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Sun H, Qiu J, Qiu J. Epigenetic regulation of innate lymphoid cells. Eur J Immunol 2024:e2350379. [PMID: 38824666 DOI: 10.1002/eji.202350379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024]
Abstract
Innate lymphoid cells (ILCs) lack antigen-specific receptors and are considered the innate arm of the immune system, phenotypically and functionally mirroring CD4+ helper T cells. ILCs are categorized into groups 1, 2, and 3 based on transcription factors and cytokine expression. ILCs predominantly reside in mucosal tissues and play important roles in regional immune responses. The development and function of ILC subsets are controlled by both transcriptional and epigenetic mechanisms, which have been extensively studied in recent years. Epigenetic regulation refers to inheritable changes in gene expression that occur without affecting DNA sequences. This mainly includes chromatin status, histone modifications, and DNA methylation. In this review, we summarize recent discoveries on epigenetic mechanisms regulating ILC development and function, and how these regulations affect disease progression under pathological conditions. Although the ablation of specific epigenetic regulators can cause global changes in corresponding epigenetic modifications to the chromatin, only partial genes with altered epigenetic modifications change their mRNA expression, resulting in specific outcomes in cell differentiation and function. Therefore, elucidating epigenetic mechanisms underlying the regulation of ILCs will provide potential targets for the diagnosis and treatment of inflammatory diseases.
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Affiliation(s)
- Hanxiao Sun
- Department of Laboratory Medicine, Department of Blood Transfusion, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinxin Qiu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ju Qiu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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2
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Vendramini-Costa DB, Francescone R, Franco-Barraza J, Luong T, Graves M, de Aquino AM, Steele N, Gardiner JC, Dos Santos SAA, Ogier C, Malloy E, Borghaei L, Martinez E, Zhigarev DI, Tan Y, Lee H, Zhou Y, Cai KQ, Klein-Szanto AJ, Wang H, Andrake M, Dunbrack RL, Campbell K, Cukierman E. Netrin G1 Ligand is a new stromal immunomodulator that promotes pancreatic cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594354. [PMID: 38798370 PMCID: PMC11118300 DOI: 10.1101/2024.05.15.594354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Understanding pancreatic cancer biology is fundamental for identifying new targets and for developing more effective therapies. In particular, the contribution of the stromal microenvironment to pancreatic cancer tumorigenesis requires further exploration. Here, we report the stromal roles of the synaptic protein Netrin G1 Ligand (NGL-1) in pancreatic cancer, uncovering its pro-tumor functions in cancer-associated fibroblasts and in immune cells. We observed that the stromal expression of NGL-1 inversely correlated with patients' overall survival. Moreover, germline knockout (KO) mice for NGL-1 presented decreased tumor burden, with a microenvironment that is less supportive of tumor growth. Of note, tumors from NGL-1 KO mice produced less immunosuppressive cytokines and displayed an increased percentage of CD8 + T cells than those from control mice, while preserving the physical structure of the tumor microenvironment. These effects were shown to be mediated by NGL-1 in both immune cells and in the local stroma, in a TGF-β-dependent manner. While myeloid cells lacking NGL-1 decreased the production of immunosuppressive cytokines, NGL-1 KO T cells showed increased proliferation rates and overall polyfunctionality compared to control T cells. CAFs lacking NGL-1 were less immunosuppressive than controls, with overall decreased production of pro-tumor cytokines and compromised ability to inhibit CD8 + T cells activation. Mechanistically, these CAFs downregulated components of the TGF-β pathway, AP-1 and NFAT transcription factor families, resulting in a less tumor-supportive phenotype. Finally, targeting NGL-1 genetically or using a functionally antagonistic small peptide phenocopied the effects of chemotherapy, while modulating the immunosuppressive tumor microenvironment (TME), rather than eliminating it. We propose NGL-1 as a new local stroma and immunomodulatory molecule, with pro-tumor roles in pancreatic cancer. Statement of Significance Here we uncovered the pro-tumor roles of the synaptic protein NGL-1 in the tumor microenvironment of pancreatic cancer, defining a new target that simultaneously modulates tumor cell, fibroblast, and immune cell functions. This study reports a new pathway where NGL-1 controls TGF-β, AP-1 transcription factor members and NFAT1, modulating the immunosuppressive microenvironment in pancreatic cancer. Our findings highlight NGL-1 as a new stromal immunomodulator in pancreatic cancer.
