51
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Munford RS, Weiss JP, Lu M. Biochemical transformation of bacterial lipopolysaccharides by acyloxyacyl hydrolase reduces host injury and promotes recovery. J Biol Chem 2020; 295:17842-17851. [PMID: 33454018 DOI: 10.1074/jbc.rev120.015254] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/22/2020] [Indexed: 12/26/2022] Open
Abstract
Animals can sense the presence of microbes in their tissues and mobilize their own defenses by recognizing and responding to conserved microbial structures (often called microbe-associated molecular patterns (MAMPs)). Successful host defenses may kill the invaders, yet the host animal may fail to restore homeostasis if the stimulatory microbial structures are not silenced. Although mice have many mechanisms for limiting their responses to lipopolysaccharide (LPS), a major Gram-negative bacterial MAMP, a highly conserved host lipase is required to extinguish LPS sensing in tissues and restore homeostasis. We review recent progress in understanding how this enzyme, acyloxyacyl hydrolase (AOAH), transforms LPS from stimulus to inhibitor, reduces tissue injury and death from infection, prevents prolonged post-infection immunosuppression, and keeps stimulatory LPS from entering the bloodstream. We also discuss how AOAH may increase sensitivity to pulmonary allergens. Better appreciation of how host enzymes modify LPS and other MAMPs may help prevent tissue injury and hasten recovery from infection.
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Affiliation(s)
- Robert S Munford
- Laboratory of Clinical Immunology and Microbiology, NIAID, National Institutes of Health, Bethesda, Maryland, USA.
| | - Jerrold P Weiss
- Inflammation Program, University of Iowa, Iowa City, Iowa, USA
| | - Mingfang Lu
- Department of Immunology and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China.
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52
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Liu Q, Zaba LC, Satpathy AT, Longmire M, Zhang W, Li K, Granja J, Guo C, Lin J, Li R, Tolentino K, Kania G, Distler O, Fiorentino D, Chung L, Qu K, Chang HY. Chromatin accessibility landscapes of skin cells in systemic sclerosis nominate dendritic cells in disease pathogenesis. Nat Commun 2020; 11:5843. [PMID: 33203843 PMCID: PMC7672105 DOI: 10.1038/s41467-020-19702-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022] Open
Abstract
Systemic sclerosis (SSc) is a disease at the intersection of autoimmunity and fibrosis. However, the epigenetic regulation and the contributions of diverse cell types to SSc remain unclear. Here we survey, using ATAC-seq, the active DNA regulatory elements of eight types of primary cells in normal skin from healthy controls, as well as clinically affected and unaffected skin from SSc patients. We find that accessible DNA elements in skin-resident dendritic cells (DCs) exhibit the highest enrichment of SSc-associated single-nucleotide polymorphisms (SNPs) and predict the degrees of skin fibrosis in patients. DCs also have the greatest disease-associated changes in chromatin accessibility and the strongest alteration of cell-cell interactions in SSc lesions. Lastly, data from an independent cohort of patients with SSc confirm a significant increase of DCs in lesioned skin. Thus, the DCs epigenome links inherited susceptibility and clinically apparent fibrosis in SSc skin, and can be an important driver of SSc pathogenesis.
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Affiliation(s)
- Qian Liu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Lisa C Zaba
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Michelle Longmire
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Wen Zhang
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Kun Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Jeffrey Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chuang Guo
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Jun Lin
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Karen Tolentino
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gabriela Kania
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Oliver Distler
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - David Fiorentino
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lorinda Chung
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China.
- CAS Center for Excellence in Molecular Cell Sciences, University of Science and Technology of China, Hefei, 230027, China.
- School of Data Sciences, University of Science and Technology of China, Hefei, 230027, China.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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53
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Ferreira RDS, Mendonça LABM, Ribeiro CFA, Calças NC, Guimarães RDCA, Nascimento VAD, Gielow KDCF, Carvalho CME, Castro APD, Franco OL. Relationship between intestinal microbiota, diet and biological systems: an integrated view. Crit Rev Food Sci Nutr 2020; 62:1166-1186. [PMID: 33115284 DOI: 10.1080/10408398.2020.1836605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The health-disease process can be influenced by the intestinal microbiota. As this plays a fundamental role in protecting the organism, the importance of studying the composition and diversity of this community becomes increasingly evident. Changes in the composition of the intestinal bacterial community may result in dysbiosis, and this process may contribute to triggering various diseases in all biological systems. This imbalance of intestinal microbiota homeostasis may alter commensal bacteria and the host metabolism, as well as immune function. Dysbiosis also causes an increase in intestinal permeability due to exposure to molecular patterns associated with the pathogen and lipopolysaccharides, leading to a chronic inflammatory process that can result in diseases for all biological systems. In this context, dietary intervention through the use of probiotics, prebiotics and antioxidant foods can be considered a contribution to the modulation of intestinal microbiota. Probiotics have been used to provide up to 10 billion colony forming units, and probiotic foods, Kefir and fermented natural yogurt are also used. Prebiotics, in turn, are found in supplemental formulations of processed foods and in functional foods that are also sources of phenolic compounds, such as flavonoids, antioxidant and anti-inflammatory substances, polyunsaturated fatty acids, vitamins, and minerals. In this review, we will discuss the relationship between an imbalance in the intestinal microbiota with the development of diseases, besides indicating the need for future studies that can establish bacterial parameters for the gastrointestinal tract by modulating the intestinal microbiota, associated with the adoption of healthy habits during all life cycles.
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Affiliation(s)
- Rosângela Dos Santos Ferreira
- S-Inova Biotech, Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Camila Fontoura Acosta Ribeiro
- S-Inova Biotech, Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Natali Camposano Calças
- S-Inova Biotech, Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Rita de Cássia Avellaneda Guimarães
- Post Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Valter Aragão do Nascimento
- Post Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Karine de Cássia Freitas Gielow
- Post Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Alinne Pereira de Castro
- S-Inova Biotech, Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Octávio Luiz Franco
- S-Inova Biotech, Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil.,Center of Proteomic and Biochemical Analysis, Post Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasilia, Brasilia, Distrito Federal, Brazil
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54
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Rapid Enhancer Remodeling and Transcription Factor Repurposing Enable High Magnitude Gene Induction upon Acute Activation of NK Cells. Immunity 2020; 53:745-758.e4. [PMID: 33010223 DOI: 10.1016/j.immuni.2020.09.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 05/08/2020] [Accepted: 09/11/2020] [Indexed: 12/24/2022]
Abstract
Innate immune responses rely on rapid and precise gene regulation mediated by accessibility of regulatory regions to transcription factors (TFs). In natural killer (NK) cells and other innate lymphoid cells, competent enhancers are primed during lineage acquisition, and formation of de novo enhancers characterizes the acquisition of innate memory in activated NK cells and macrophages. Here, we investigated how primed and de novo enhancers coordinate to facilitate high-magnitude gene induction during acute activation. Epigenomic and transcriptomic analyses of regions near highly induced genes (HIGs) in NK cells both in vitro and in a model of Toxoplasma gondii infection revealed de novo chromatin accessibility and enhancer remodeling controlled by signal-regulated TFs STATs. Acute NK cell activation redeployed the lineage-determining TF T-bet to de novo enhancers, independent of DNA-sequence-specific motif recognition. Thus, acute stimulation reshapes enhancer function through the combinatorial usage and repurposing of both lineage-determining and signal-regulated TFs to ensure an effective response.
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55
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Singh A, Kazer SW, Roider J, Krista KC, Millar J, Asowata OE, Ngoepe A, Ramsuran D, Fardoos R, Ardain A, Muenchhoff M, Kuhn W, Karim F, Ndung'u T, Shalek AK, Goulder P, Leslie A, Kløverpris HN. Innate Lymphoid Cell Activation and Sustained Depletion in Blood and Tissue of Children Infected with HIV from Birth Despite Antiretroviral Therapy. Cell Rep 2020; 32:108153. [PMID: 32937142 PMCID: PMC7495043 DOI: 10.1016/j.celrep.2020.108153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/14/2020] [Accepted: 08/25/2020] [Indexed: 12/04/2022] Open
Abstract
Innate lymphoid cells (ILCs) are important for response to infection and for immune development in early life. HIV infection in adults depletes circulating ILCs, but the impact on children infected from birth remains unknown. We study vertically HIV-infected children from birth to adulthood and find severe and persistent depletion of all circulating ILCs that, unlike CD4+ T cells, are not restored by long-term antiretroviral therapy unless initiated at birth. Remaining ILCs upregulate genes associated with cellular activation and metabolic perturbation. Unlike HIV-infected adults, ILCs are also profoundly depleted in tonsils of vertically infected children. Transcriptional profiling of remaining ILCs reveals ongoing cell-type-specific activity despite antiretroviral therapy. Collectively, these data suggest an important and ongoing role for ILCs in lymphoid tissue of HIV-infected children from birth, where persistent depletion and sustained transcriptional activity are likely to have long-term immune consequences that merit further investigation.
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Affiliation(s)
- Alveera Singh
- Africa Health Research Institute (AHRI), Durban 4001, South Africa
| | - Samuel W Kazer
- Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139
| | - Julia Roider
- Africa Health Research Institute (AHRI), Durban 4001, South Africa; Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Rd, Oxford OX1 3SY, UK; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa; Medizinische Klinik IV, Department of Infectious Diseases, Ludwig-Maximilians-University, Munich 80802, Germany
| | - Kami C Krista
- Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139
| | - Jane Millar
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Rd, Oxford OX1 3SY, UK; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | | | - Abigail Ngoepe
- Africa Health Research Institute (AHRI), Durban 4001, South Africa
| | - Duran Ramsuran
- Africa Health Research Institute (AHRI), Durban 4001, South Africa
| | - Rabiah Fardoos
- Africa Health Research Institute (AHRI), Durban 4001, South Africa; Department of Immunology and Microbiology, University of Copenhagen, Copenhagen 2200N, Denmark
| | - Amanda Ardain
- Africa Health Research Institute (AHRI), Durban 4001, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Maximilian Muenchhoff
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Rd, Oxford OX1 3SY, UK; Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich 81377, Germany; German Center for Infection Research (DZIF), partner site Munich 80333, Germany
| | - Warren Kuhn
- ENT Department General Justice Gizenga Mpanza Regional Hospital (Stanger Hospital), University of KwaZulu-Natal, Durban 4001, South Africa
| | - Farina Karim
- Africa Health Research Institute (AHRI), Durban 4001, South Africa
| | - Thumbi Ndung'u
- Africa Health Research Institute (AHRI), Durban 4001, South Africa; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa; University College London, Division of Infection and Immunity, London WC1E 6AE, UK; Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Alex K Shalek
- Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139
| | - Philip Goulder
- Africa Health Research Institute (AHRI), Durban 4001, South Africa; Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Rd, Oxford OX1 3SY, UK; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Alasdair Leslie
- Africa Health Research Institute (AHRI), Durban 4001, South Africa; University College London, Division of Infection and Immunity, London WC1E 6AE, UK; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Henrik N Kløverpris
- Africa Health Research Institute (AHRI), Durban 4001, South Africa; Department of Immunology and Microbiology, University of Copenhagen, Copenhagen 2200N, Denmark; University College London, Division of Infection and Immunity, London WC1E 6AE, UK; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
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56
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Meininger I, Carrasco A, Rao A, Soini T, Kokkinou E, Mjösberg J. Tissue-Specific Features of Innate Lymphoid Cells. Trends Immunol 2020; 41:902-917. [PMID: 32917510 DOI: 10.1016/j.it.2020.08.009] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023]
Abstract
Although the function of the circulating immune cell compartment has been studied in detail for decades, limitations in terms of access and cell yields from peripheral tissues have restricted our understanding of tissue-based immunity, particularly in humans. Recent advances in high-throughput protein analyses, transcriptional profiling, and epigenetics have partially overcome these obstacles. Innate lymphoid cells (ILCs) are predominantly tissue-resident, and accumulating data indicate that they have significant tissue-specific functions. We summarize current knowledge of ILC phenotypes in various tissues in mice and humans, aiming to clarify ILC immunity in distinct anatomical locations.
