Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment

Nature Immunology volume 17, pages 169–178 (2016)Cite this article

Subjects

An Erratum to this article was published on 22 March 2016

An Erratum to this article was published on 19 January 2016

This article has been updated

Abstract

The transcription factor GATA-3 is indispensable for the development of all innate lymphoid cells (ILCs) that express the interleukin 7 receptor α-chain (IL-7Rα). However, the function of low GATA-3 expression in committed group 3 ILCs (ILC3 cells) has not been identified. We found that GATA-3 regulated the homeostasis of ILC3 cells by controlling IL-7Rα expression. In addition, GATA-3 served a critical function in the development of the NKp46+ ILC3 subset by regulating the balance between the transcription factors T-bet and RORγt. Among NKp46+ ILC3 cells, although GATA-3 positively regulated genes specific to the NKp46+ ILC3 subset, it negatively regulated genes specific to lymphoid tissue–inducer (LTi) or LTi-like ILC3 cells. Furthermore, GATA-3 was required for IL-22 production in both ILC3 subsets. Thus, despite its low expression, GATA-3 was critical for the homeostasis, development and function of ILC3 subsets.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: GATA-3 regulates IL-7Rα expression and ILC3 homeostasis.
Figure 2: GATA-3 is indispensable for the development of NKp46+ ILC3 cells.
Figure 3: GATA-3 negatively regulates RORγt without affecting T-bet expression.
Figure 4: The interplay among RORγt, GATA-3 and T-bet regulates the development of NKp46+ ILC3 cells at different stages.
Figure 5: GATA-3 globally regulates 'lineage-preferred' genes selectively expressed by CCR6+ or NKp46+ ILC3 subsets.
Figure 6: GATA-3 regulates IL-22 production by ILC3 cells and thus regulates the susceptibility of mice to infection with C. rodentium.

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

Change history

  • 08 December 2015

    In the version of this article initially published online, in the third and fourth paragraphs of the Discussion section, the mice are incorrectly identified as Rorcgfb/+. The correct genotype is Rorcgfp/+. The error has been corrected for the print, PDF and HTML versions of this article.

References

  1. Spits, H. et al. Innate lymphoid cells–a proposal for uniform nomenclature. Nat. Rev. Immunol. 13, 145–149 (2013).

    Article  CAS  Google Scholar 

  2. Hoyler, T. et al. The transcription factor GATA-3 controls cell fate and maintenance of type 2 innate lymphoid cells. Immunity 37, 634–648 (2012).

    Article  CAS  Google Scholar 

  3. Yagi, R. et al. The transcription factor GATA-3 is critical for the development of all IL-7Ralpha-expressing innate lymphoid cells. Immunity 40, 378–388 (2014).

    Article  CAS  Google Scholar 

  4. Klein Wolterink, R.G. et al. Essential, dose-dependent role for the transcription factor Gata3 in the development of IL-5+ and IL-13+ type 2 innate lymphoid cells. Proc. Natl. Acad. Sci. USA 110, 10240–10245 (2013).

    Article  Google Scholar 

  5. Mjösberg, J. et al. The transcription factor GATA-3 is essential for the function of human type 2 innate lymphoid cells. Immunity 37, 649–659 (2012).

    Article  Google Scholar 

  6. Moro, K. et al. Innate production of TH2 cytokines by adipose tissue-associated c-Kit+Sca-1+ lymphoid cells. Nature 463, 540–544 (2010).

    Article  CAS  Google Scholar 

  7. Neill, D.R. et al. Nuocytes represent a new innate effector leukocyte that mediates type-2 immunity. Nature 464, 1367–1370 (2010).

    Article  CAS  Google Scholar 

  8. Price, A.E. et al. Systemically dispersed innate IL-13-expressing cells in type 2 immunity. Proc. Natl. Acad. Sci. USA 107, 11489–11494 (2010).

    Article  CAS  Google Scholar 

  9. Satoh-Takayama, N. et al. Microbial flora drives interleukin 22 production in intestinal NKp46+ cells that provide innate mucosal immune defense. Immunity 29, 958–970 (2008).

