chromatin regulation and ikaros. Nat. Rev. Immunol. 2, 162–174 (2002).

    CAS  PubMed  Google Scholar 

  6. Ji, H. et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 467, 338–342 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Novershtern, N. et al. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144, 296–309 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Chambers, S.M. et al. Hematopoietic fingerprints: an expression database of stem cells and their progeny. Cell Stem Cell 1, 578–591 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Månsson, R. et al. Molecular Evidence for hierarchical transcriptional lineage priming in fetal and adult stem cells and multipotent progenitors. Immunity 26, 407–419 (2007).

    PubMed  Google Scholar 

  10. Ng, S.Y.-M., Yoshida, T., Zhang, J. & Georgopoulos, K. Genome-wide lineage-specific transcriptional networks underscore Ikaros-dependent lymphoid priming in hematopoietic stem cells. Immunity 30, 493–507 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Hu, M. et al. Multilineage gene expression precedes commitment in the hemopoietic system. Genes Dev. 11, 774–785 (1997).

    CAS  PubMed  Google Scholar 

  12. Akashi, K., Traver, D., Miyamoto, T. & Weissman, I.L. A clonogenic common myeloid progenitor that gives rise to all myeloid lineages. Nature 404, 193–197 (2000).

    CAS  PubMed  Google Scholar 

  13. Doulatov, S. et al. Revised map of the human progenitor hierarchy shows the origin of macrophages and dendritic cells in early lymphoid development. Nat. Immunol. 11, 585–593 (2010).

    CAS  PubMed  Google Scholar 

  14. Luc, S. et al. The earliest thymic T cell progenitors sustain B cell and myeloid lineage potential. Nat. Immunol. 13, 412–419 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Goardon, N. et al. Coexistence of LMPP-like and GMP-like leukemia stem cells in acute myeloid leukemia. Cancer Cell 19, 138–152 (2011).

    CAS  PubMed  Google Scholar 

  16. Adolfsson, J. et al. Identification of Flt3+ lympho-myeloid stem cells lacking erythro-megakaryocytic potential a revised road map for adult blood lineage commitment. Cell 121, 295–306 (2005).

    CAS  PubMed  Google Scholar 

  17. Kohn, L.A. et al. Lymphoid priming in human bone marrow begins before expression of CD10 with upregulation of L-selectin. Nat. Immunol. 13, 963–971 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Notta, F. et al. Isolation of single human hematopoietic stem cells capable of long-term multilineage engraftment. Science 333, 218–221 (2011).

    CAS  PubMed  Google Scholar 

  19. Hao, Q.-L. et al. Human intrathymic lineage commitment is marked by differential CD7 expression: identification of CD7− lympho-myeloid thymic progenitors. Blood 111, 1318–1326 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Doulatov, S., Notta, F., Laurenti, E. & Dick, J.E. Hematopoiesis: a human perspective. Cell Stem Cell 10, 120–136 (2012).

    CAS  PubMed  Google Scholar 

  21. Zhang, Q., Iida, R., Shimazu, T. & Kincade, P.W. Replenishing B lymphocytes in health and disease. Curr. Opin. Immunol. 24, 196–203 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Ernst, J., Nau, G.J. & Bar-Joseph, Z. Clustering short time series gene expression data. Bioinformatics 21, i159–i168 (2005).

    CAS  PubMed  Google Scholar 

  23. Ernst, J., Vainas, O., Harbison, C.T., Simon, I. & Bar-Joseph, Z. Reconstructing dynamic regulatory maps. Mol. Syst. Biol. 3 (2007).

  24. Itoh, K. et al. Reproducible establishment of hemopoietic supportive stromal cell lines from murine bone marrow. Exp. Hematol. 17, 145–153 (1989).

    CAS  PubMed  Google Scholar 

  25. Rossi, M.I. et al. Relatively normal human lymphopoiesis but rapid turnover of newly formed B cells in transplanted nonobese diabetic/SCID mice. J. Immunol. 167, 3033–3042 (2001).

    CAS  PubMed  Google Scholar 

  26. Lin, Y.C. et al. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat. Immunol. 11, 635–643 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Kawamoto, H., Ikawa, T., Masuda, K., Wada, H. & Katsura, Y. A map for lineage restriction of progenitors during hematopoiesis: the essence of the myeloid-based model. Immunol. Rev. 238, 23–36 (2010).

    CAS  PubMed  Google Scholar 

  28. Zhang, J.A., Mortazavi, A., Williams, B.A., Wold, B.J. & Rothenberg, E.V. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell 149, 467–482 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Santos, P.M. & Borghesi, L. Molecular resolution of the B cell landscape. Curr. Opin. Immunol. 23, 163–170 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Basso, K. & Dalla-Favera, R. Roles of BCL6 in normal and transformed germinal center B cells. Immunol. Rev. 247, 172–183 (2012).

    PubMed  Google Scholar 

  31. Duy, C. et al. BCL6 is critical for the development of a diverse primary B cell repertoire. J. Exp. Med. 207, 1209–1221 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Schilham, M.W. et al. Defects in cardiac outflow tract formation and pro-B-lymphocyte expansion in mice lacking Sox-4. Nature 380, 711–714 (1996).