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Affiliation(s)
- Isabel Meininger
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Carrasco
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Rao
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tea Soini
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Efthymia Kokkinou
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.
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57
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Nagel S, Pommerenke C, MacLeod RAF, Meyer C, Kaufmann M, Drexler HG. The NKL-code for innate lymphoid cells reveals deregulated expression of NKL homeobox genes HHEX and HLX in anaplastic large cell lymphoma (ALCL). Oncotarget 2020; 11:3208-3226. [PMID: 32922661 PMCID: PMC7456612 DOI: 10.18632/oncotarget.27683] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/07/2020] [Indexed: 12/26/2022] Open
Abstract
NKL homeobox genes encode developmental transcription factors and display an NKL-code according to their physiological expression pattern in hematopoiesis. Here, we analyzed public transcriptome data from primary innate lymphoid cells (ILCs) for NKL homeobox gene activities and found that ILC3 expressed exclusively HHEX while in ILC1 and ILC2 these genes were silenced. Deregulation of the NKL-code promotes hematopoietic malignancies, including anaplastic large cell lymphoma (ALCL) which reportedly may derive from ILC3. Accordingly, we analyzed NKL homeobox gene activities in ALCL cell lines and investigated their role in this malignancy. Transcriptome analyses demonstrated low expression levels of HHEX but powerfully activated HLX. Forced expression of HHEX in ALCL cell lines induced genes involved in apoptosis and ILC3 differentiation, indicating tumor suppressor activity. ALCL associated NPM1-ALK and JAK-STAT3-signalling drove enhanced expression of HLX while discounting HHEX. Genomic profiling revealed copy number gains at the loci of HLX and STAT3 in addition to genes encoding both STAT3 regulators (AURKA, BCL3, JAK3, KPNB1, NAMPT, NFAT5, PIM3, ROCK1, SIX1, TPX2, WWOX) and targets (BATF3, IRF4, miR135b, miR21, RORC). Transcriptome data of ALCL cell lines showed absence of STAT3 mutations while MGA was mutated and downregulated, encoding a novel potential STAT3 repressor. Furthermore, enhanced IL17F-signalling activated HLX while TGFbeta-signalling inhibited HHEX expression. Taken together, our data extend the scope of the NKL-code for ILCs and spotlight aberrant expression of NKL homeobox gene HLX in ALCL. HLX represents a direct target of ALCL hallmark factor STAT3 and deregulates cell survival and differentiation in this malignancy.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A F MacLeod
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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58
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Wang Q, Robinette ML, Billon C, Collins PL, Bando JK, Fachi JL, Sécca C, Porter SI, Saini A, Gilfillan S, Solt LA, Musiek ES, Oltz EM, Burris TP, Colonna M. Circadian rhythm-dependent and circadian rhythm-independent impacts of the molecular clock on type 3 innate lymphoid cells. Sci Immunol 2020; 4:4/40/eaay7501. [PMID: 31586012 DOI: 10.1126/sciimmunol.aay7501] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/29/2019] [Indexed: 11/02/2022]
Abstract
Many gut functions are attuned to circadian rhythm. Intestinal group 3 innate lymphoid cells (ILC3s) include NKp46+ and NKp46- subsets, which are RORγt dependent and provide mucosal defense through secretion of interleukin-22 (IL-22) and IL-17. Because ILC3s highly express some key circadian clock genes, we investigated whether ILC3s are also attuned to circadian rhythm. We noted circadian oscillations in the expression of clock and cytokine genes, such as REV-ERBα, IL-22, and IL-17, whereas acute disruption of the circadian rhythm affected cytokine secretion by ILC3s. Because of prominent and rhythmic expression of REV-ERBα in ILC3s, we also investigated the impact of constitutive deletion of REV-ERBα, which has been previously shown to inhibit the expression of a RORγt repressor, NFIL3, while also directly antagonizing DNA binding of RORγt. Development of the NKp46+ ILC3 subset was markedly impaired, with reduced cell numbers, RORγt expression, and IL-22 production in REV-ERBα-deficient mice. The NKp46- ILC3 subsets developed normally, potentially due to compensatory expression of other clock genes, but IL-17 secretion paradoxically increased, probably because RORγt was not antagonized by REV-ERBα. We conclude that ILC3s are attuned to circadian rhythm, but clock regulator REV-ERBα also has circadian-independent impacts on ILC3 development and functions due to its roles in the regulation of RORγt.
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Affiliation(s)
- Qianli Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michelle L Robinette
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cyrielle Billon
- Center for Clinical Pharmacology, Washington University School of Medicine and St. Louis College of Pharmacy, St. Louis, MO 63110, USA
| | - Patrick L Collins
- Department of Microbial Infection and Immunity, Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Jennifer K Bando
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - José Luís Fachi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP 13083-862, Brazil
| | - Cristiane Sécca
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sofia I Porter
- Department of Microbial Infection and Immunity, Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Ankita Saini
- Department of Microbial Infection and Immunity, Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Susan Gilfillan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A Solt
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Erik S Musiek
- Hope Center for Neurological Disorders, Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Thomas P Burris
- Center for Clinical Pharmacology, Washington University School of Medicine and St. Louis College of Pharmacy, St. Louis, MO 63110, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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59
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DNA double-strand breaks induce H2Ax phosphorylation domains in a contact-dependent manner. Nat Commun 2020; 11:3158. [PMID: 32572033 PMCID: PMC7308414 DOI: 10.1038/s41467-020-16926-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/29/2020] [Indexed: 01/20/2023] Open
Abstract
Efficient repair of DNA double-strand breaks (DSBs) requires a coordinated DNA Damage Response (DDR), which includes phosphorylation of histone H2Ax, forming γH2Ax. This histone modification spreads beyond the DSB into neighboring chromatin, generating a DDR platform that protects against end disassociation and degradation, minimizing chromosomal rearrangements. However, mechanisms that determine the breadth and intensity of γH2Ax domains remain unclear. Here, we show that chromosomal contacts of a DSB site are the primary determinants for γH2Ax landscapes. DSBs that disrupt a topological border permit extension of γH2Ax domains into both adjacent compartments. In contrast, DSBs near a border produce highly asymmetric DDR platforms, with γH2Ax nearly absent from one broken end. Collectively, our findings lend insights into a basic DNA repair mechanism and how the precise location of a DSB may influence genome integrity. Formation of γH2Ax serves as a checkpoint for double-strand break (DSB) repair pathways. Here the authors reveal via integrated chromatin analysis that γH2Ax domains are established by chromosomal contacts with the DSB site.
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60
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Zhou S, Li Q, Wu H, Lu Q. The pathogenic role of innate lymphoid cells in autoimmune-related and inflammatory skin diseases. Cell Mol Immunol 2020; 17:335-346. [PMID: 32203190 PMCID: PMC7109064 DOI: 10.1038/s41423-020-0399-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 02/27/2020] [Indexed: 12/31/2022] Open
Abstract
Innate lymphoid cells (ILCs), as an important component of the innate immune system, arise from a common lymphoid progenitor and are located in mucosal barriers and various tissues, including the intestine, skin, lung, and adipose tissue. ILCs are heterogeneous subsets of lymphocytes that have emerging roles in orchestrating immune response and contribute to maintain metabolic homeostasis and regulate tissue inflammation. Currently, more details about the pathways for the development and differentiation of ILCs have largely been elucidated, and cytokine secretion and downstream immune cell responses in disease pathogenesis have been reported. Recent research has identified that several distinct subsets of ILCs at skin barriers are involved in the complex regulatory network in local immunity, potentiating adaptive immunity and the inflammatory response. Of note, additional studies that assess the effects of ILCs are required to better define how ILCs regulate their development and functions and how they interact with other immune cells in autoimmune-related and inflammatory skin disorders. In this review, we will distill recent research progress in ILC biology, abnormal functions and potential pathogenic mechanisms in autoimmune-related skin diseases, including systemic lupus erythematosus (SLE), scleroderma and inflammatory diseases, as well as psoriasis and atopic dermatitis (AD), thereby giving a comprehensive review of the diversity and plasticity of ILCs and their unique functions in disease conditions with the aim to provide new insights into molecular diagnosis and suggest potential value in immunotherapy.
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Affiliation(s)
- Suqing Zhou
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, 139 Middle Renmin Road, Changsha, Hunan, 410011, China
| | - Qianwen Li
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, 139 Middle Renmin Road, Changsha, Hunan, 410011, China
| | - Haijing Wu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, 139 Middle Renmin Road, Changsha, Hunan, 410011, China.
| | - Qianjin Lu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Medical Epigenomics, 139 Middle Renmin Road, Changsha, Hunan, 410011, China.
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62
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Kee BL, Morman RE, Sun M. Transcriptional regulation of natural killer cell development and maturation. Adv Immunol 2020; 146:1-28. [PMID: 32327150 DOI: 10.1016/bs.ai.2020.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Natural killer cells are lymphocytes that respond rapidly to intracellular pathogens or cancer/stressed cells by producing pro-inflammatory cytokines or chemokines and by killing target cells through direct cytolysis. NK cells are distinct from B and T lymphocytes in that they become activated through a series of broadly expressed germ line encoded activating and inhibitory receptors or through the actions of inflammatory cytokines. They are the founding member of the innate lymphoid cell family, which mirror the functions of T lymphocytes, with NK cells being the innate counterpart to CD8 T lymphocytes. Despite the functional relationship between NK cells and CD8 T cells, the mechanisms controlling their specification, differentiation and maturation are distinct, with NK cells emerging from multipotent lymphoid progenitors in the bone marrow under the control of a unique transcriptional program. Over the past few years, substantial progress has been made in understanding the developmental pathways and the factors involved in generating mature and functional NK cells. NK cells have immense therapeutic potential and understanding how to acquire large numbers of functional cells and how to endow them with potent activity to control hematopoietic and non-hematopoietic malignancies and autoimmunity is a major clinical goal. In this review, we examine basic aspects of conventional NK cell development in mice and humans and discuss multiple transcription factors that are known to guide the development of these cells.
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Affiliation(s)
- Barbara L Kee
- Department of Pathology and Committee on Immunology, The University of Chicago, Chicago, IL, United States.
| | - Rosmary E Morman
- Department of Pathology and Committee on Immunology, The University of Chicago, Chicago, IL, United States
| | - Mengxi Sun
- Department of Pathology and Committee on Immunology, The University of Chicago, Chicago, IL, United States
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63
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Ercolano G, Wyss T, Salomé B, Romero P, Trabanelli S, Jandus C. Distinct and shared gene expression for human innate versus adaptive helper lymphoid cells. J Leukoc Biol 2020; 108:723-737. [PMID: 32017245 PMCID: PMC7496918 DOI: 10.1002/jlb.5ma0120-209r] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
Innate lymphoid cells (ILCs) are the latest identified innate immune cell family. Given their similarity in transcription factor expression and cytokine secretion profiles, ILCs have been considered as the innate phenocopy of CD4 Th cells. Here, we explored the transcriptome of circulating human ILC subsets as opposed to CD4 Th cell subsets. We describe transcriptomic differences between total ILCs and total CD4 Th cells, as well as between paired innate and adaptive cell subsets (ILC1 vs. Th1; ILC2 vs. Th2; and ILC3 vs. Th17 cells). In particular, we observed differences in expression of genes involved in cell trafficking such as CCR1, CCR6 and CXCR3, innate activation and inhibitory functions, including CD119, 2B4, TIGIT, and CTLA‐4, and neuropeptide receptors, such as VIPR2. Moreover, we report for the first time on distinct expression of long noncoding RNAs (lncRNAs) in innate vs. adaptive cells, arguing for a potential role of lncRNA in shaping human ILC biology. Altogether, our results point for unique, rather than redundant gene organization in ILCs compared to CD4 Th cells, in regard to kinetics, fine‐tuning and spatial organization of the immune response.