    Article  CAS  Google Scholar 

  10. Buonocore, S. et al. Innate lymphoid cells drive interleukin-23-dependent innate intestinal pathology. Nature 464, 1371–1375 (2010).

    Article  CAS  Google Scholar 

  11. Sonnenberg, G.F., Monticelli, L.A., Elloso, M.M., Fouser, L.A. & Artis, D. CD4+ lymphoid tissue-inducer cells promote innate immunity in the gut. Immunity 34, 122–134 (2011).

    Article  CAS  Google Scholar 

  12. Klose, C.S. et al. Differentiation of type 1 ILCs from a common progenitor to all helper-like innate lymphoid cell lineages. Cell 157, 340–356 (2014).

    Article  CAS  Google Scholar 

  13. Fuchs, A. et al. Intraepithelial type 1 innate lymphoid cells are a unique subset of IL-12- and IL-15-responsive IFN-γ-producing cells. Immunity 38, 769–781 (2013).

    Article  CAS  Google Scholar 

  14. Halim, T.Y. et al. Group 2 innate lymphoid cells are critical for the initiation of adaptive T helper 2 cell-mediated allergic lung inflammation. Immunity 40, 425–435 (2014).

    Article  CAS  Google Scholar 

  15. Basu, R. et al. Th22 cells are an important source of IL-22 for host protection against enteropathogenic bacteria. Immunity 37, 1061–1075 (2012).

    Article  CAS  Google Scholar 

  16. Qiu, J. et al. Group 3 innate lymphoid cells inhibit T-cell-mediated intestinal inflammation through aryl hydrocarbon receptor signaling and regulation of microflora. Immunity 39, 386–399 (2013).

    Article  CAS  Google Scholar 

  17. Hepworth, M.R. et al. Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria. Nature 498, 113–117 (2013).

    Article  CAS  Google Scholar 

  18. Oliphant, C.J. et al. MHCII-mediated dialog between group 2 innate lymphoid cells and CD4+ T cells potentiates type 2 immunity and promotes parasitic helminth expulsion. Immunity 41, 283–295 (2014).

    Article  CAS  Google Scholar 

  19. Gasteiger, G. & Rudensky, A.Y. Interactions between innate and adaptive lymphocytes. Nat. Rev. Immunol. 14, 631–639 (2014).

    Article  CAS  Google Scholar 

  20. Klose, C.S. et al. A T-bet gradient controls the fate and function of CCR6-RORγt+ innate lymphoid cells. Nature 494, 261–265 (2013).

    Article  CAS  Google Scholar 

  21. Cella, M. et al. A human natural killer cell subset provides an innate source of IL-22 for mucosal immunity. Nature 457, 722–725 (2009).

    Article  CAS  Google Scholar 

  22. Constantinides, M.G., McDonald, B.D., Verhoef, P.A. & Bendelac, A. A committed precursor to innate lymphoid cells. Nature 508, 397–401 (2014).

    Article  CAS  Google Scholar 

  23. Sawa, S. et al. Lineage relationship analysis of RORγt+ innate lymphoid cells. Science 330, 665–669 (2010).

    Article  CAS  Google Scholar 

  24. Wang, L. et al. Distinct functions for the transcription factors GATA-3 and ThPOK during intrathymic differentiation of CD4+ T cells. Nat. Immunol. 9, 1122–1130 (2008).

    Article  CAS  Google Scholar 

  25. Serafini, N. et al. Gata3 drives development of RORγt+ group 3 innate lymphoid cells. J. Exp. Med. 211, 199–208 (2014).

    Article  CAS  Google Scholar 

  26. Zhu, J. et al. Conditional deletion of Gata3 shows its essential function in TH1-TH2 responses. Nat. Immunol. 5, 1157–1165 (2004).

    Article  CAS  Google Scholar 

  27. Eberl, G. & Littman, D.R. Thymic origin of intestinal αβ T cells revealed by fate mapping of RORγt+ cells. Science 305, 248–251 (2004).

    Article  CAS  Google Scholar 

  28. Sciumé, G. et al. Distinct requirements for T-bet in gut innate lymphoid cells. J. Exp. Med. 209, 2331–2338 (2012).

    Article  Google Scholar 

  29. Rankin, L.C. et al. The transcription factor T-bet is essential for the development of NKp46+ innate lymphocytes via the Notch pathway. Nat. Immunol. 14, 389–395 (2013).

