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Single-cell analysis defines the divergence between the innate lymphoid cell lineage and lymphoid tissue–inducer cell lineage

Nature Immunology volume 17, pages 269–276 (2016)Cite this article

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Abstract

The precise lineage relationship between innate lymphoid cells (ILCs) and lymphoid tissue–inducer (LTi) cells is poorly understood. Using single-cell multiplex transcriptional analysis of 100 lymphoid genes and single-cell cultures of fetal liver precursor cells, we identified the common proximal precursor to these lineages and found that its bifurcation was marked by differential induction of the transcription factors PLZF and TCF1. Acquisition of individual effector programs specific to the ILC subsets ILC1, ILC2 and ILC3 was initiated later, at the common ILC precursor stage, by transient expression of mixed ILC1, ILC2 and ILC3 transcriptional patterns, whereas, in contrast, the development of LTi cells did not go through multilineage priming. Our findings provide insight into the divergent mechanisms of the differentiation of the ILC lineage and LTi cell lineage and establish a high-resolution 'blueprint' of their development.

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Figure 1: Identification of distinct subpopulations of α4β7-expressing lymphoid precursors in fetal liver.
Figure 2: Colonies derived from single-cell cultures of α4β7-expressing lymphoid precursors in fetal liver.
Figure 3: Hierarchical clustering distinguishes αLP and ILCP transcriptional profiles.
Figure 4: Clusters define the developmental progression of key transcription factors.
Figure 5: Transitional cluster B includes two distinct subsets, on the basis of expression of Tcf7 and Zbtb16.
Figure 6: Multilineage transcriptional priming in ILCPs.
Figure 7: ILCP subsets with biased progeny in single-cell cultures.

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Acknowledgements

We thank J.C. Zúñiga-Pflücker (University of Toronto) for stocks of OP9 and OP9-DL1 stromal cells. Supported by the US National Institutes of Health (R01 HL118092, AI038339 and AI108643) and by the Digestive Diseases Research Center of Excellence (P30DK42086).

Author information

Author notes

  1. Isabel E Ishizuka, Sylvestre Chea and Herman Gudjonson: These authors contributed equally to this work.

  2. Albert Bendelac and Rachel Golub: These authors jointly directed this work.

Authors and Affiliations

  1. Committee on Immunology, University of Chicago, Chicago, Illinois, USA

    Isabel E Ishizuka, Herman Gudjonson, Michael G Constantinides & Albert Bendelac

  2. Department of Pathology, University of Chicago, Chicago, Illinois, USA

    Isabel E Ishizuka, Michael G Constantinides & Albert Bendelac

  3. Immunology Department, Institut Pasteur, Lymphopoiesis Unit, Inserm U668, University Paris Diderot, Paris, France

    Sylvestre Chea & Rachel Golub

  4. Institute of Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA

    Herman Gudjonson & Aaron R Dinner

  5. Department of Chemistry, University of Chicago, Chicago, Illinois, USA

    Herman Gudjonson & Aaron R Dinner

Authors
  1. Isabel E Ishizuka
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Contributions

I.E.I., H.G., M.G.C. and A.B. designed the experiments; I.E.I. performed single-cell sorting and culture experiments; S.C. designed and performed the lymphoid Biomark assay; H.G. performed computational analysis of the Biomark experiments; M.G.C. designed and performed experiments; A.R.D. supervised computational analysis; A.B. supervised experiments; R.G. supervised Biomark experiments; and I.E.I., H.G. and A.B. wrote the manuscript with contributions from all authors.

Corresponding author

Correspondence to Albert Bendelac.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Intercellular transcriptional distances confirm hierarchical clustering analysis.

Euclidean distance between all pairs of measured transcriptional profiles. Dendrograms shown are those obtained from the hierarchical clustering of these intercellular distances. Outer bar, sorted cell type; αLP (red), ILCP (green), LTiP (blue). Inner bar, cluster assignment of each cell; AI-III (red), B (purple), CI-IV (green).

Supplementary Figure 2 α4β7+IL-33Rαhi cells represent contaminating mast cell precursors.

a, Biomark analysis of the Il33r+ cluster excluded from the study suggested that they were not innate lymphoid cells, as evidenced by the nearly uniform lack of Tcf7 and Tox, as well as other key markers. b, FACS analysis suggested the mast cell nature of these cells. α4β7-MACS-enriched fetal liver cells obtained from the Zbtb16-GFPCre reporter strain were gated as Lin− cells (this is the same population that was used to sort single αLP and ILCP) and stained for IL-33Rα. The IL-33Rα+ cells expressed intermediate amounts of PLZF (GFP) and α4β7, possibly explaining why they were found as contaminants in the Biomark analysis of ‘purified’ αLP and ILCP. 16% of these cells expressed the mast cell marker FcεRIα, indicating that they were mast cell lineage precursors.

Supplementary Figure 3 Expression frequencies of key transcription factors in αLP and ILCP transcription-state clusters define their developmental progression.

In each cluster, the proportion of cells with detectable levels of transcript is calculated for genes defining early developmental transitions. Similar to the trends observed in average transcript levels by cluster, Id2 is first expressed at a low level in AI, followed by Tox and Nfil3 in AII, Sox4 and Runx1 in AIII, and finally by Tcf7 and Zbtb16 in B.

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Supplementary Figures 1–3 and Supplementary Tables 1 and 2 (PDF 655 kb)

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Ishizuka, I., Chea, S., Gudjonson, H. et al. Single-cell analysis defines the divergence between the innate lymphoid cell lineage and lymphoid tissue–inducer cell lineage. Nat Immunol 17, 269–276 (2016). https://doi.org/10.1038/ni.3344

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