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3
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Kosanovich JL, Eichinger KM, Lipp MA, Gidwani SV, Brahmbhatt D, Yondola MA, Chi DH, Perkins TN, Empey KM. Lung ILC2s are activated in BALB/c mice born to immunized mothers despite complete protection against respiratory syncytial virus. Front Immunol 2024; 15:1374818. [PMID: 38827738 PMCID: PMC11140082 DOI: 10.3389/fimmu.2024.1374818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/03/2024] [Indexed: 06/04/2024] Open
Abstract
Activated lung ILC2s produce large quantities of IL-5 and IL-13 that contribute to eosinophilic inflammation and mucus production following respiratory syncytial virus infection (RSV). The current understanding of ILC2 activation during RSV infection, is that ILC2s are activated by alarmins, including IL-33, released from airway epithelial cells in response to viral-mediated damage. Thus, high levels of RSV neutralizing maternal antibody generated from maternal immunization would be expected to reduce IL-33 production and mitigate ILC2 activation. Here we report that lung ILC2s from mice born to RSV-immunized dams become activated despite undetectable RSV replication. We also report, for the first time, expression of activating and inhibitory Fcgamma receptors on ILC2s that are differentially expressed in offspring born to immunized versus unimmunized dams. Alternatively, ex vivo IL-33-mediated activation of ILC2s was mitigated following the addition of antibody: antigen immune complexes. Further studies are needed to confirm the role of Fcgamma receptor ligation by immune complexes as an alternative mechanism of ILC2 regulation in RSV-associated eosinophilic lung inflammation.
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Affiliation(s)
- Jessica L. Kosanovich
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States
| | - Katherine M. Eichinger
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States
- Center for Clinical Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States
| | - Madeline A. Lipp
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States
- Center for Clinical Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States
| | | | | | | | - David H. Chi
- Division of Pediatric Otolaryngology, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh PA, United States
| | - Timothy N. Perkins
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Kerry M. Empey
- Department of Pharmacy and Therapeutics, University of Pittsburgh School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Immunology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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4
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Liu C, Nagashima H, Fernando N, Bass V, Gopalakrishnan J, Signorella S, Montgomery W, Lim AI, Harrison O, Reich L, Yao C, Sun HW, Brooks SR, Jiang K, Nagarajan V, Zhao Y, Jung S, Phillips R, Mikami Y, Lareau CA, Kanno Y, Jankovic D, Aryee MJ, Pękowska A, Belkaid Y, O'Shea J, Shih HY. A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification. Immunity 2024; 57:1005-1018.e7. [PMID: 38697116 PMCID: PMC11108081 DOI: 10.1016/j.immuni.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/12/2023] [Accepted: 04/10/2024] [Indexed: 05/04/2024]
Abstract
Cytokine expression during T cell differentiation is a highly regulated process that involves long-range promoter-enhancer and CTCF-CTCF contacts at cytokine loci. Here, we investigated the impact of dynamic chromatin loop formation within the topologically associating domain (TAD) in regulating the expression of interferon gamma (IFN-γ) and interleukin-22 (IL-22); these cytokine loci are closely located in the genome and are associated with complex enhancer landscapes, which are selectively active in type 1 and type 3 lymphocytes. In situ Hi-C analyses revealed inducible TADs that insulated Ifng and Il22 enhancers during Th1 cell differentiation. Targeted deletion of a 17 bp boundary motif of these TADs imbalanced Th1- and Th17-associated immunity, both in vitro and in vivo, upon Toxoplasma gondii infection. In contrast, this boundary element was dispensable for cytokine regulation in natural killer cells. Our findings suggest that precise cytokine regulation relies on lineage- and developmental stage-specific interactions of 3D chromatin architectures and enhancer landscapes.
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Affiliation(s)
- Chunhong Liu
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hiroyuki Nagashima
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nilisha Fernando
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Victor Bass
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jaanam Gopalakrishnan
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sadie Signorella
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Will Montgomery
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Oliver Harrison
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Reich
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chen Yao
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kan Jiang
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vijayaraj Nagarajan
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yongbing Zhao
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seolkyoung Jung
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rachael Phillips
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yohei Mikami
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Caleb A Lareau
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yuka Kanno
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dragana Jankovic
- Immunoparasitology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aleksandra Pękowska
- Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Han-Yu Shih
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
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5
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Ver Heul AM, Mack M, Zamidar L, Tamari M, Yang TL, Trier AM, Kim DH, Janzen-Meza H, Van Dyken SJ, Hsieh CS, Karo JM, Sun JC, Kim BS. RAG suppresses group 2 innate lymphoid cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590767. [PMID: 38712036 PMCID: PMC11071423 DOI: 10.1101/2024.04.23.590767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Antigen specificity is the central trait distinguishing adaptive from innate immune function. Assembly of antigen-specific T cell and B cell receptors occurs through V(D)J recombination mediated by the Recombinase Activating Gene endonucleases RAG1 and RAG2 (collectively called RAG). In the absence of RAG, mature T and B cells do not develop and thus RAG is critically associated with adaptive immune function. In addition to adaptive T helper 2 (Th2) cells, group 2 innate lymphoid cells (ILC2s) contribute to type 2 immune responses by producing cytokines like Interleukin-5 (IL-5) and IL-13. Although it has been reported that RAG expression modulates the function of innate natural killer (NK) cells, whether other innate immune cells such as ILC2s are affected by RAG remains unclear. We find that in RAG-deficient mice, ILC2 populations expand and produce increased IL-5 and IL-13 at steady state and contribute to increased inflammation in atopic dermatitis (AD)-like disease. Further, we show that RAG modulates ILC2 function in a cell-intrinsic manner independent of the absence or presence of adaptive T and B lymphocytes. Lastly, employing multiomic single cell analyses of RAG1 lineage-traced cells, we identify key transcriptional and epigenomic ILC2 functional programs that are suppressed by a history of RAG expression. Collectively, our data reveal a novel role for RAG in modulating innate type 2 immunity through suppression of ILC2s.
