Dudakov, J.A., Hanash, A.M. & van den Brink, M.R. Interleukin-22: immunobiology and pathology. Annu. Rev. Immunol. 33, 747–785 (2015).
Spits, H. et al. Innate lymphoid cells–a proposal for uniform nomenclature. Nat. Rev. Immunol. 13, 145–149 (2013).
McKenzie, A.N., Spits, H. & Eberl, G. Innate lymphoid cells in inflammation and immunity. Immunity 41, 366–374 (2014).
Diefenbach, A., Colonna, M. & Koyasu, S. Development, differentiation, and diversity of innate lymphoid cells. Immunity 41, 354–365 (2014).
Montaldo, E., Juelke, K. & Romagnani, C. Group 3 innate lymphoid cells (ILC3s): Origin, differentiation, and plasticity in humans and mice. Eur. J. Immunol. 45, 2171–2182 (2015).
Eberl, G., Di Santo, J.P. & Vivier, E. The brave new world of innate lymphoid cells. Nat. Immunol. 16, 1–5 (2015).
Eberl, G., Colonna, M., Di Santo, J.P. & McKenzie, A.N. Innate lymphoid cells: a new paradigm in immunology. Science 348, aaa6566 (2015).
Mebius, R.E., Rennert, P. & Weissman, I.L. Developing lymph nodes collect CD4+CD3− LTβ+ cells that can differentiate to APC, NK cells, and follicular cells but not T or B cells. Immunity 7, 493–504 (1997).
Constantinides, M.G. et al. PLZF expression maps the early stages of ILC1 lineage development. Proc. Natl. Acad. Sci. USA 112, 5123–5128 (2015).
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).
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).
Kirchberger, S. et al. Innate lymphoid cells sustain colon cancer through production of interleukin-22 in a mouse model. J. Exp. Med. 210, 917–931 (2013).
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).
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).
Sonnenberg, G.F., Fouser, L.A. & Artis, D. Functional biology of the IL-22-IL-22R pathway in regulating immunity and inflammation at barrier surfaces. Adv. Immunol. 107, 1–29 (2010).
Zheng, Y. et al. Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens. Nat. Med. 14, 282–289 (2008).
Satoh-Takayama, N. et al. The chemokine receptor CXCR6 controls the functional topography of interleukin-22 producing intestinal innate lymphoid cells. Immunity 41, 776–788 (2014).
Artis, D. & Spits, H. The biology of innate lymphoid cells. Nature 517, 293–301 (2015).
van de Pavert, S.A. & Vivier, E. Differentiation and function of group 3 innate lymphoid cells, from embryo to adult. Int. Immunol. doi:10.1093/intimm/dxv052 (22 September 2015).
Robinette, M.L. et al. Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets. Nat. Immunol. 16, 306–317 (2015).
Sciumé, G. et al. Distinct requirements for T-bet in gut innate lymphoid cells. J. Exp. Med. 209, 2331–2338 (2012).
Guo, X. et al. Induction of innate lymphoid cell-derived interleukin-22 by the transcription factor STAT3 mediates protection against intestinal infection. Immunity 40, 25–39 (2014).
Sathe, P. et al. Innate immunodeficiency following genetic ablation of Mcl1 in natural killer cells. Nat. Commun. 5, 4539 (2014).
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).
Guo, X. et al. Innate lymphoid cells control early colonization resistance against intestinal pathogens through ID2-dependent regulation of the microbiota. Immunity 42, 731–743 (2015).
Basu, R. et al. Th22 cells are an important source of IL-22 for host protection against enteropathogenic bacteria. Immunity 37, 1061–1075 (2012).
Ahlfors, H. et al. IL-22 fate reporter reveals origin and control of IL-22 production in homeostasis and infection. J. Immunol. 193, 4602–4613 (2014).
Vonarbourg, C. et al. Regulated expression of nuclear receptor RORγt confers distinct functional fates to NK cell receptor-expressing RORγt+ innate lymphocytes. Immunity 33, 736–751 (2010).
Dhiman, R. et al. IL-22 produced by human NK cells inhibits growth of Mycobacterium tuberculosis by enhancing phagolysosomal fusion. J. Immunol. 183, 6639–6645 (2009).
Guo, H. & Topham, D.J. Interleukin-22 (IL-22) production by pulmonary Natural killer cells and the potential role of IL-22 during primary influenza virus infection. J. Virol. 84, 7750–7759 (2010).
Male, V. et al. Immature NK cells, capable of producing IL-22, are present in human uterine mucosa. J. Immunol. 185, 3913–3918 (2010).
Tang, Q. et al. Development of IL-22-producing NK lineage cells from umbilical cord blood hematopoietic stem cells in the absence of secondary lymphoid tissue. Blood 117, 4052–4055 (2011).
Xu, X. et al. Conventional NK cells can produce IL-22 and promote host defense in Klebsiella pneumoniae pneumonia. J. Immunol. 192, 1778–1786 (2014).
Macho-Fernandez, E. et al. Lymphotoxin β receptor signaling limits mucosal damage through driving IL-23 production by epithelial cells. Mucosal Immunol. 8, 403–413 (2015).
Sonnenberg, G.F. et al. Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria. Science 336, 1321–1325 (2012).
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).
Hepworth, M.R. et al. Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria. Nature 498, 113–117 (2013).
Gasteiger, G. & Rudensky, A.Y. Interactions between innate and adaptive lymphocytes. Nat. Rev. Immunol. 14, 631–639 (2014).
Wiles, S. et al. Organ specificity, colonization and clearance dynamics in vivo following oral challenges with the murine pathogen Citrobacter rodentium. Cell. Microbiol. 6, 963–972 (2004).
Smith, H.F. et al. Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. J. Evol. Biol. 22, 1984–1999 (2009).
Frisch, M., Pedersen, B.V. & Andersson, R.E. Appendicitis, mesenteric lymphadenitis, and subsequent risk of ulcerative colitis: cohort studies in Sweden and Denmark. Br. Med. J. 338, b716 (2009).
Alonzi, T. et al. Essential role of STAT3 in the control of the acute-phase response as revealed by inducible gene inactivation [correction of activation] in the liver. Mol. Cell. Biol. 21, 1621–1632 (2001).
Eberl, M., Jomaa, H. & Hayday, A.C. Integrated immune responses to infection - cross-talk between human γδ T cells and dendritic cells. Immunology 112, 364–368 (2004).
Nieuwenhuis, E.E. et al. Disruption of T helper 2-immune responses in Epstein-Barr virus-induced gene 3-deficient mice. Proc. Natl. Acad. Sci. USA 99, 16951–16956 (2002).
Narni-Mancinelli, E. et al. Fate mapping analysis of lymphoid cells expressing the NKp46 cell surface receptor. Proc. Natl. Acad. Sci. USA 108, 18324–18329 (2011).
Thakur, C. et al. Increased expression of mdig predicts poorer survival of the breast cancer patients. Gene 535, 218–224 (2014).
Liao, Y., Smyth, G.K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
Ritchie, M.E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
Smyth, G.K. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, 3 (2004).
McCarthy, D.J. & Smyth, G.K. Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics 25, 765–771 (2009).
Yu, Z. & Morrison, M. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36, 808–812 (2004).