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Affiliation(s)
- Giuseppe Ercolano
- Department of Oncology UNIL CHUV and Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Tania Wyss
- Department of Oncology UNIL CHUV and Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Bérengère Salomé
- Department of Oncology UNIL CHUV and Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Pedro Romero
- Department of Oncology UNIL CHUV, University of Lausanne, Lausanne, Switzerland
| | - Sara Trabanelli
- Department of Oncology UNIL CHUV and Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Camilla Jandus
- Department of Oncology UNIL CHUV and Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
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64
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An Z, Flores-Borja F, Irshad S, Deng J, Ng T. Pleiotropic Role and Bidirectional Immunomodulation of Innate Lymphoid Cells in Cancer. Front Immunol 2020; 10:3111. [PMID: 32117199 PMCID: PMC7010811 DOI: 10.3389/fimmu.2019.03111] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/20/2019] [Indexed: 12/20/2022] Open
Abstract
Innate lymphoid cells (ILCs) are largely tissue resident and respond rapidly toward the environmental signals from surrounding tissues and other immune cells. The pleiotropic function of ILCs in diverse contexts underpins its importance in the innate arm of immune system in human health and disease. ILCs derive from common lymphoid progenitors but lack adaptive antigen receptors and functionally act as the innate counterpart to T-cell subsets. The classification of different subtypes is based on their distinct transcription factor requirement for development as well as signature cytokines that they produce. The discovery and subsequent characterization of ILCs over the past decade have mainly focused on the regulation of inflammation, tissue remodeling, and homeostasis, whereas the understanding of the multiple roles and mechanisms of ILCs in cancer is still limited. Emerging evidence of the potent immunomodulatory properties of ILCs in early host defense signifies a major advance in the use of ILCs as promising targets in cancer immunotherapy. In this review, we will decipher the non-exclusive roles of ILCs associated with both protumor and antitumor activities. We will also dissect the heterogeneity, plasticity, genetic evidence, and dysregulation in different cancer contexts, providing a comprehensive understanding of the complexity and diversity. These will have implications for the therapeutic targeting in cancer.
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Affiliation(s)
- Zhengwen An
- KCL Breast Cancer Now Research Unit, Guys Cancer Centre, King's College London, London, United Kingdom
| | - Fabian Flores-Borja
- Centre for Immunobiology and Regenerative Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Sheeba Irshad
- KCL Breast Cancer Now Research Unit, Guys Cancer Centre, King's College London, London, United Kingdom
| | - Jinhai Deng
- Richard Dimbleby Department of Cancer Research, Comprehensive Cancer Centre, Kings College London, London, United Kingdom
| | - Tony Ng
- KCL Breast Cancer Now Research Unit, Guys Cancer Centre, King's College London, London, United Kingdom
- Richard Dimbleby Department of Cancer Research, Comprehensive Cancer Centre, Kings College London, London, United Kingdom
- UCL Cancer Institute, University College London, London, United Kingdom
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65
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de la Calle-Fabregat C, Morante-Palacios O, Ballestar E. Understanding the Relevance of DNA Methylation Changes in Immune Differentiation and Disease. Genes (Basel) 2020; 11:E110. [PMID: 31963661 PMCID: PMC7017047 DOI: 10.3390/genes11010110] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Immune cells are one of the most complex and diverse systems in the human organism. Such diversity implies an intricate network of different cell types and interactions that are dependently interconnected. The processes by which different cell types differentiate from progenitors, mature, and finally exert their function requires an orchestrated succession of molecular processes that determine cell phenotype and function. The acquisition of these phenotypes is highly dependent on the establishment of unique epigenetic profiles that confer identity and function on the various types of effector cells. These epigenetic mechanisms integrate microenvironmental cues into the genome to establish specific transcriptional programs. Epigenetic modifications bridge environment and genome regulation and play a role in human diseases by their ability to modulate physiological programs through external stimuli. DNA methylation is one of the most ubiquitous, stable, and widely studied epigenetic modifications. Recent technological advances have facilitated the generation of a vast amount of genome-wide DNA methylation data, providing profound insights into the roles of DNA methylation in health and disease. This review considers the relevance of DNA methylation to immune system cellular development and function, as well as the participation of DNA methylation defects in immune-mediated pathologies, illustrated by selected paradigmatic diseases.
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Affiliation(s)
| | | | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain; (C.d.l.C.-F.); (O.M.-P.)
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66
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Zhong C, Zheng M, Cui K, Martins AJ, Hu G, Li D, Tessarollo L, Kozlov S, Keller JR, Tsang JS, Zhao K, Zhu J. Differential Expression of the Transcription Factor GATA3 Specifies Lineage and Functions of Innate Lymphoid Cells. Immunity 2020; 52:83-95.e4. [PMID: 31882362 PMCID: PMC6962539 DOI: 10.1016/j.immuni.2019.12.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/18/2019] [Accepted: 12/03/2019] [Indexed: 01/06/2023]
Abstract
Lymphoid tissue inducer (LTi) cells are regarded as a subset of innate lymphoid cells (ILCs). However, these cells are not derived from the ILC common progenitor, which generates other ILC subsets and is defined by the expression of the transcription factor PLZF. Here, we examined transcription factor(s) determining the fate of LTi progenitors versus non-LTi ILC progenitors. Conditional deletion of Gata3 resulted in the loss of PLZF+ non-LTi progenitors but not the LTi progenitors that expressed the transcription factor RORγt. Consistently, PLZF+ non-LTi progenitors expressed high amounts of GATA3, whereas GATA3 expression was low in RORγt+ LTi progenitors. The generation of both progenitors required the transcriptional regulator Id2, which defines the common helper-like innate lymphoid progenitor (ChILP), but not cytokine signaling. Nevertheless, low GATA3 expression was necessary for the generation of functionally mature LTi cells. Thus, differential expression of GATA3 determines the fates and functions of distinct ILC progenitors.
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Affiliation(s)
- Chao Zhong
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Systems Biomedicine, Department of Immunology, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, PRC.
| | - Mingzhu Zheng
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kairong Cui
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Martins
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gangqing Hu
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Microbiology, Immunology, and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Dan Li
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, PRC; Department of Clinical Laboratory, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, PRC
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, NCI, Frederick, MD 21702, USA
| | - Serguei Kozlov
- Center for Advanced Preclinical Research, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jonathan R Keller
- Mouse Cancer Genetics Program, Center for Cancer Research, NCI, Frederick, MD 21702, USA; Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - John S Tsang
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinfang Zhu
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Berrett H, Qian L, Roman O, Cordova A, Simmons A, Sun XH, Alberola-Ila J. Development of Type 2 Innate Lymphoid Cells Is Selectively Inhibited by Sustained E Protein Activity. Immunohorizons 2019; 3:593-605. [PMID: 31852728 PMCID: PMC6938226 DOI: 10.4049/immunohorizons.1900045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/02/2019] [Indexed: 11/25/2022] Open
Abstract
Innate lymphoid cells (ILCs) are tissue-resident lymphoid cells that reside mostly at barrier surfaces and participate in the initial response against pathogens. They are classified into different types based on effector programs that are based on cytokine production and transcription factor expression. They all derive from the common lymphoid precursor, but the molecular mechanisms regulating ILC subset development is not well understood. Experiments using Id2 knockout mice have previously shown that E protein activity inhibition is an absolute requirement for the development of all ILC subsets. In this study, we use a genetic approach to demonstrate that small increases in E protein activity during ILC development selectively inhibit type 2 ILC development. Type 1 ILCs are mostly unperturbed, and type 3 ILC show only a minor inhibition. This effect is first evident at the ILC2 progenitor stage and is ILC intrinsic. Therefore, our results demonstrate that modulation of E protein activity can bias cell fate decisions in developing ILCs.
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Affiliation(s)
- Hannah Berrett
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104; and.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Liangyue Qian
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104; and
| | - Olga Roman
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104; and
| | - Alanis Cordova
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104; and
| | - Amie Simmons
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104; and
| | - Xiao-Hong Sun
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104; and.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - José Alberola-Ila
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104; and .,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
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68
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McGinty JW, von Moltke J. A three course menu for ILC and bystander T cell activation. Curr Opin Immunol 2019; 62:15-21. [PMID: 31830683 DOI: 10.1016/j.coi.2019.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023]
Abstract
The varied list of agonists that activate innate lymphoid cells (ILCs) continues to grow, but whether and how these signals interact is not well defined, especially in vivo. ILC subsets share master transcription factors, chromatin landscapes, and effector cytokines with their corresponding T helper (Th) cell subsets. Here we discuss how studies of these two cell types can inform each other. Specifically, we outline a framework in which ILC agonists are grouped by the transcription factors they activate. Optimal ILC activation requires at least three items from a 'menu' of non-redundant signals that collectively replicate the STAT and TCR signaling that drives effector Th cell function. This conceptual model may also apply to TCR-independent 'bystander' activation of Th cells.
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Affiliation(s)
- John W McGinty
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Jakob von Moltke
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, 98109, USA.
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69
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Abstract
In this review, Rothenburg discusses the gene regulatory network and chromatin-based kinetic constraints that determine activities of transcription factors in the primary establishment of T-cell identity. T-cell development in mammals is a model for lineage choice and differentiation from multipotent stem cells. Although T-cell fate choice is promoted by signaling in the thymus through one dominant pathway, the Notch pathway, it entails a complex set of gene regulatory network and chromatin state changes even before the cells begin to express their signature feature, the clonal-specific T-cell receptors (TCRs) for antigen. This review distinguishes three developmental modules for T-cell development, which correspond to cell type specification, TCR expression and selection, and the assignment of cells to different effector types. The first is based on transcriptional regulatory network events, the second is dominated by somatic gene rearrangement and mutation and cell selection, and the third corresponds to establishing a poised state of latent regulator priming through an unknown mechanism. Interestingly, in different lineages, the third module can be deployed at variable times relative to the completion of the first two modules. This review focuses on the gene regulatory network and chromatin-based kinetic constraints that determine activities of transcription factors TCF1, GATA3, PU.1, Bcl11b, Runx1, and E proteins in the primary establishment of T-cell identity.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
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70
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Di Luccia B, Gilfillan S, Cella M, Colonna M, Huang SCC. ILC3s integrate glycolysis and mitochondrial production of reactive oxygen species to fulfill activation demands. J Exp Med 2019; 216:2231-2241. [PMID: 31296736 PMCID: PMC6781001 DOI: 10.1084/jem.20180549] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/12/2019] [Accepted: 06/19/2019] [Indexed: 12/29/2022] Open
Abstract
Group 3 innate lymphoid cells (ILC3s) are the innate counterparts of Th17 that require the transcription factor RORγt for development and contribute to the defense against pathogens through IL-22 and IL-17 secretion. Proliferation and effector functions of Th17 require a specific mTOR-dependent metabolic program that utilizes high-rate glycolysis, while mitochondrial lipid oxidation and production of reactive oxygen species (mROS) support alternative T reg cell differentiation. Whether ILC3s employ a specific metabolic program is not known. Here, we find that ILC3s rely on mTOR complex 1 (mTORC1) for proliferation and production of IL-22 and IL-17A after in vitro activation and Citrobacter rodentium infection. mTORC1 induces activation of HIF1α, which reprograms ILC3 metabolism toward glycolysis and sustained expression of RORγt. However, in contrast to Th17, ILC3 activation requires mROS production; rather than inducing an alternative regulatory fate as it does in CD4 T cells, mROS stabilizes HIF1α and RORγt in ILC3s and thereby promotes their activation. We conclude that ILC3 activation relies on a metabolic program that integrates glycolysis with mROS production.
