101
|
Shih HY, Sciumè G, Mikami Y, Guo L, Sun HW, Brooks SR, Urban JF, Davis FP, Kanno Y, O'Shea JJ. Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality. Cell 2016; 165:1120-1133. [PMID: 27156451 PMCID: PMC4874839 DOI: 10.1016/j.cell.2016.04.029] [Citation(s) in RCA: 261] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/17/2016] [Accepted: 04/06/2016] [Indexed: 12/31/2022]
Abstract
Innate lymphoid cells (ILCs) play key roles in host defense, barrier integrity, and homeostasis and mirror adaptive CD4(+) T helper (Th) cell subtypes in both usage of effector molecules and transcription factors. To better understand the relationship between ILC subsets and their Th cell counterparts, we measured genome-wide chromatin accessibility. We find that chromatin in proximity to effector genes is selectively accessible in ILCs prior to high-level transcription upon activation. Accessibility of these regions is acquired in a stepwise manner during development and changes little after in vitro or in vivo activation. Conversely, dramatic chromatin remodeling occurs in naive CD4(+) T cells during Th cell differentiation using a type-2-infection model. This alteration results in a substantial convergence of Th2 cells toward ILC2 regulomes. Our data indicate extensive sharing of regulatory circuitry across the innate and adaptive compartments of the immune system, in spite of their divergent developing pathways.
Collapse
Affiliation(s)
- Han-Yu Shih
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Giuseppe Sciumè
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yohei Mikami
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liying Guo
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph F Urban
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Fred P Davis
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuka Kanno
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
102
|
Chea S, Perchet T, Petit M, Verrier T, Guy-Grand D, Banchi EG, Vosshenrich CAJ, Di Santo JP, Cumano A, Golub R. Notch signaling in group 3 innate lymphoid cells modulates their plasticity. Sci Signal 2016; 9:ra45. [DOI: 10.1126/scisignal.aaf2223] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
103
|
Viant C, Rankin LC, Girard-Madoux MJH, Seillet C, Shi W, Smyth MJ, Bartholin L, Walzer T, Huntington ND, Vivier E, Belz GT. Transforming growth factor-β and Notch ligands act as opposing environmental cues in regulating the plasticity of type 3 innate lymphoid cells. Sci Signal 2016; 9:ra46. [PMID: 27141930 DOI: 10.1126/scisignal.aaf2176] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Group 3 innate lymphoid cells (ILC3s) are composed of subsets that are either positive or negative for the natural cytotoxicity receptor (NCR) NKp46 (encoded by Ncr1). ILC3s are located at mucosal sites, such as in the intestine and lung, where they are exposed to billions of commensal microbes and potentially harmful pathogens. Together with T cells, the various ILC3 subsets maintain the balance between homeostasis and immune activation. Through genetic mapping, we identified a previously uncharacterized subset of NCR(-) ILC3s in mice that transiently express Ncr1, demonstrating previously undescribed heterogeneity within the ILC3 population. In addition, we showed that sustained Notch signaling was required for the maintenance of the NCR(+) phenotype and that the cytokine transforming growth factor-β (TGF-β) impaired the development of NCR(+) ILC3s. Thus, the plasticity of ILC3s is regulated by the balance between the opposing effects of Notch and TGF-β signaling, maintaining homeostasis in the face of continual challenges.
Collapse
Affiliation(s)
- Charlotte Viant
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, INSERM, U1104, CNRS UMR 7280, 13288 Marseille, France
| | - Lucille C Rankin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mathilde J H Girard-Madoux
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, INSERM, U1104, CNRS UMR 7280, 13288 Marseille, France
| | - Cyril Seillet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Wei Shi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia. Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Laurent Bartholin
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR 5286, Université Lyon 1, Centre Léon Bérard, 69373 Lyon, France
| | - Thierry Walzer
- Centre International de Recherche en Infectiologie, INSERM U1111, 69364 Lyon, France
| | - Nicholas D Huntington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université UM2, INSERM, U1104, CNRS UMR 7280, 13288 Marseille, France. Immunologie, Hôpital de la Conception, Assistance Publique-Hôpitaux de Marseille, 13385 Marseille, France.
