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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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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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.
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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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DOI: https://doi.org/10.1038/ni.2615
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