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Affiliation(s)
- Blanda Di Luccia
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Susan Gilfillan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Stanley Ching-Cheng Huang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH
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71
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Riggan L, Freud AG, O'Sullivan TE. True Detective: Unraveling Group 1 Innate Lymphocyte Heterogeneity. Trends Immunol 2019; 40:909-921. [PMID: 31500958 DOI: 10.1016/j.it.2019.08.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 01/26/2023]
Abstract
Innate lymphoid cells (ILCs) consist of a heterogeneous family of lymphocytes that regulate tissue homeostasis and can contribute to pathology in mice and humans. Mammalian group 1 ILCs are defined by the production of interferon (IFN)-γ and the functional dependence on the transcription factor T-bet. While recent studies demonstrate that group 1 ILCs consist of circulating mature natural killer (NK) cells and tissue-resident ILC1s, the functional, phenotypic, and developmental properties that distinguish these two cell lineages are often confusing and difficult to dissect. In this review, we critically evaluate the current knowledge of mammalian group 1 ILC heterogeneity and propose new inclusive nomenclature to clarify the roles of ILC1s and NK cells during homeostasis and disease.
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Affiliation(s)
- Luke Riggan
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 900953, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aharon G Freud
- Department of Pathology, Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Timothy E O'Sullivan
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 900953, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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72
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Hawiger J, Zienkiewicz J. Decoding inflammation, its causes, genomic responses, and emerging countermeasures. Scand J Immunol 2019; 90:e12812. [PMID: 31378956 PMCID: PMC6883124 DOI: 10.1111/sji.12812] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/03/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022]
Abstract
Inflammation is the mechanism of diseases caused by microbial, autoimmune, allergic, metabolic and physical insults that produce distinct types of inflammatory responses. This aetiologic view of inflammation informs its classification based on a cause‐dependent mechanism as well as a cause‐directed therapy and prevention. The genomic era ushered in a new understanding of inflammation by highlighting the cell's nucleus as the centre of the inflammatory response. Exogenous or endogenous inflammatory insults evoke genomic responses in immune and non‐immune cells. These genomic responses depend on transcription factors, which switch on and off a myriad of inflammatory genes through their regulatory networks. We discuss the transcriptional paradigm of inflammation based on denying transcription factors’ access to the nucleus. We present two approaches that control proinflammatory signalling to the nucleus. The first approach constitutes a novel intracellular protein therapy with bioengineered physiologic suppressors of cytokine signalling. The second approach entails control of proinflammatory transcriptional cascades by targeting nuclear transport with a cell‐penetrating peptide that inhibits the expression of 23 out of the 26 mediators of inflammation along with the nine genes required for metabolic responses. We compare these emerging anti‐inflammatory countermeasures to current therapies. The transcriptional paradigm of inflammation offers nucleocentric strategies for microbial, autoimmune, metabolic, physical and other types of inflammation afflicting millions of people worldwide.
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Affiliation(s)
- Jacek Hawiger
- Immunotherapy Program at Vanderbilt University School of Medicine, Nashville, TN, USA.,Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Veterans Affairs, Tennessee Valley Health Care System, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jozef Zienkiewicz
- Immunotherapy Program at Vanderbilt University School of Medicine, Nashville, TN, USA.,Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Veterans Affairs, Tennessee Valley Health Care System, Nashville, TN, USA
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73
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Cella M, Gamini R, Sécca C, Collins PL, Zhao S, Peng V, Robinette ML, Schettini J, Zaitsev K, Gordon W, Bando JK, Yomogida K, Cortez V, Fronick C, Fulton R, Lin LL, Gilfillan S, Flavell RA, Shan L, Artyomov MN, Bowman M, Oltz EM, Jelinsky SA, Colonna M. Subsets of ILC3-ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues. Nat Immunol 2019; 20:980-991. [PMID: 31209406 PMCID: PMC6685551 DOI: 10.1038/s41590-019-0425-y] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 05/15/2019] [Indexed: 12/19/2022]
Abstract
Innate lymphoid cells (ILCs) are tissue-resident lymphocytes categorized on the basis of their core regulatory programs and the expression of signature cytokines. Human ILC3s that produce the cytokine interleukin-22 convert into ILC1-like cells that produce interferon-γ in vitro, but whether this conversion occurs in vivo remains unclear. In the present study we found that ILC3s and ILC1s in human tonsils represented the ends of a spectrum that included additional discrete subsets. RNA velocity analysis identified an intermediate ILC3-ILC1 cluster, which had strong directionality toward ILC1s. In humanized mice, the acquisition of ILC1 features by ILC3s showed tissue dependency. Chromatin studies indicated that the transcription factors Aiolos and T-bet cooperated to repress regulatory elements active in ILC3s. A transitional ILC3-ILC1 population was also detected in the human intestine. We conclude that ILC3s undergo conversion into ILC1-like cells in human tissues in vivo, and that tissue factors and Aiolos were required for this process.
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Affiliation(s)
- Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- These authors contributed equally
| | - Ramya Gamini
- Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
- These authors contributed equally
| | - Cristiane Sécca
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Patrick L. Collins
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Present address: Department of Microbial Infection and Immunity, Ohio State University, Wexner School of Medicine, Columbus, OH 43210, USA
| | - Shanrong Zhao
- Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Vincent Peng
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Michelle L. Robinette
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Present address: Brigham and Women’s Hospital, Harvard Medical School, Boston MA 02115, USA
| | - Jorge Schettini
- Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Konstantin Zaitsev
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Present Address: Computer Technologies Department, ITMO University, St. Petersburg, Russia
| | - William Gordon
- Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
- Present address: Cogen Therapeutics, Cambridge MA 02139, USA
| | - Jennifer K. Bando
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Kentaro Yomogida
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Victor Cortez
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Present address: Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
| | - Catrina Fronick
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert Fulton
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Lih-Ling Lin
- Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
- Present address: Immunology and Inflammation, Sanofi, Cambridge MA 02139, USA
| | - Susan Gilfillan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Richard A. Flavell
- Department of Immunobiology Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Liang Shan
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N. Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Michael Bowman
- Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
- Present address: Immunology and Inflammation, Sanofi, Cambridge MA 02139, USA
| | - Eugene M. Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Present address: Department of Microbial Infection and Immunity, Ohio State University, Wexner School of Medicine, Columbus, OH 43210, USA
| | - Scott A. Jelinsky
- Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
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Pokrovskii M, Hall JA, Ochayon DE, Yi R, Chaimowitz NS, Seelamneni H, Carriero N, Watters A, Waggoner SN, Littman DR, Bonneau R, Miraldi ER. Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells. Immunity 2019; 51:185-197.e6. [PMID: 31278058 PMCID: PMC6863506 DOI: 10.1016/j.immuni.2019.06.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/12/2019] [Accepted: 06/04/2019] [Indexed: 12/14/2022]
Abstract
Innate lymphoid cells (ILCs) promote tissue homeostasis and immune defense but also contribute to inflammatory diseases. ILCs exhibit phenotypic and functional plasticity in response to environmental stimuli, yet the transcriptional regulatory networks (TRNs) that control ILC function are largely unknown. Here, we integrate gene expression and chromatin accessibility data to infer regulatory interactions between transcription factors (TFs) and genes within intestinal type 1, 2, and 3 ILC subsets. We predicted the "core" TFs driving ILC identities, organized TFs into cooperative modules controlling distinct gene programs, and validated roles for c-MAF and BCL6 as regulators affecting type 1 and type 3 ILC lineages. The ILC network revealed alternative-lineage-gene repression, a mechanism that may contribute to reported plasticity between ILC subsets. By connecting TFs to genes, the TRNs suggest means to selectively regulate ILC effector functions, while our network approach is broadly applicable to identifying regulators in other in vivo cell populations.
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Affiliation(s)
- Maria Pokrovskii
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Jason A Hall
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - David E Ochayon
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Ren Yi
- Departments of Biology and Computer Science, New York University, NY 10003, USA
| | - Natalia S Chaimowitz
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Harsha Seelamneni
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Nicholas Carriero
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Aaron Watters
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Stephen N Waggoner
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Dan R Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute.
| | - Richard Bonneau
- Departments of Biology and Computer Science, New York University, NY 10003, USA; Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA.
| | - Emily R Miraldi
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Divisions of Immunobiology and Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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75
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STAT3 Genotypic Variant rs744166 and Increased Tyrosine Phosphorylation of STAT3 in IL-23 Responsive Innate Lymphoid Cells during Pathogenesis of Crohn's Disease. J Immunol Res 2019; 2019:9406146. [PMID: 31321245 PMCID: PMC6610725 DOI: 10.1155/2019/9406146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/17/2019] [Accepted: 05/27/2019] [Indexed: 02/08/2023] Open
Abstract
Crohn's disease (CD) results from dysregulated immune responses to gut microbiota in genetically susceptible individuals, affecting multiple areas of the gastrointestinal tract. Innate lymphoid cells (ILCs) are tissue-resident innate effector lymphocytes which play crucial roles in mucosal immune defense, tissue repair, and maintenance of homeostasis. The accumulation of IFN-γ-producing ILC1s and increased level of proinflammatory cytokines produced by ILCs has been observed in the inflamed terminal ileum of CD patients. To date, the precise mechanisms of ILC plasticity and gene regulatory pathways in ILCs remain unclear. Signal transducer and activator of transcription 3 (STAT3) regulates gene expression in a cell-specific, cytokine-dependent manner, involving multiple immune responses. This study proposes the positive correlation between the prevalence of STAT3 rs744166 risky allele "A" with the severity of disease in a cohort of 94 CD patients. In addition, the results suggest an increased STAT3 activity in the inflamed ileum of CD patients, compared to unaffected ileum sections. Notably, IL-23 triggers the differentiation of CD117+NKp44- ILC3s and induces the activation of STAT3 in both CD117+NKp44- and CD117-NKp44- ILC subsets, implying the involvement of STAT3 in the initiation of ILC plasticity. Moreover, carriage of STAT3 "A" risk allele exhibited a higher basal level of STAT3 tyrosine phosphorylation, and an increased IL-23 triggered the pSTAT3 level. We also demonstrated that there was no delayed dephosphorylation of STAT3 in ILCs of both A/A and G/G donors. Overall, the results of this study suggest that IL-23-induced activation of STAT3 in the CD117-NKp44- ILC1s involves in ILC1-to-ILC3 plasticity and a potential regulatory role of ILC1 function. Those genetically susceptible individuals carried STAT3 rs744166 risky allele appear to have higher basal and cytokine-stimulated activation of STAT3 signal, leading to prolonged inflammation and chronic relapse.
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76
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Vivier E, Artis D, Colonna M, Diefenbach A, Di Santo JP, Eberl G, Koyasu S, Locksley RM, McKenzie ANJ, Mebius RE, Powrie F, Spits H. Innate Lymphoid Cells: 10 Years On. Cell 2019; 174:1054-1066. [PMID: 30142344 DOI: 10.1016/j.cell.2018.07.017] [Citation(s) in RCA: 1319] [Impact Index Per Article: 263.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/27/2018] [Accepted: 07/11/2018] [Indexed: 12/20/2022]
Abstract
Innate lymphoid cells (ILCs) are lymphocytes that do not express the type of diversified antigen receptors expressed on T cells and B cells. ILCs are largely tissue-resident cells and are deeply integrated into the fabric of tissues. The discovery and investigation of ILCs over the past decade has changed our perception of immune regulation and how the immune system contributes to the maintenance of tissue homeostasis. We now know that cytokine-producing ILCs contribute to multiple immune pathways by, for example, sustaining appropriate immune responses to commensals and pathogens at mucosal barriers, potentiating adaptive immunity, and regulating tissue inflammation. Critically, the biology of ILCs also extends beyond classical immunology to metabolic homeostasis, tissue remodeling, and dialog with the nervous system. The last 10 years have also contributed to our greater understanding of the transcriptional networks that regulate lymphocyte commitment and delineation. This, in conjunction with the recent advances in our understanding of the influence of local tissue microenvironments on the plasticity and function of ILCs, has led to a re-evaluation of their existing categorization. In this review, we distill the advances in ILC biology over the past decade to refine the nomenclature of ILCs and highlight the importance of ILCs in tissue homeostasis, morphogenesis, metabolism, repair, and regeneration.