| | - Gabrielle T Belz
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
104
|
IL-33 in T Cell Differentiation, Function, and Immune Homeostasis. Trends Immunol 2016; 37:321-333. [DOI: 10.1016/j.it.2016.03.007] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 01/01/2023]
|
105
|
Verrier T, Satoh-Takayama N, Serafini N, Marie S, Di Santo JP, Vosshenrich CAJ. Phenotypic and Functional Plasticity of Murine Intestinal NKp46+ Group 3 Innate Lymphoid Cells. THE JOURNAL OF IMMUNOLOGY 2016; 196:4731-8. [PMID: 27183613 DOI: 10.4049/jimmunol.1502673] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/21/2016] [Indexed: 12/17/2022]
Abstract
Group 3 innate lymphoid cells (ILC3) actively participate in mucosal defense and homeostasis through prompt secretion of IL-17A, IL-22, and IFN-γ. Reports identify two ILC3 lineages: a CCR6(+)T-bet(-) subset that appears early in embryonic development and promotes lymphoid organogenesis and a CCR6(-)T-bet(+) subset that emerges after microbial colonization and harbors NKp46(+) ILC3. We demonstrate that NKp46 expression in the ILC3 subset is highly unstable. Cell fate mapping using Ncr1(CreGFP) × Rosa26(RFP) mice revealed the existence of an intestinal RFP(+) ILC3 subset (Ncr1(FM)) lacking NKp46 expression at the transcript and protein levels. Ncr1(FM) ILC3 produced more IL-22 and were distinguishable from NKp46(+) ILC3 by differential CD117, CD49a, DNAX accessory molecule-1, and, surprisingly, CCR6 expression. Ncr1(FM) ILC3 emerged after birth and persisted in adult mice following broad-spectrum antibiotic treatment. These results identify an unexpected phenotypic instability within NKp46(+) ILC3 that suggests a major role for environmental signals in tuning ILC3 functional plasticity.
Collapse
Affiliation(s)
- Thomas Verrier
- Unité d'Immunité Innée, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75724 Paris, France; Paris Diderot University, 75205 Paris, France; and
| | - Naoko Satoh-Takayama
- Unité d'Immunité Innée, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75724 Paris, France; Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Science, Yokohama 230-0045, Japan
| | - Nicolas Serafini
- Unité d'Immunité Innée, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75724 Paris, France
| | - Solenne Marie
- Unité d'Immunité Innée, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75724 Paris, France
| | - James P Di Santo
- Unité d'Immunité Innée, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75724 Paris, France;
| | | |
Collapse
|
106
|
Geiger TL, Sun JC. Development and maturation of natural killer cells. Curr Opin Immunol 2016; 39:82-9. [PMID: 26845614 PMCID: PMC4801705 DOI: 10.1016/j.coi.2016.01.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 12/21/2022]
Abstract
Natural killer (NK) cells are innate lymphocytes that are critical for host protection against pathogens and cancer due to their ability to rapidly release inflammatory cytokines and kill infected or transformed cells. In the 40 years since their initial discovery, much has been learned about how this important cellular lineage develops and functions. We now know that NK cells are the founding members of an expanded family of lymphocyte known as innate lymphoid cells (ILC). Furthermore, we have recently discovered that NK cells can possess features of adaptive immunity such as antigen specificity and long-lived memory responses. Here we will review our current understanding of the molecular mechanisms driving development of NK cells from the common lymphoid progenitor (CLP) to mature NK cells, and from activated effectors to long-lived memory NK cells.
Collapse
Affiliation(s)
- Theresa L Geiger
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, New York, NY 10065, United States; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Joseph C Sun
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, New York, NY 10065, United States; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States; Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, United States.
| |
Collapse
|