    Article  CAS  Google Scholar 

  30. Wei, G. et al. Genome-wide analyses of transcription factor GATA-3-mediated gene regulation in distinct T cell types. Immunity 35, 299–311 (2011).

    Article  CAS  Google Scholar 

  31. Zhu, J. et al. The transcription factor T-bet is induced by multiple pathways and prevents an endogenous Th2 cell program during Th1 cell responses. Immunity 37, 660–673 (2012).

    Article  CAS  Google Scholar 

  32. Robinette, M.L. et al. Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets. Nat. Immunol. 16, 306–317 (2015).

    Article  CAS  Google Scholar 

  33. Qiu, J. et al. The aryl hydrocarbon receptor regulates gut immunity through modulation of innate lymphoid cells. Immunity 36, 92–104 (2012).

    Article  CAS  Google Scholar 

  34. Yu, Q., Erman, B., Park, J.H., Feigenbaum, L. & Singer, A. IL-7 receptor signals inhibit expression of transcription factors TCF-1, LEF-1, and RORγt: impact on thymocyte development. J. Exp. Med. 200, 797–803 (2004).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank D.R. Littman (New York University) for Rorc-Cre mice on the C57BL/6 background; A. Singer (National Cancer Institute) for Tg-hCD2-Il7ra mice on the C57BL/6 background; C. Dulac (Harvard) for Tbx21-Cre mice; D. Artis (University of Pennsylvania) for C. rodentium strain DBS100; A. Bhandoola, R. Germain, J. O'Shea, P. Schwartzberg and A. Sher for critical reading of our manuscript; L. Guo for suggestions and technical assistance in analyzing ILCs; K. Weng for assistance in cell sorting; L. Feigenbaum for assistance in generating RORγt–E2-Crimson mice; and the DNA Sequencing and Computational Biology Core of the National Heart, Lung, and Blood Institute for sequencing the RNA-Seq and ChIP-Seq libraries. Supported by the Intramural Research Program of the US National Institutes of Health, the National Institute of Allergy and Infectious Diseases and the National Heart, Lung, and Blood Institute.

Author information

Authors and Affiliations

  1. Molecular and Cellular Immunoregulation Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA

    Chao Zhong & Jinfang Zhu

  2. Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA

    Kairong Cui, Gangqing Hu & Keji Zhao

  3. Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA

    Christoph Wilhelm & Yasmine Belkaid

  4. Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, University of Bonn, Bonn, Germany

    Christoph Wilhelm

  5. Laboratory of System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA

    Kairui Mao

Authors
  1. Chao Zhong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kairong Cui
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Christoph Wilhelm
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Gangqing Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kairui Mao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yasmine Belkaid
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Keji Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jinfang Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

C.Z. performed all experiments; K.C. helped with constructing libraries for RNA-Seq and ChIP-Seq; C.W. helped with C. rodentium–infection experiments; G.H. performed initial analyses of the RNA-Seq and ChIP-Seq data; K.M. performed imaging experiments; K.C., C.W., G.H., K.M., Y.B. and K.Z. offered suggestions on the project and edited the paper; and C.Z. and J.Z. conceived of the project, designed the experiments, analyzed the data and wrote the paper.

Corresponding author

Correspondence to Jinfang Zhu.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Deletion of GATA3 in ILC3 cells.

(a) Gating strategy for ILC3s from small intestine lamina propria (siLP). (b) Flow cytometry analysis of GATA3 in ILC2s and ILC3s of Gata3fl/fl and Gata3ΔILC3 mice. Data are representative of more than three independent experiments.

Supplementary Figure 2 Characterization of Gata3-deficient ILC3 cells.

(a) Expression of the indicated cell-surface markers by CCR6+ and CCR6- siLP ILC3 subsets after Gata3 deletion. Data are representative of at least two independent experiments. (b) Heatmap of the expression of selected genes in ILC3s affected by Gata3 deletion, normalized by expression within each row. Live lineage-CD127+Thy-1highKLRG-1- ILC3s were sorted from siLP of Gata3fl/fl and Gata3ΔILC3 mice and subjected to RNA-Seq analysis. Signature genes in ILC3s affected after Gata3 deletion were selectively shown. Data are from two individual mice (n = 2 replicates) in each group.