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Affiliation(s)
- Eric Vivier
- Innate Pharma Research Labs, Innate Pharma, Marseille, France; Aix Marseille University, CNRS, INSERM, APHM, CIML, Hôpital de la Timone, Immunologie, Marseille-Immunopole, Marseille, France.
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine and Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Andreas Diefenbach
- Laboratory of Innate Immunity, Department of Microbiology and Infection Immunology, Charité - Universitätsmedizin, Berlin, Germany; Berlin Institute of Health, Berlin, Germany; Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum, Berlin, Germany
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, Paris, France; Inserm U1223, Paris, France
| | - Gérard Eberl
- Microenvironment & Immunity Unit, Institut Pasteur, Paris, France; INSERM U1224, Paris, France
| | - Shigeo Koyasu
- Laboratory for Immune Cell Systems, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Richard M Locksley
- HHMI and Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Reina E Mebius
- Department of Molecular Cell Biology and Immunology, Vrije Universiteit Medical Center, Amsterdam, the Netherlands
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Hergen Spits
- Department of Experimental Immunology Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands
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77
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Amariuta T, Luo Y, Gazal S, Davenport EE, van de Geijn B, Ishigaki K, Westra HJ, Teslovich N, Okada Y, Yamamoto K, Price AL, Raychaudhuri S. IMPACT: Genomic Annotation of Cell-State-Specific Regulatory Elements Inferred from the Epigenome of Bound Transcription Factors. Am J Hum Genet 2019; 104:879-895. [PMID: 31006511 PMCID: PMC6506796 DOI: 10.1016/j.ajhg.2019.03.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/14/2019] [Indexed: 12/18/2022] Open
Abstract
Despite significant progress in annotating the genome with experimental methods, much of the regulatory noncoding genome remains poorly defined. Here we assert that regulatory elements may be characterized by leveraging local epigenomic signatures where specific transcription factors (TFs) are bound. To link these two features, we introduce IMPACT, a genome annotation strategy that identifies regulatory elements defined by cell-state-specific TF binding profiles, learned from 515 chromatin and sequence annotations. We validate IMPACT using multiple compelling applications. First, IMPACT distinguishes between bound and unbound TF motif sites with high accuracy (average AUPRC 0.81, SE 0.07; across 8 tested TFs) and outperforms state-of-the-art TF binding prediction methods, MocapG, MocapS, and Virtual ChIP-seq. Second, in eight tested cell types, RNA polymerase II IMPACT annotations capture more cis-eQTL variation than sequence-based annotations, such as promoters and TSS windows (25% average increase in enrichment). Third, integration with rheumatoid arthritis (RA) summary statistics from European (N = 38,242) and East Asian (N = 22,515) populations revealed that the top 5% of CD4+ Treg IMPACT regulatory elements capture 85.7% of RA h2, the most comprehensive explanation for RA h2 to date. In comparison, the average RA h2 captured by compared CD4+ T histone marks is 42.3% and by CD4+ T specifically expressed gene sets is 36.4%. Lastly, we find that IMPACT may be used in many different cell types to identify complex trait associated regulatory elements.
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Affiliation(s)
- Tiffany Amariuta
- Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA; Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Graduate School of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Yang Luo
- Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA; Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven Gazal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Emma E Davenport
- Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA; Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bryce van de Geijn
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kazuyoshi Ishigaki
- Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA; Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Harm-Jan Westra
- Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA; Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Faculty of Medical Sciences, University of Groningen, Groningen, the Netherlands
| | - Nikola Teslovich
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yukinori Okada
- Osaka University Graduate School of Medicine, Osaka, Japan; Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Kazuhiko Yamamoto
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Alkes L Price
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA; Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Graduate School of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA; Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
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78
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Castro-Dopico T, Clatworthy MR. IgG and Fcγ Receptors in Intestinal Immunity and Inflammation. Front Immunol 2019; 10:805. [PMID: 31031776 PMCID: PMC6473071 DOI: 10.3389/fimmu.2019.00805] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
Fcγ receptors (FcγR) are cell surface glycoproteins that mediate cellular effector functions of immunoglobulin G (IgG) antibodies. Genetic variation in FcγR genes can influence susceptibility to a variety of antibody-mediated autoimmune and inflammatory disorders, including systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). More recently, however, genetic studies have implicated altered FcγR signaling in the pathogenesis of inflammatory bowel disease (IBD), a condition classically associated with dysregulated innate and T cell immunity. Specifically, a variant of the activating receptor, FcγRIIA, with low affinity for IgG, confers protection against the development of ulcerative colitis, a subset of IBD, leading to a re-evaluation of the role of IgG and FcγRs in gastrointestinal tract immunity, an organ system traditionally associated with IgA. In this review, we summarize our current understanding of IgG and FcγR function at this unique host-environment interface, from the pathogenesis of colitis and defense against enteropathogens, its contribution to maternal-fetal cross-talk and susceptibility to cancer. Finally, we discuss the therapeutic implications of this information, both in terms of how FcγR signaling pathways may be targeted for the treatment of IBD and how FcγR engagement may influence the efficacy of therapeutic monoclonal antibodies in IBD.
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Affiliation(s)
- Tomas Castro-Dopico
- Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Menna R. Clatworthy
- Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research CentreCambridge, United Kingdom
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
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79
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Belarif L, Danger R, Kermarrec L, Nerrière-Daguin V, Pengam S, Durand T, Mary C, Kerdreux E, Gauttier V, Kucik A, Thepenier V, Martin JC, Chang C, Rahman A, Guen NSL, Braudeau C, Abidi A, David G, Malard F, Takoudju C, Martinet B, Gérard N, Neveu I, Neunlist M, Coron E, MacDonald TT, Desreumaux P, Mai HL, Le Bas-Bernardet S, Mosnier JF, Merad M, Josien R, Brouard S, Soulillou JP, Blancho G, Bourreille A, Naveilhan P, Vanhove B, Poirier N. IL-7 receptor influences anti-TNF responsiveness and T cell gut homing in inflammatory bowel disease. J Clin Invest 2019; 129:1910-1925. [PMID: 30939120 DOI: 10.1172/jci121668] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
It remains unknown what causes inflammatory bowel disease (IBD), including signaling networks perpetuating chronic gastrointestinal inflammation in Crohn's disease (CD) and ulcerative colitis (UC), in humans. According to an analysis of up to 500 patients with IBD and 100 controls, we report that key transcripts of the IL-7 receptor (IL-7R) pathway are accumulated in inflamed colon tissues of severe CD and UC patients not responding to either immunosuppressive/corticosteroid, anti-TNF, or anti-α4β7 therapies. High expression of both IL7R and IL-7R signaling signature in the colon before treatment is strongly associated with nonresponsiveness to anti-TNF therapy. While in mice IL-7 is known to play a role in systemic inflammation, we found that in humans IL-7 also controlled α4β7 integrin expression and imprinted gut-homing specificity on T cells. IL-7R blockade reduced human T cell homing to the gut and colonic inflammation in vivo in humanized mouse models, and altered effector T cells in colon explants from UC patients grown ex vivo. Our findings show that failure of current treatments for CD and UC is strongly associated with an overexpressed IL-7R signaling pathway and point to IL-7R as a relevant therapeutic target and potential biomarker to fill an unmet need in clinical IBD detection and treatment.
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Affiliation(s)
| | - Richard Danger
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire de Nantes (CHU Nantes), Nantes, France
| | - Laetitia Kermarrec
- Institut des Maladies de l'Appareil Digestif (IMAD), The Enteric Nervous System in Gut and Brain Disorders, Université de Nantes, INSERM, Nantes, France
| | - Véronique Nerrière-Daguin
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire de Nantes (CHU Nantes), Nantes, France
| | | | - Tony Durand
- Institut des Maladies de l'Appareil Digestif (IMAD), The Enteric Nervous System in Gut and Brain Disorders, Université de Nantes, INSERM, Nantes, France
| | | | | | | | - Aneta Kucik
- Blizard Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | | | - Jerome C Martin
- Precision Immunology Institute.,Tisch Cancer Institute.,Department of Oncological Sciences
| | - Christie Chang
- Precision Immunology Institute.,Tisch Cancer Institute.,Department of Oncological Sciences
| | - Adeeb Rahman
- Precision Immunology Institute.,Charles Bronfman Institute for Personalized Medicine, and.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nina Salabert-Le Guen
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,CHU Nantes, Laboratoire d'Immunologie, Center for Immuno Monitoring Nantes-Atlantique (CIMNA), Nantes, France.,LabEx Immunograft Oncology (IGO), Nantes, France.,Université de Nantes, Faculté de Médecine, Nantes, France
| | - Cécile Braudeau
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,CHU Nantes, Laboratoire d'Immunologie, Center for Immuno Monitoring Nantes-Atlantique (CIMNA), Nantes, France.,LabEx Immunograft Oncology (IGO), Nantes, France
| | - Ahmed Abidi
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,Université de Tunis El Manar, Laboratoire de génétique, immunologie et pathologies humaines, Faculté des sciences de Tunis, Tunis, Tunisia
| | - Grégoire David
- Institut des Maladies de l'Appareil Digestif (IMAD), The Enteric Nervous System in Gut and Brain Disorders, Université de Nantes, INSERM, Nantes, France
| | - Florent Malard
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France
| | - Celine Takoudju
- Institut des Maladies de l'Appareil Digestif (IMAD), The Enteric Nervous System in Gut and Brain Disorders, Université de Nantes, INSERM, Nantes, France
| | - Bernard Martinet
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire de Nantes (CHU Nantes), Nantes, France
| | - Nathalie Gérard
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire de Nantes (CHU Nantes), Nantes, France
| | - Isabelle Neveu
- Institut des Maladies de l'Appareil Digestif (IMAD), The Enteric Nervous System in Gut and Brain Disorders, Université de Nantes, INSERM, Nantes, France.,CHU Nantes, IMAD, Nantes, France
| | - Michel Neunlist
- Institut des Maladies de l'Appareil Digestif (IMAD), The Enteric Nervous System in Gut and Brain Disorders, Université de Nantes, INSERM, Nantes, France.,CHU Nantes, IMAD, Nantes, France
| | - Emmanuel Coron
- Institut des Maladies de l'Appareil Digestif (IMAD), The Enteric Nervous System in Gut and Brain Disorders, Université de Nantes, INSERM, Nantes, France.,CHU Nantes, IMAD, Nantes, France
| | - Thomas T MacDonald
- Blizard Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Pierre Desreumaux
- Hepato-Gastroenterology Department, Claude Huriez Hospital, University of Lille 2, Lille, France
| | - Hoa-Le Mai
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire de Nantes (CHU Nantes), Nantes, France
| | - Stephanie Le Bas-Bernardet
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire de Nantes (CHU Nantes), Nantes, France
| | - Jean-François Mosnier
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,CHU Nantes, Service d'Anatomie et Cytologie Pathologiques, Nantes, France
| | - Miriam Merad
- Precision Immunology Institute.,Tisch Cancer Institute.,Department of Oncological Sciences.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Régis Josien
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire de Nantes (CHU Nantes), Nantes, France.,CHU Nantes, Laboratoire d'Immunologie, Center for Immuno Monitoring Nantes-Atlantique (CIMNA), Nantes, France.,Université de Nantes, Faculté de Médecine, Nantes, France
| | - Sophie Brouard
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire de Nantes (CHU Nantes), Nantes, France
| | - Jean-Paul Soulillou
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France
| | - Gilles Blancho
- Centre de Recherche en Transplantation et Immunologie (CRTI), UMR 1064, Inserm, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire de Nantes (CHU Nantes), Nantes, France
| | - Arnaud Bourreille
- Institut des Maladies de l'Appareil Digestif (IMAD), The Enteric Nervous System in Gut and Brain Disorders, Université de Nantes, INSERM, Nantes, France.,CHU Nantes, IMAD, Nantes, France
| | - Philippe Naveilhan
- Institut des Maladies de l'Appareil Digestif (IMAD), The Enteric Nervous System in Gut and Brain Disorders, Université de Nantes, INSERM, Nantes, France.,CHU Nantes, IMAD, Nantes, France
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80
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Hagihara Y, Yoshimatsu Y, Mikami Y, Takada Y, Mizuno S, Kanai T. Epigenetic regulation of T helper cells and intestinal pathogenicity. Semin Immunopathol 2019; 41:379-399. [DOI: 10.1007/s00281-019-00732-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/05/2019] [Indexed: 02/06/2023]
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81
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Pulmonary group 2 innate lymphoid cells: surprises and challenges. Mucosal Immunol 2019; 12:299-311. [PMID: 30664706 PMCID: PMC6436699 DOI: 10.1038/s41385-018-0130-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 02/04/2023]
Abstract
Group 2 innate lymphoid cells (ILC2s) are a recently described subset of innate lymphocytes with important immune and homeostatic functions at multiple tissue sites, especially the lung. These cells expand locally after birth and during postnatal lung maturation and are present in the lung and other peripheral organs. They are modified by a variety of processes and mediate inflammatory responses to respiratory pathogens, inhaled allergens and noxious particles. Here, we review the emerging roles of ILC2s in pulmonary homeostasis and discuss recent and surprising advances in our understanding of how hormones, age, neurotransmitters, environmental challenges, and infection influence ILC2s. We also review how these responses may underpin the development, progression and severity of pulmonary inflammation and chronic lung diseases and highlight some of the remaining challenges for ILC2 biology.
