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Diverse and heritable lineage imprinting of early haematopoietic progenitors


Haematopoietic stem cells (HSCs) and their subsequent progenitors produce blood cells, but the precise nature and kinetics of this production is a contentious issue. In one model, lymphoid and myeloid production branch after the lymphoid-primed multipotent progenitor (LMPP)1, with both branches subsequently producing dendritic cells2. However, this model is based mainly on in vitro clonal assays and population-based tracking in vivo, which could miss in vivo single-cell complexity3,4,5,6,7. Here we avoid these issues by using a new quantitative version of ‘cellular barcoding’8,9,10 to trace the in vivo fate of hundreds of LMPPs and HSCs at the single-cell level. These data demonstrate that LMPPs are highly heterogeneous in the cell types that they produce, separating into combinations of lymphoid-, myeloid- and dendritic-cell-biased producers. Conversely, although we observe a known lineage bias of some HSCs11,12,13,14, most cellular output is derived from a small number of HSCs that each generates all cell types. Crucially, in vivo analysis of the output of sibling cells derived from single LMPPs shows that they often share a similar fate, suggesting that the fate of these progenitors was imprinted. Furthermore, as this imprinting is also observed for dendritic-cell-biased LMPPs, dendritic cells may be considered a distinct lineage on the basis of separate ancestry. These data suggest a ‘graded commitment’ model of haematopoiesis, in which heritable and diverse lineage imprinting occurs earlier than previously thought.

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Figure 1: Single LMPP output to different cell types.
Figure 2: Classification of lineage bias in LMPPs and HSCs.
Figure 3: Kinetics of lineage production do not explain LMPP fate heterogeneity.
Figure 4: Pre-existing and heritable lineage imprinting within LMPPs.


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We thank G. Filion, U. Braunschweig, L. Pagie, M. Hauptmann, P. Lio, R. van der Wath and the NKI Genomics Facility for computational assistance; J. van Heijst, J. Rohr and J. Urbanus for useful discussions; for illustrations in Fig. 1a and Supplementary Fig. 1; NKI cytometry and animal facilities; D. Leone, Z. Ping and M. Lodder for technical assistance; and P. Hodgkin, K. Duffy and J. Coquet for critical reading of the manuscript. This work was supported by ERC grant LIFE-HIS-T and HFSP grant RGP0060/2012, S.H.N. was supported by the National Health and Medical Research Council Australia, Marie Curie Incoming International FP6 Fellowship, and the Leukemia and Lymphoma Society; and L.P. was supported by a Marie Curie Intra European FP7 Fellowship and the Bettencourt Schueller Fondation.

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Authors and Affiliations



S.H.N. conceived, developed, executed and analysed experiments; L.P. developed and carried out data analysis, advised by R.J.d.B.; E.S., C.G. and N.v.R. contributed to lineage-tracing technology development. T.N.S. conceived the approach and advised on data analysis and interpretation. All authors discussed results and wrote the manuscript.

Corresponding authors

Correspondence to Shalin H. Naik or Ton N. Schumacher.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, Supplementary References, Supplementary Tables 1-3 and Supplementary Figures 1-15. (PDF 3526 kb)

3D Principal Component Analysis of LMPPs by the first 3 principal components

PCA of the LMPPs was used to identify groups of progenitors, and resulted in 3 distinct groups with some 'intermediate' LMPPs between them. Backgating of LMPPs (i.e. a manual selection of LMPPs by their 3-dimensional coordinates on the principal components, and visualization of their corresponding LMPPs in the clustered heatmap) was done using in-software tools for Supplementary Fig. 7. (MOV 15098 kb)

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Naik, S., Perié, L., Swart, E. et al. Diverse and heritable lineage imprinting of early haematopoietic progenitors. Nature 496, 229–232 (2013).

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