    CAS  PubMed  Google Scholar 

  33. Liu, P. et al. Bcl11a is essential for normal lymphoid development. Nat. Immunol. 4, 525–532 (2003).

    CAS  PubMed  Google Scholar 

  34. Yu, Y. et al. Bcl11a is essential for lymphoid development and negatively regulates p53. J. Exp. Med. 209, 2467–2483 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Zhao, B., Tumaneng, K. & Guan, K.-L. The Hippo pathway in organ size control, tissue regeneration and stem cell self-renewal. Nat. Cell Biol. 13, 877–883 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Jansson, L. & Larsson, J. Normal hematopoietic stem cell function in mice with enforced expression of the Hippo signaling effector YAP1. PLoS ONE 7, e32013 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Eppert, K. et al. Stem cell gene expression programs influence clinical outcome in human leukemia. Nat. Med. 17, 1086–1093 (2011).

    CAS  PubMed  Google Scholar 

  38. Zhang, J. et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 481, 157–163 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Fan, J.-B. et al. Highly parallel genome-wide expression analysis of single mammalian cells. PLoS ONE 7, e30794 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. April, C. et al. Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples. PLoS ONE 4, e8162 (2009).

    PubMed  PubMed Central  Google Scholar 

  41. Yeung, K.Y., Haynor, D.R. & Ruzzo, W.L. Validating clustering for gene expression data. Bioinformatics 17, 309–318 (2001).

    CAS  PubMed  Google Scholar 

  42. Kel, A.E. et al. MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 31, 3576–3579 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Chekmenev, D.S., Haid, C. & Kel, A.E. P-Match: transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res. 33, W432–W437 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Ci, W. et al. The BCL6 transcriptional program features repression of multiple oncogenes in primary B cells and is deregulated in DLBCL. Blood 113, 5536–5548 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Basso, K. et al. Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood 115, 975–984 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283–1298 (2006).

    CAS  PubMed  Google Scholar 

  47. Mazurier, F., Gan, O.I., McKenzie, J.L., Doedens, M. & Dick, J.E. Lentivector-mediated clonal tracking reveals intrinsic heterogeneity in the human hematopoietic stem cell compartment and culture-induced stem cell impairment. Blood 103, 545–552 (2004).

    CAS  PubMed  Google Scholar 

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Acknowledgements

We thank the obstetrics unit of Trillium Hospital for cord blood samples; P.A. Penttilä, A. Khandi, L. Jamieson and S. Zhao at the SickKids Flow Cytometry Facility for cell sorting; V. Voisin and G. Bader for advice on bioinformatics and critical review of the manuscript; S. Bashir for statistical advice; A. Neumann for help with cloning and plasmids; M. Doedens for help with intrafemoral injections; and O. Gan for critical review of the manuscript. Supported by the Swiss National Science Foundation (E.L.), Roche (E.L.), the Fondation Suisse pour les Bourses en Médecine et Biologie (E.L.), the Swedish Research Council (S.Z.), Genome Canada (through the Ontario Genomics Institute), Ontario Institute for Cancer Research with funds from the province of Ontario, the Canadian Institutes for Health Research, Canada Research Chairs Program, the Princess Margaret Hospital Foundation, the Terry Fox Research Institute, Canadian Cancer Society Research Institute and the Ontario Ministry of Health and Long Term Care. The views expressed do not necessarily reflect those of the Ontario Ministry of Health and Long Term Care.

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Author notes

  1. Sergei Doulatov

    Present address: Present address: Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Harvard Stem Cell Institute, Boston, Massachusetts, USA.,

  2. Sergei Doulatov and Sasan Zandi: These authors contributed equally to this work.

Authors and Affiliations

  1. Campbell Family Institute for Cancer Research, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada

    Elisa Laurenti, Sergei Doulatov, Sasan Zandi, Ian Plumb & John E Dick

  2. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

    John E Dick

  3. Illumina, San Diego, California, USA

    Jing Chen, Craig April & Jian-Bing Fan

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  1. Elisa Laurenti
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Contributions

E.L. designed and did experiments, analyzed data and wrote the manuscript; S.D. designed and did experiments, analyzed data and edited the manuscript; S.Z. designed and did experiments and edited the manuscript; I.P. cloned lentiviral vectors plasmids and did RT-PCR; J.C. and C.A. did gene-expression profiling experiments; J.-B.F. supervised gene-expression profile experiments, and J.E.D. supervised the study and wrote the manuscript.

Corresponding author

Correspondence to John E Dick.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6, Supplementary Tables 1–3 and 5 and Supplementary Note 1 (PDF 4384 kb)

Supplementary Table 4

Gene expression profiles determined with the STEM algorithm and K-means. (XLSX 1216 kb)

Supplementary Table 6

Transcription factors differentially expressed throughout the hierarchy. (XLSX 35 kb)

Supplementary Table 7

Gene-lists used for transcription factor binding motif enrichment. (XLSX 93 kb)

Supplementary Table 8

Data for MS5-MBN assay. (XLSX 72 kb)

Supplementary Table 9

Human chimerism and proportions of B and myeloid cells in all mice analyzed. (XLSX 63 kb)

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Laurenti, E., Doulatov, S., Zandi, S. et al. The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment. Nat Immunol 14, 756–763 (2013). https://doi.org/10.1038/ni.2615

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