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82
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Sagebiel AF, Steinert F, Lunemann S, Körner C, Schreurs RRCE, Altfeld M, Perez D, Reinshagen K, Bunders MJ. Tissue-resident Eomes + NK cells are the major innate lymphoid cell population in human infant intestine. Nat Commun 2019; 10:975. [PMID: 30816112 PMCID: PMC6395753 DOI: 10.1038/s41467-018-08267-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/18/2018] [Indexed: 01/20/2023] Open
Abstract
Innate lymphoid cells (ILC), including natural killer (NK) cells, are implicated in host-defense and tissue-growth. However, the composition and kinetics of NK cells in the intestine during the first year of life, when infants are first broadly exposed to exogenous antigens, are still unclear. Here we show that CD103+ NK cells are the major ILC population in the small intestines of infants. When compared to adult intestinal NK cells, infant intestinal NK cells exhibit a robust effector phenotype, characterized by Eomes, perforin and granzyme B expression, and superior degranulation capacity. Absolute intestinal NK cell numbers decrease gradually during the first year of life, coinciding with an influx of intestinal Eomes+ T cells; by contrast, epithelial NKp44+CD69+ NK cells with less cytotoxic capacity persist in adults. In conclusion, NK cells are abundant in infant intestines, where they can provide effector functions while Eomes+ T cell responses mature. Innate lymphoid cells (ILC), including natural killer (NK) cells, are important innate immune regulators. Here the authors show that, in human infant intestines, CD103+Eomes+ NK cells are the predominant ILC population, but are replaced gradually by Eomes+ T cells, while NKp44+ NK cells persist in adult intestines.
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Affiliation(s)
- Adrian F Sagebiel
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany
| | - Fenja Steinert
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany
| | - Sebastian Lunemann
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany
| | - Christian Körner
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany
| | - Renée R C E Schreurs
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Marcus Altfeld
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany
| | - Daniel Perez
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Konrad Reinshagen
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Madeleine J Bunders
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany. .,Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands. .,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands.
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83
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Cherrier DE, Serafini N, Di Santo JP. Innate Lymphoid Cell Development: A T Cell Perspective. Immunity 2019; 48:1091-1103. [PMID: 29924975 DOI: 10.1016/j.immuni.2018.05.010] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/15/2018] [Accepted: 05/25/2018] [Indexed: 02/08/2023]
Abstract
Innate lymphoid cells (ILCs) and natural killer (NK) cells have garnered considerable interest due to their unique functional properties in immune defense and tissue homeostasis. Our current understanding of how these cells develop has been greatly facilitated by knowledge of T cell biology. Models of T cell differentiation provided the basis for a conceptual classification of these innate effectors and inspired a scheme of their activation and regulation. In this review, we discuss NK cell and ILC development from a "T cell standpoint" in an attempt to extend the analogy between adaptive T cells and their innate ILC and NK cell counterparts.
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Affiliation(s)
- Dylan E Cherrier
- Innate Immunity Unit, Institut Pasteur, Paris 75015, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1223, Paris 75015, France; Université Paris Diderot, Paris 75013, France
| | - Nicolas Serafini
- Innate Immunity Unit, Institut Pasteur, Paris 75015, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1223, Paris 75015, France
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, Paris 75015, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1223, Paris 75015, France.
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84
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Colonna M. Innate Lymphoid Cells: Diversity, Plasticity, and Unique Functions in Immunity. Immunity 2019; 48:1104-1117. [PMID: 29924976 DOI: 10.1016/j.immuni.2018.05.013] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 05/13/2018] [Accepted: 05/30/2018] [Indexed: 01/12/2023]
Abstract
Type 1, 2, and 3 innate lymphoid cells (ILCs) have emerged as tissue-resident innate correlates of T helper 1 (Th1), Th2, and Th17 cells. Recent studies suggest that ILCs are more diverse than originally proposed; this might reflect truly distinct lineages or adaptation of ILCs to disparate tissue microenvironments, known as plasticity. Given that ILCs strikingly resemble T cells, are they redundant? While the regulation, timing, and magnitude of ILC and primary T cell responses differ, tissue-resident memory T cells may render ILCs redundant during secondary responses. The unique impact of ILCs in immunity is probably embodied in the extensive array of surface and intracellular receptors that endow these cells with the ability to distinguish between normal and pathogenic components, interact with other cells, and calibrate their cytokine secretion accordingly. Here I review recent advances in elucidating the diversity of ILCs and discuss their unique and redundant functions.
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Affiliation(s)
- Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA.
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85
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Zook EC, Li ZY, Xu Y, de Pooter RF, Verykokakis M, Beaulieu A, Lasorella A, Maienschein-Cline M, Sun JC, Sigvardsson M, Kee BL. Transcription factor ID2 prevents E proteins from enforcing a naïve T lymphocyte gene program during NK cell development. Sci Immunol 2019; 3:3/22/eaao2139. [PMID: 29703840 DOI: 10.1126/sciimmunol.aao2139] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 01/04/2018] [Accepted: 02/27/2018] [Indexed: 12/14/2022]
Abstract
All innate lymphoid cells (ILCs) require the small helix-loop-helix transcription factor ID2, but the functions of ID2 are not well understood in these cells. We show that mature natural killer (NK) cells, the prototypic ILCs, developed in mice lacking ID2 but remained as precursor CD27+CD11b- cells that failed to differentiate into CD27-CD11b+ cytotoxic effectors. We show that ID2 limited chromatin accessibility at E protein binding sites near naïve T lymphocyte-associated genes including multiple chemokine receptors, cytokine receptors, and signaling molecules and altered the NK cell response to inflammatory cytokines. In the absence of ID2, CD27+CD11b- NK cells expressed ID3, a helix-loop-helix protein associated with naïve T cells, and they transitioned from a CD8 memory precursor-like to a naïve-like chromatin accessibility state. We demonstrate that ID3 was required for the development of ID2-deficient NK cells, indicating that completely unfettered E protein function is incompatible with NK cell development. These data solidify the roles of ID2 and ID3 as mediators of effector and naïve gene programs, respectively, and revealed a critical role for ID2 in promoting a chromatin state and transcriptional program in CD27+CD11b- NK cells that supports cytotoxic effector differentiation and cytokine responses.
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Affiliation(s)
- Erin C Zook
- Department of Pathology and Committee on Immunology, University of Chicago, Chicago, IL 60657, USA
| | - Zhong-Yin Li
- Department of Pathology and Committee on Immunology, University of Chicago, Chicago, IL 60657, USA
| | - Yiying Xu
- Department of Pathology and Committee on Immunology, University of Chicago, Chicago, IL 60657, USA
| | - Renée F de Pooter
- Department of Pathology and Committee on Immunology, University of Chicago, Chicago, IL 60657, USA
| | - Mihalis Verykokakis
- Department of Pathology and Committee on Immunology, University of Chicago, Chicago, IL 60657, USA
| | - Aimee Beaulieu
- Department of Immunology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna Lasorella
- Institute for Cancer Genetics and Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA
| | - Mark Maienschein-Cline
- Core for Research Informatics, Research Resources Center, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Joseph C Sun
- Department of Immunology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Barbara L Kee
- Department of Pathology and Committee on Immunology, University of Chicago, Chicago, IL 60657, USA.
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86
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Collins PL, Cella M, Porter SI, Li S, Gurewitz GL, Hong HS, Johnson RP, Oltz EM, Colonna M. Gene Regulatory Programs Conferring Phenotypic Identities to Human NK Cells. Cell 2019; 176:348-360.e12. [PMID: 30595449 PMCID: PMC6329660 DOI: 10.1016/j.cell.2018.11.045] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/09/2018] [Accepted: 11/28/2018] [Indexed: 01/03/2023]
Abstract
Natural killer (NK) cells develop from common progenitors but diverge into distinct subsets, which differ in cytokine production, cytotoxicity, homing, and memory traits. Given their promise in adoptive cell therapies for cancer, a deeper understanding of regulatory modules controlling clinically beneficial NK phenotypes is of high priority. We report integrated "-omics" analysis of human NK subsets, which revealed super-enhancers associated with gene cohorts that may coordinate NK functions and localization. A transcription factor-based regulatory scheme also emerged, which is evolutionarily conserved and shared by innate and adaptive lymphocytes. For both NK and T lineages, a TCF1-LEF1-MYC axis dominated the regulatory landscape of long-lived, proliferative subsets that traffic to lymph nodes. In contrast, effector populations circulating between blood and peripheral tissues shared a PRDM1-dominant landscape. This resource defines transcriptional modules, regulated by feedback loops, which may be leveraged to enhance phenotypes for NK cell-based therapies.
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Affiliation(s)
- Patrick L Collins
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sofia I Porter
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shasha Li
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Greer L Gurewitz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | | | - R Paul Johnson
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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87
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Colbey C, Cox AJ, Pyne DB, Zhang P, Cripps AW, West NP. Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes. Sports Med 2018; 48:65-77. [PMID: 29363055 PMCID: PMC5790851 DOI: 10.1007/s40279-017-0846-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Upper respiratory symptoms remain the most common illness in athletes. Upper respiratory symptoms during heavy training and competition may impair performance. Preventing illness is the primary reason for the use of supplements, such as probiotics and prebiotics, for maintaining or promoting gut health and immune function. While exercise-induced perturbations in the immune system may increase susceptibility to illness and infection, growing evidence indicates that upper respiratory symptoms are related to a breakdown in the homeostatic regulation of the mucosal immune system of the airways. Balancing protection of the respiratory tract with normal physiological functioning requires dynamic orchestration between a wide array of immune parameters. The intestinal microbiota regulates extra-intestinal immunity via the common mucosal immune system and new evidence implicates the microbiota of the nose, mouth and respiratory tract in upper respiratory symptoms. Omics’ approaches now facilitate comprehensive profiling at the molecular and proteomic levels to reveal new pathways and molecules of immune regulation. New targets may provide for personalised nutritional and training interventions to maintain athlete health.