Supplementary Figure 3 GATA3 affects the homeostasis of ILC3 cells in a cell-intrinsic manner.

(a) Schematic diagram of the mixed bone marrow (BM) chimera experiments. BM cells from Gata3fl/fl or Gata3ΔILC3 mice were mixed at 1:1 ratio with BM cells from wild type mice with a congenic CD45.1 marker, and transferred into irradiated Rag2-/-Il2rg-/- recipient mice. Repopulation of the transferred BM cell derived lymphocytes in recipient mice were analyzed 4-6 weeks later. (b) Flow cytometry analysis of repopulated lLC3s in the siLP and cLP, and B cells in the spleens of recipient mice. (c) Analysis of lLC3 and B cell repopulation from Gata3fl/fl and Gata3ΔILC3 BM, relative to the internal control cells derived from CD45.1+ BM. Data are representative of three independent experiments with 3-5 mice in each group. ***, p value < 0.001. NS, non-significant.

Supplementary Figure 4 Deletion of GATA3 affects the development of ‘ex-ILC3’ cells.

(a) Gating strategy and flow cytometry analysis of exILC3s from wild type and Gata3ΔILC3 mice. Gata3ΔILC3 mice were crossed with the RORγt fate mapping reporter mice (RORγtfm: Rosa26TdTomatoRorc-Cre) to generate Gata3ΔILC3RORγtfm. Gata3+/+RORγtfm mice were used as a wild type control. (b) Analysis of ILC1 and exILC3 cell number in Gata3+/+RORγtfm and Gata3ΔILC3RORγtfm mice. Three mice per each group were analyzed. **, p value < 0.01. NS, non-significant. Data are from one experiment.

Supplementary Figure 5 Deletion of Gata3 affects the NKp46+ ILC3 subset.

Gata3fl/fl mice and Gata3fl/flCre-ERT2 mice were treated with tamoxifen every other day for three times. Three month later, mice were sacrificed and NKp46+ ILC3s from siLP were analyzed. Data are representative of two independent experiments with more than three mice per group in each experiment.

Supplementary Figure 6 GATA3 suppresses RORγt expression in all ILC3 subsets independently of the regulation of IL-7R.

(a) Flow cytometry analysis of RORγt level in CCR6+ and CCR6- ILC3 subsets from Gata3fllfl and Gata3ΔILC3 mice. (b) Gating strategy of small intestine LTi cells from Gata3fllfl and Gata3ΔILC3 embryos at E15.5 days and analysis of the RORγt expression. (c) GATA3 negatively regulates RORγt expression by ILC3s in a cell intrinsic manner. Gata3fllfl and Gata3ΔILC3 BM were mixed with wild type congenic CD45.1 BM and transferred into irradiated Rag2-/-Il2rg-/- recipient mice. RORγt expression in repopulated ILC3s from different chimeras were analyzed by flow cytometry 4-6 weeks after transfer. (d) RORγt expression in siLP ILC3s from indicated mice were detected by flow cytometry. All data are representative of at least two independent experiments with more than three mice per group in each experiment.

Supplementary Figure 7 Expression of IL-7R and RORγt, as well as the development of NKp46+ ILC3 cells, are dysregulated in Rag1−/− Gata3ΔILC3 mice.

Flow cytometry analysis of CD127 and RORγt expression in siLP ILC3s (a) and of siLP ILC3 subsets (b) in the Rag1-/-Gata3fl/fl (n=4) and Rag1-/-Gata3ΔILC3 (n=6) mice. **, p value < 0.01; ***, p value < 0.001. Data are representative of two independent experiments.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 (PDF 771 kb)

Supplementary Table 1

Gene lists (XLSX 80 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhong, C., Cui, K., Wilhelm, C. et al. Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment. Nat Immunol 17, 169–178 (2016). https://doi.org/10.1038/ni.3318

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ni.3318

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing