Abstract
Group 2 innate lymphoid cells (ILC2 cells) are important for type 2 immune responses and are activated by the epithelial cytokines interleukin 33 (IL-33), IL-25 and thymic stromal lymphopoietin (TSLP). Here we demonstrated that IL-1β was a critical activator of ILC2 cells, inducing proliferation and cytokine production and regulating the expression of epithelial cytokine receptors. IL-1β also governed ILC2 plasticity by inducing low expression of the transcription factor T-bet and the cytokine receptor chain IL-12Rβ2, which enabled the conversion of these cells into an ILC1 phenotype in response to IL-12. This transition was marked by an atypical chromatin landscape characterized by the simultaneous transcriptional accessibility of the locus encoding interferon-γ (IFN-γ) and the loci encoding IL-5 and IL-13. Finally, IL-1β potentiated ILC2 activation and plasticity in vivo, and IL-12 acted as the switch that determined an ILC2-versus-ILC1 response. Thus, we have identified a previously unknown role for IL-1β in facilitating ILC2 maturation and plasticity.
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29 April 2016
In the version of this article initially published online, the interferon (IFN-α) in the fourth sentence of the abstract is incorrect. That section should read "the locus encoding interferon-γ (IFN-γ)...." Also, sentence two in paragraph three of the introduction includes a typographical error ("zand"); that should read "IL-18 and IL-1...." The errors have been corrected for the print, PDF and HTML versions of this article.
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Acknowledgements
We thank H. Ueno, S. Hanabuchi, T. Kim and M. Ramaswamy for discussions; C. Harrod and C. Kiefer for critical reading of the manuscript; N. Loof, C. Boudreaux, K. Kayembe, C. Groves and R. Rayanki for support with cell sorting; H. Lu and A. Berlin for laboratory support; the LAR staff for maintaining the experimental animals; N. Baldwin for help in depositing RNA-sequencing data; and A. O'Bar and S. Zurawski for performing Luminex experiment. Supported by the Cancer Prevention and Research Institute of Texas (RP110319 (“Targeting Dendritic Cells to Block Immunosuppression in Breast Cancer”) to Y.-J.L.) and by the Japan Society for the Promotion of Science (KAKENHI Grant-in-Aid 23-10890 to Y.O.)
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Y.O. and Y.-J.L. conceived of the idea for this project; Y.O., J.S.S., L.T.-S., A.A.H. and Y.-J.L. designed experiments; Y.O., J.S.S., L.T.-S., M.A.C., J.P.B. and A.M.C. performed experiments and analyzed data; Y.O. and B.L.C. performed analysis of RNA sequencing data; and Y.O., J.S.S., L.T.-S., A.H.H. and Y.-J.L. wrote the manuscript.
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Y.O., J.S.S., A.M.C., A.A.H. and Y.-J.L. are employed by and shareholders of Medimmune.
Integrated supplementary information
Supplementary Figure 1 Identification of human ILC2s in peripheral blood and tonsils.
(a) List of cytokines tested for the ability to promote proliferation of ILC2s. (b) Expression of T-bet and GATA-3 in ILCs in PBMC examined by intra-nuclear transcription staining followed by flow cytometry. Subsets of ILCs were defined as in Fig. 1a. (c) Purity and yield of ILC2s from blood after cell sorting. (d) Purity and yield ILC2s after FACS sorting. (e) Schematic of identification of ILCs in human tonsils by flow cytometry. Antibodies against the following lineage makers (Lin) are used: CD3, CD4, CD14, CD16, CD19, CD20, CD34, CD123, TCRαβ, HLA-DR. ILC2s were identified as Lin- CD127+ CD56- CRTH2+. CD56brigtht NK cells were identified as Lin-CD127int c-Kit- CD56hi.
Supplementary Figure 2 IL-1β enhances the response of ILC2s to epithelial cytokines.
(a) Expression of CRLF2 in CD56brigtht NK cells, ILC2s and c-Kit+ CD127+ cells freshly isolated from peripheral blood or stimulated with IL-2 and IL-1β for 7 days. Expression of CRLF2 was normalized to GUSB and shown as arbitrary unit. (b) Cell numbers of ILC2s recovered after culturing with IL-2, IL-25 and IL-1β for 7 days (300 cells plated per well at day 0). (c) Scheme of the experiments comparing freshly isolated ILC2s and IL-1β-primed ILC2s. (d) Frequencies of phospho-NF-κB positive cells in Fig. 3f. (e) NF-κB phosphorylation in CD56brigtht NK cells, ILC2s and c-Kit+ CD127+ cells in freshly isolated from peripheral blood stimulated with IL-1β, IL-18 and IL-33 for 5 min. *P < 0.05, **P < 0.01 and *** P < 0.001 using one-way ANOVA followed by two-tailed t-test (a), one-way ANOVA followed by Dunnet’s test (b), or followed by Turkey’s test (d). Data are from 6 (a) and 5 (b) and 4 (d) independent experiments with independent donors or from one experiment representative of four (e) experiments with similar results. Data are represented as mean (± s.e.m.) (a,b).
Supplementary Figure 3 Validation of the expression changes in ILC2s stimulated with IL-1β.
(a) The surface expression of HLA-DR/DP/DQ, CD80 and CD40L measured by flow cytometry in ILC2s freshly isolated from peripheral blood or cultured with IL-2 and IL-1β for 7 days. (b) mRNA levels of GATA3, RORC and RORA in freshly isolated ILC2s, CD56bright NK cells and ILC2s stimulated with IL-2 and IL-1β for 5 days. Data are normalized to GUSB and shown as relative values and represented as mean (± s.e.m.). *P<0.05, ** P < 0.01, *** P < 0.001 analyzed using one-way ANOVA followed by Turkey’s test (b). Data are representative of 6 experiments with similar results (a), or 6 (b) experiments with independent donors.
Supplementary Figure 4 IL-12 affects ILC2 functional gene expression and phenotype plasticity.
(a) Viabilities of ILC2s cultured with IL-2 and IL-1β with or without IL-12 for 7 days. (b) Schematic of identification of human c-Kit+ and c-Kit- subpopulations of ILC2s in human PBMC by flow cytometry. CD56brigtht NK cells and ILC2s were defined as in Fig. 1a and ILC2s were further divided by expression of c-Kit. Numbers adjacent to outlined areas indicate percent of parent population. (c) Recovery of c-Kit+ and c-Kit- ILC2s subpopulations from 150 ml whole blood. (d) Intracellular staining of IL-13, IL-5 and IFN-γ in c-Kit+ and c-Kit- ILC2s, and CD56brigtht NK cells cultured with or without IL-12 in the presence of IL-2 and IL-1β for 7 days followed by re-stimulation with PMA and ionomycin for 6 h in the presence of protein secretion inhibitors. (e) Frequencies of IL-5 and IL-13 double positive cells (left) and IFN-γ and IL-13 double positive cells (right) measured in d. (f) Expression of IL1RL1, IL17RB, CRLF2 and GATA3 in ILC2s freshly isolated from peripheral blood or cultured with IL-2 and IL-1β with or without IL-12 for 7 days. Data are normalized to GUSB and shown as relative values. * P < 0.05, **P < 0.01 and ***P < 0.001 as analyzed by two-tailed t-test (a), one-way ANOVA followed by Turkey’s test (e,f). Data are from 9 (a) or 6 (c,e,f) experiments with independent donors or from one experiment representative of 6 experiments (d) with similar results. Data are represented as mean (± s.e.m.) (f).
Supplementary Figure 5 IFNG and type-2-cytokine-encoding loci.
(a) IFNG locus and (b) Type 2 cytokine loci are shown with gray boxes depicting the distal regulatory regions for each locus. The red boxes approximately refer to the regions amplified by qPCR using specific primers as shown in Fig. 6. CNS, conserved non-coding sequences. CGRE, conserved GATA-3 response element. IE, IL4 intronic enhancer. HS, hyper sensitive site.
Supplementary Figure 6 Identification of ILC2 cells and NK cells in vivo and the effect of anti-IL-12 on IL-1-mediated ILC2 activation.
(a) The expression of lineage markers CD3, CD19, B220, CD5, TCRβ, TCRγδ, CD11c, F4/80, Gr1, Ter119, and CD27 on CD45+ cells, ILC2s and CD49b+ NKs measured by flow cytometry. (b) The concentration of IL-13 in the culture supernatant of ILC2 isolated from the lungs of the mice administered and stimulated as in Fig. 7g. Data are representative of 7 independent experiments (a). Data are represented as mean (b).
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Ohne, Y., Silver, J., Thompson-Snipes, L. et al. IL-1 is a critical regulator of group 2 innate lymphoid cell function and plasticity. Nat Immunol 17, 646–655 (2016). https://doi.org/10.1038/ni.3447
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DOI: https://doi.org/10.1038/ni.3447
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