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Affiliation(s)
- Candice Colbey
- Menzies Health Institute Queensland and School of Medical Science, Griffith University, Griffith Health Gold Coast Campus, Southport, QLD, 4222, Australia
| | - Amanda J Cox
- Menzies Health Institute Queensland and School of Medical Science, Griffith University, Griffith Health Gold Coast Campus, Southport, QLD, 4222, Australia
| | - David B Pyne
- Menzies Health Institute Queensland and School of Medical Science, Griffith University, Griffith Health Gold Coast Campus, Southport, QLD, 4222, Australia
- Faculty of Health, University of Canberra Research Institute for Sport and Exercise, University of Canberra, Canberra, ACT, Australia
- Discipline of Physiology, Australian Institute of Sport, Canberra, ACT, Australia
| | - Ping Zhang
- Menzies Health Institute Queensland and School of Medical Science, Griffith University, Griffith Health Gold Coast Campus, Southport, QLD, 4222, Australia
| | - Allan W Cripps
- Menzies Health Institute Queensland and School of Medical Science, Griffith University, Griffith Health Gold Coast Campus, Southport, QLD, 4222, Australia
| | - Nicholas P West
- Menzies Health Institute Queensland and School of Medical Science, Griffith University, Griffith Health Gold Coast Campus, Southport, QLD, 4222, Australia.
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88
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A conserved enhancer regulates Il9 expression in multiple lineages. Nat Commun 2018; 9:4803. [PMID: 30442929 PMCID: PMC6237898 DOI: 10.1038/s41467-018-07202-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 10/23/2018] [Indexed: 12/12/2022] Open
Abstract
Cytokine genes are regulated by multiple regulatory elements that confer tissue-specific and activation-dependent expression. The cis-regulatory elements of the gene encoding IL-9, a cytokine that promotes allergy, autoimmune inflammation and tumor immunity, have not been defined. Here we identify an enhancer (CNS-25) upstream of the Il9 gene that binds most transcription factors (TFs) that promote Il9 gene expression. Deletion of the enhancer in the mouse germline alters transcription factor binding to the remaining Il9 regulatory elements, and results in diminished IL-9 production in multiple cell types including Th9 cells, and attenuates IL-9-dependent immune responses. Moreover, deletion of the homologous enhancer (CNS-18) in primary human Th9 cultures results in significant decrease of IL-9 production. Thus, Il9 CNS-25/IL9 CNS-18 is a critical and conserved regulatory element for IL-9 production. Interleukin-9 (IL-9) is important for allergy, autoimmunity and tumor immunity, but how its expression is regulated is unclear. Here the authors show the essential function of an enhancer, CNS-25 in mouse and CNS-18 in human, for IL-9 expression, with the deletion of this enhancer severely hampering IL-9 production in mice or human cells.
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89
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Crittenden S, Cheyne A, Adams A, Forster T, Robb CT, Felton J, Ho G, Ruckerl D, Rossi AG, Anderton SM, Ghazal P, Satsangi J, Howie SE, Yao C. Purine metabolism controls innate lymphoid cell function and protects against intestinal injury. Immunol Cell Biol 2018; 96:1049-1059. [PMID: 29758102 PMCID: PMC6248310 DOI: 10.1111/imcb.12167] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 12/31/2022]
Abstract
Inflammatory bowel disease (IBD) is a condition of chronic inflammatory intestinal disorder with increasing prevalence but limited effective therapies. The purine metabolic pathway is involved in various inflammatory processes including IBD. However, the mechanisms through which purine metabolism modulates IBD remain to be established. Here, we found that mucosal expression of genes involved in the purine metabolic pathway is altered in patients with active ulcerative colitis (UC), which is associated with elevated gene expression signatures of the group 3 innate lymphoid cell (ILC3)-interleukin (IL)-22 pathway. In mice, blockade of ectonucleotidases (NTPDases), critical enzymes for purine metabolism by hydrolysis of extracellular adenosine 5'-triphosphate (eATP) into adenosine, exacerbates dextran-sulfate sodium-induced intestinal injury. This exacerbation of colitis is associated with reduction of colonic IL-22-producing ILC3s, which afford essential protection against intestinal inflammation, and is rescued by exogenous IL-22. Mechanistically, activation of ILC3s for IL-22 production is reciprocally mediated by eATP and adenosine. These findings reveal that the NTPDase-mediated balance between eATP and adenosine regulates ILC3 cell function to provide protection against intestinal injury and suggest potential therapeutic strategies for treating IBD by targeting the purine-ILC3 axis.
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Affiliation(s)
- Siobhan Crittenden
- Medical Research Council (MRC) Centre for Inflammation ResearchQueen's Medical Research InstituteThe University of EdinburghEdinburghEH16 4TJUK
| | - Ashleigh Cheyne
- Medical Research Council (MRC) Centre for Inflammation ResearchQueen's Medical Research InstituteThe University of EdinburghEdinburghEH16 4TJUK
| | - Alexander Adams
- Gastrointestinal UnitInstitute of Genetics and Molecular MedicineWestern General HospitalThe University of EdinburghEdinburghEH4 2XUUK
| | - Thorsten Forster
- Division of Pathway MedicineEdinburgh Infectious DiseasesThe University of EdinburghEdinburghEH16 4SBUK
| | - Calum T Robb
- Medical Research Council (MRC) Centre for Inflammation ResearchQueen's Medical Research InstituteThe University of EdinburghEdinburghEH16 4TJUK
| | - Jennifer Felton
- Medical Research Council (MRC) Centre for Inflammation ResearchQueen's Medical Research InstituteThe University of EdinburghEdinburghEH16 4TJUK
| | - Gwo‐Tzer Ho
- Medical Research Council (MRC) Centre for Inflammation ResearchQueen's Medical Research InstituteThe University of EdinburghEdinburghEH16 4TJUK
| | - Dominik Ruckerl
- Faculty of Biology, Medicine and HealthSchool of Biological SciencesThe University of ManchesterManchesterM13 9PTUK
| | - Adriano G Rossi
- Medical Research Council (MRC) Centre for Inflammation ResearchQueen's Medical Research InstituteThe University of EdinburghEdinburghEH16 4TJUK
| | - Stephen M Anderton
- Medical Research Council (MRC) Centre for Inflammation ResearchQueen's Medical Research InstituteThe University of EdinburghEdinburghEH16 4TJUK
| | - Peter Ghazal
- Division of Pathway MedicineEdinburgh Infectious DiseasesThe University of EdinburghEdinburghEH16 4SBUK
- Centre for Synthetic and Systems Biology (SynthSys)The University of EdinburghEdinburghEH9 3JDUK
| | - Jack Satsangi
- Gastrointestinal UnitInstitute of Genetics and Molecular MedicineWestern General HospitalThe University of EdinburghEdinburghEH4 2XUUK
| | - Sarah E Howie
- Medical Research Council (MRC) Centre for Inflammation ResearchQueen's Medical Research InstituteThe University of EdinburghEdinburghEH16 4TJUK
| | - Chengcan Yao
- Medical Research Council (MRC) Centre for Inflammation ResearchQueen's Medical Research InstituteThe University of EdinburghEdinburghEH16 4TJUK
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90
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Cooper MA, Fehniger TA, Colonna M. Is There Natural Killer Cell Memory and Can It Be Harnessed by Vaccination? Vaccination Strategies Based on NK Cell and ILC Memory. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a029512. [PMID: 29254976 DOI: 10.1101/cshperspect.a029512] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Studies over the last decade have decisively shown that innate immune natural killer (NK) cells exhibit enhanced long-lasting functional responses following a single activation event. With the increased recognition of memory and memory-like properties of NK cells, questions have arisen with regard to their ability to effectively mediate vaccination responses in humans. Moreover, recently discovered innate lymphoid cells (ILCs) could also potentially exhibit memory-like functions. Here, we review different forms of NK cell memory, and speculate about the ability of these cells and ILCs to meaningfully contribute to vaccination responses.
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Affiliation(s)
- Megan A Cooper
- Department of Pediatrics, Division of Rheumatology, Washington University School of Medicine, St. Louis, Missouri 63110.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Todd A Fehniger
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110
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91
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Zhu J. T Helper Cell Differentiation, Heterogeneity, and Plasticity. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a030338. [PMID: 28847903 DOI: 10.1101/cshperspect.a030338] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Naïve CD4 T cells, on activation, differentiate into distinct T helper (Th) subsets that produce lineage-specific cytokines. By producing unique sets of cytokines, effector Th subsets play critical roles in orchestrating immune responses to a variety of infections and are involved in the pathogenesis of many inflammatory diseases including autoimmunity, allergy, and asthma. The differentiation of Th cells relies on the strength of T-cell receptor (TCR) signaling and signals triggered by polarizing cytokines that activate and/or up-regulate particular transcription factors. Several lineage-specific master transcription factors dictate Th cell fates and functions. Although these master regulators cross-regulate each other, their expression can be dynamic. Sometimes, they are even coexpressed, resulting in massive Th-cell heterogeneity and plasticity. Similar regulation mediated by these master regulators is also found in innate lymphoid cells (ILCs) that are innate counterparts of Th cells.
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Affiliation(s)
- Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
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92
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Sciumè G. Guest editorial: Innate lymphocytes: Development, homeostasis, and disease. Cytokine Growth Factor Rev 2018; 42:1-4. [PMID: 30219180 DOI: 10.1016/j.cytogfr.2018.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/13/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Giuseppe Sciumè
- Department of Molecular Medicine, Sapienza University of Rome, Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Viale Regina Elena, 291 00161, Rome, Italy.
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93
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Bugide S, Janostiak R, Wajapeyee N. Epigenetic Mechanisms Dictating Eradication of Cancer by Natural Killer Cells. Trends Cancer 2018; 4:553-566. [PMID: 30064663 PMCID: PMC6085095 DOI: 10.1016/j.trecan.2018.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/07/2018] [Accepted: 06/11/2018] [Indexed: 12/27/2022]
Abstract
Natural killer (NK) cells of the innate immune system are the first line of defense against infectious agents and cancer cells. However, only a few mechanisms that regulate eradication of tumors by NK cells have been identified. In this review, we present an account of epigenetic mechanisms that modulate the ability of NK cells to eradicate cancer cells. To date, several drugs that target epigenetic modifiers have shown clinical efficacy in cancer. Therefore, once a given epigenetic modifier is validated as a regulator of NK cell function, it can be targeted for NK cell-based cancer immunotherapies.
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Affiliation(s)
- Suresh Bugide
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Radoslav Janostiak
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Narendra Wajapeyee
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
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94
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Smith NL, Patel RK, Reynaldi A, Grenier JK, Wang J, Watson NB, Nzingha K, Yee Mon KJ, Peng SA, Grimson A, Davenport MP, Rudd BD. Developmental Origin Governs CD8 + T Cell Fate Decisions during Infection. Cell 2018; 174:117-130.e14. [PMID: 29909981 DOI: 10.1016/j.cell.2018.05.029] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/03/2018] [Accepted: 05/11/2018] [Indexed: 12/22/2022]
Abstract
Heterogeneity is a hallmark feature of the adaptive immune system in vertebrates. Following infection, naive T cells differentiate into various subsets of effector and memory T cells, which help to eliminate pathogens and maintain long-term immunity. The current model suggests there is a single lineage of naive T cells that give rise to different populations of effector and memory T cells depending on the type and amounts of stimulation they encounter during infection. Here, we have discovered that multiple sub-populations of cells exist in the naive CD8+ T cell pool that are distinguished by their developmental origin, unique transcriptional profiles, distinct chromatin landscapes, and different kinetics and phenotypes after microbial challenge. These data demonstrate that the naive CD8+ T cell pool is not as homogeneous as previously thought and offers a new framework for explaining the remarkable heterogeneity in the effector and memory T cell subsets that arise after infection.
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Affiliation(s)
- Norah L Smith
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Ravi K Patel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Arnold Reynaldi
- Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW 2052, Australia
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Jocelyn Wang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Neva B Watson
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Kito Nzingha
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Kristel J Yee Mon
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Seth A Peng
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Miles P Davenport
- Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW 2052, Australia
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA.
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95
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Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network. Proc Natl Acad Sci U S A 2018; 114:5800-5807. [PMID: 28584128 DOI: 10.1073/pnas.1610617114] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
T-cell development from hematopoietic progenitors depends on multiple transcription factors, mobilized and modulated by intrathymic Notch signaling. Key aspects of T-cell specification network architecture have been illuminated through recent reports defining roles of transcription factors PU.1, GATA-3, and E2A, their interactions with Notch signaling, and roles of Runx1, TCF-1, and Hes1, providing bases for a comprehensively updated model of the T-cell specification gene regulatory network presented herein. However, the role of lineage commitment factor Bcl11b has been unclear. We use self-organizing maps on 63 RNA-seq datasets from normal and perturbed T-cell development to identify functional targets of Bcl11b during commitment and relate them to other regulomes. We show that both activation and repression target genes can be bound by Bcl11b in vivo, and that Bcl11b effects overlap with E2A-dependent effects. The newly clarified role of Bcl11b distinguishes discrete components of commitment, resolving how innate lymphoid, myeloid, and dendritic, and B-cell fate alternatives are excluded by different mechanisms.
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96
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Abstract
It had been a great honor for me to work with the late Dr. William E. Paul for 17 years in the Laboratory of Immunology (LI) from 1998 until his passing in 2015. He was such a master in the immunology field. Under his outstanding guidance, my research has been focusing on transcriptional regulation of T helper (Th) cell differentiation, especially, on the role of a master transcription factor GATA3 during Th2 cell differentiation. Just as enormous scientific contributions of Dr. Paul (we all call him Bill) to the immunology community are far beyond his serving as the Chief of the LI, GATA3 also plays important roles in different lymphocytes at various developmental stages besides its critical functions in Th2 cells. In this special review dedicated to the memory of Bill, I will summarize the research that I have carried out in Bill's lab working on GATA3 in the context of related studies by other groups in the field of T cell differentiation and innate lymphoid cell (ILC) development. These include the essential role of GATA3 in regulating Th2/ILC2 differentiation/development and their functions, the critical role of GATA3 during the development of T cells and innate lymphoid cells, and dynamic and quantitative expression of GATA3 in controlling lymphocyte homeostasis and functions.
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Affiliation(s)
- Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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97
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Schleussner N, Merkel O, Costanza M, Liang HC, Hummel F, Romagnani C, Durek P, Anagnostopoulos I, Hummel M, Jöhrens K, Niedobitek A, Griffin PR, Piva R, Sczakiel HL, Woessmann W, Damm-Welk C, Hinze C, Stoiber D, Gillissen B, Turner SD, Kaergel E, von Hoff L, Grau M, Lenz G, Dörken B, Scheidereit C, Kenner L, Janz M, Mathas S. The AP-1-BATF and -BATF3 module is essential for growth, survival and TH17/ILC3 skewing of anaplastic large cell lymphoma. Leukemia 2018; 32:1994-2007. [PMID: 29588546 PMCID: PMC6127090 DOI: 10.1038/s41375-018-0045-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 12/20/2017] [Accepted: 01/08/2018] [Indexed: 01/26/2023]
Abstract
Transcription factor AP-1 is constitutively activated and IRF4 drives growth and survival in ALK+ and ALK- anaplastic large cell lymphoma (ALCL). Here we demonstrate high-level BATF and BATF3 expression in ALCL. Both BATFs bind classical AP-1 motifs and interact with in ALCL deregulated AP-1 factors. Together with IRF4, they co-occupy AP-1-IRF composite elements, differentiating ALCL from non-ALCL. Gene-specific inactivation of BATFs, or global AP-1 inhibition results in ALCL growth retardation and/or cell death in vitro and in vivo. Furthermore, the AP-1-BATF module establishes TH17/group 3 innate lymphoid cells (ILC3)-associated gene expression in ALCL cells, including marker genes such as AHR, IL17F, IL22, IL26, IL23R and RORγt. Elevated IL-17A and IL-17F levels were detected in a subset of children and adolescents with ALK+ ALCL. Furthermore, a comprehensive analysis of primary lymphoma data confirms TH17-, and in particular ILC3-skewing in ALCL compared with PTCL. Finally, pharmacological inhibition of RORC as single treatment leads to cell death in ALCL cell lines and, in combination with the ALK inhibitor crizotinib, enforces death induction in ALK+ ALCL. Our data highlight the crucial role of AP-1/BATFs in ALCL and lead to the concept that some ALCL might originate from ILC3.
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Affiliation(s)
- Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Olaf Merkel
- Institute of Clinical Pathology, Medical University of Vienna, Vienna, Austria.,European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
| | - Mariantonia Costanza
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany.,European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
| | - Huan-Chang Liang
- Institute of Clinical Pathology, Medical University of Vienna, Vienna, Austria.,European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
| | - Franziska Hummel
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Chiara Romagnani
- German Rheumatism Research Centre, German Rheumatism Research Centre (DRFZ), A Leibniz Institute, 10117, Berlin, Germany.,Medical Department I, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Pawel Durek
- German Rheumatism Research Centre, German Rheumatism Research Centre (DRFZ), A Leibniz Institute, 10117, Berlin, Germany
| | | | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Korinna Jöhrens
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Antonia Niedobitek
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | | | - Roberto Piva
- Department of Molecular Biotechnology and Health Sciences, Center for Experimental Research and Medical Studies, University of Torino, Torino, Italy
| | - Henrike L Sczakiel
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Wilhelm Woessmann
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK.,NHL-BFM Study Centre and Department of Paediatric Haematology and Oncology, Justus-Liebig-University, Giessen, Germany
| | - Christine Damm-Welk
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK.,NHL-BFM Study Centre and Department of Paediatric Haematology and Oncology, Justus-Liebig-University, Giessen, Germany
| | - Christian Hinze
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Department of Nephrology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Dagmar Stoiber
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria.,Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria
| | - Bernd Gillissen
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Suzanne D Turner
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK.,Department of Pathology, University of Cambridge, Cambridge, CB21QP, UK
| | - Eva Kaergel
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Linda von Hoff
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Michael Grau
- Department of Medicine A, Albert-Schweitzer-Campus 1, University Hospital Münster, 48149, Münster, Germany.,Cluster of Excellence EXC 1003, Cells in Motion, 48149, Münster, Germany
| | - Georg Lenz
- Department of Medicine A, Albert-Schweitzer-Campus 1, University Hospital Münster, 48149, Münster, Germany.,Cluster of Excellence EXC 1003, Cells in Motion, 48149, Münster, Germany
| | - Bernd Dörken
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | | | - Lukas Kenner
- Institute of Clinical Pathology, Medical University of Vienna, Vienna, Austria. .,European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK. .,Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria. .,University of Veterinary Medicine, Vienna, Austria. .,CBmed, Center for Biomarker Research in Medicine, 8010, Graz, Austria.
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany.,Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, 13125, Berlin, Germany
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany. .,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany. .,European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. .,Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, 13125, Berlin, Germany.
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98
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Mortha A, Burrows K. Cytokine Networks between Innate Lymphoid Cells and Myeloid Cells. Front Immunol 2018; 9:191. [PMID: 29467768 PMCID: PMC5808287 DOI: 10.3389/fimmu.2018.00191] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/22/2018] [Indexed: 12/30/2022] Open
Abstract
Innate lymphoid cells (ILCs) are an essential component of the innate immune system in vertebrates. They are developmentally rooted in the lymphoid lineage and can diverge into at least three transcriptionally distinct lineages. ILCs seed both lymphoid and non-lymphoid tissues and are locally self-maintained in tissue-resident pools. Tissue-resident ILCs execute important effector functions making them key regulator in tissue homeostasis, repair, remodeling, microbial defense, and anti-tumor immunity. Similar to T lymphocytes, ILCs possess only few sensory elements for the recognition of non-self and thus depend on extrinsic cellular sensory elements residing within the tissue. Myeloid cells, including mononuclear phagocytes (MNPs), are key sentinels of the tissue and are able to translate environmental cues into an effector profile that instructs lymphocyte responses. The adaptation of myeloid cells to the tissue state thus influences the effector program of ILCs and serves as an example of how environmental signals are integrated into the function of ILCs via a tissue-resident immune cell cross talks. This review summarizes our current knowledge on the role of myeloid cells in regulating ILC functions and discusses how feedback communication between ILCs and myeloid cells contribute to stabilize immune homeostasis in order to maintain the healthy state of an organ.
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Affiliation(s)
- Arthur Mortha
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Kyle Burrows
- Department of Immunology, University of Toronto, Toronto, ON, Canada
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99
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von Moltke J, Pepper M. Sentinels of the Type 2 Immune Response. Trends Immunol 2018; 39:99-111. [PMID: 29122456 PMCID: PMC6181126 DOI: 10.1016/j.it.2017.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/25/2022]
Abstract
Type 2 immune responses have evolved to sense and respond to large, non-replicating infections or non-microbial noxious compounds in tissues. The development of these responses therefore depends upon highly coordinated and tightly regulated tissue-residing cellular sensors and responders. Multiple exposure to type 2 helper T cell (Th2)-inducing stimuli further enhances both the diversity and potency of the response. This review discusses advances in our understanding of the interacting cellular subsets that comprise both primary and secondary type 2 responses. Current knowledge regarding type 2 immune responses in the lung are initially presented and are then contrasted with what is known about the small intestine. The studies described portray an immune response that depends upon well-organized tissue structures, and suggest their modulation as a therapeutic strategy.
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Affiliation(s)
- Jakob von Moltke
- Department of Immunology, University of Washington School of Medicine, 750 Republican Street, Seattle, WA 98109, USA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, 750 Republican Street, Seattle, WA 98109, USA.
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100
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Robinette ML, Cella M, Telliez JB, Ulland TK, Barrow AD, Capuder K, Gilfillan S, Lin LL, Notarangelo LD, Colonna M. Jak3 deficiency blocks innate lymphoid cell development. Mucosal Immunol 2018; 11:50-60. [PMID: 28513593 PMCID: PMC5693788 DOI: 10.1038/mi.2017.38] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 03/21/2017] [Indexed: 02/04/2023]
Abstract
Loss-of-function mutations in the tyrosine kinase JAK3 cause autosomal recessive severe combined immunodeficiency (SCID). Defects in this form of SCID are restricted to the immune system, which led to the development of immunosuppressive JAK inhibitors. We find that the B6.Cg-Nr1d1tm1Ven/LazJ mouse line purchased from Jackson Laboratories harbors a spontaneous mutation in Jak3, generating a SCID phenotype and an inability to generate antigen-independent professional cytokine-producing innate lymphoid cells (ILCs). Mechanistically, Jak3 deficiency blocks ILC differentiation in the bone marrow at the ILC precursor and the pre-NK cell progenitor. We further demonstrate that the pan-JAK inhibitor tofacitinib and the specific JAK3 inhibitor PF-06651600 impair the ability of human intraepithelial ILC1 (iILC1) to produce IFN-γ, without affecting ILC3 production of IL-22. Both inhibitors impaired the proliferation of iILC1 and ILC3 and differentiation of human ILC in vitro. Tofacitinib is currently approved for the treatment of moderate-to-severely active rheumatoid arthritis. Both tofacitinib and PF-06651600 are currently in clinical trials for several other immune-mediated conditions. Our data suggest that therapeutic inhibition of JAK may also impact ILCs and, to some extent, underlie clinical efficacy.
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Affiliation(s)
- Michelle L. Robinette
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marina Cella
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Tyler K. Ulland
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexander D. Barrow
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kelly Capuder
- Division of Immunology, Harvard Medical School, Boston Children’s Hospital, Boston, MA
| | - Susan Gilfillan
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lih-Ling Lin
- Inflammation and Immunology Research Unit, Pfizer
| | - Luigi D. Notarangelo
- Division of Immunology, Harvard Medical School, Boston Children’s Hospital, Boston, MA,Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Marco Colonna
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
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