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Affiliation(s)
- Aaron M. Ver Heul
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Madison Mack
- Immunology & Inflammation Research Therapeutic Area, Sanofi, Cambridge, MA 02141, USA
| | - Lydia Zamidar
- Kimberly and Eric J. Waldman Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mark Lebwohl Center for Neuroinflammation and Sensation, Icahn School of Medicine at Mount Sinai, New York, NY 10019, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Masato Tamari
- Kimberly and Eric J. Waldman Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mark Lebwohl Center for Neuroinflammation and Sensation, Icahn School of Medicine at Mount Sinai, New York, NY 10019, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ting-Lin Yang
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Anna M. Trier
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Do-Hyun Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63130, USA
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Hannah Janzen-Meza
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Steven J. Van Dyken
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Chyi-Song Hsieh
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jenny M. Karo
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA
| | - Joseph C. Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA
| | - Brian S. Kim
- Kimberly and Eric J. Waldman Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mark Lebwohl Center for Neuroinflammation and Sensation, Icahn School of Medicine at Mount Sinai, New York, NY 10019, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Allen Discovery Center for Neuroimmune Interactions, Icahn School of Medicine at Mount Sinai 10019
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6
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Dong X, Qi M, Cai C, Zhu Y, Li Y, Coulter S, Sun F, Liddle C, Uboha NV, Halberg R, Xu W, Marker P, Fu T. Farnesoid X receptor mediates macrophage-intrinsic responses to suppress colitis-induced colon cancer progression. JCI Insight 2024; 9:e170428. [PMID: 38258906 PMCID: PMC10906220 DOI: 10.1172/jci.insight.170428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 12/05/2023] [Indexed: 01/24/2024] Open
Abstract
Bile acids (BAs) affect the intestinal environment by ensuring barrier integrity, maintaining microbiota balance, regulating epithelium turnover, and modulating the immune system. As a master regulator of BA homeostasis, farnesoid X receptor (FXR) is severely compromised in patients with inflammatory bowel disease (IBD) and colitis-associated colorectal cancer (CAC). At the front line, gut macrophages react to the microbiota and metabolites that breach the epithelium. We aim to study the role of the BA/FXR axis in macrophages. This study demonstrates that inflammation-induced epithelial abnormalities compromised FXR signaling and altered BAs' profile in a mouse CAC model. Further, gut macrophage-intrinsic FXR sensed aberrant BAs, leading to pro-inflammatory cytokines' secretion, which promoted intestinal stem cell proliferation. Mechanistically, activation of FXR ameliorated intestinal inflammation and inhibited colitis-associated tumor growth, by regulating gut macrophages' recruitment, polarization, and crosstalk with Th17 cells. However, deletion of FXR in bone marrow or gut macrophages escalated the intestinal inflammation. In summary, our study reveals a distinctive regulatory role of FXR in gut macrophages, suggesting its potential as a therapeutic target for addressing IBD and CAC.
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Affiliation(s)
- Xingchen Dong
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin Carbone Cancer Center (UWCCC), University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ming Qi
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin Carbone Cancer Center (UWCCC), University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Chunmiao Cai
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin Carbone Cancer Center (UWCCC), University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Yu Zhu
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, California, USA
| | - Yuwenbin Li
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Sally Coulter
- Storr Liver Centre, The Westmead Institute for Medical Research and Sydney Medical School, University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia
| | - Fei Sun
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin Carbone Cancer Center (UWCCC), University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Christopher Liddle
- Storr Liver Centre, The Westmead Institute for Medical Research and Sydney Medical School, University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia
| | | | - Richard Halberg
- McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Wei Xu
- McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Paul Marker
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin Carbone Cancer Center (UWCCC), University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ting Fu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin Carbone Cancer Center (UWCCC), University of Wisconsin–Madison, Madison, Wisconsin, USA
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Santana-Hernández S, Suarez-Olmos J, Servitja S, Berenguer-Molins P, Costa-Garcia M, Comerma L, Rea A, Perera-Bel J, Menendez S, Arpí O, Bermejo B, Martínez MT, Cejalvo JM, Comino-Méndez I, Pascual J, Alba E, López-Botet M, Rojo F, Rovira A, Albanell J, Muntasell A. NK cell-triggered CCL5/IFNγ-CXCL9/10 axis underlies the clinical efficacy of neoadjuvant anti-HER2 antibodies in breast cancer. J Exp Clin Cancer Res 2024; 43:10. [PMID: 38167224 PMCID: PMC10763072 DOI: 10.1186/s13046-023-02918-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The variability in responses to neoadjuvant treatment with anti-HER2 antibodies prompts to personalized clinical management and the development of innovative treatment strategies. Tumor-infiltrating Natural Killer (TI-NK) cells can predict the efficacy of HER2-targeted antibodies independently from clinicopathological factors in primary HER2-positive breast cancer patients. Understanding the mechanism/s underlying this association would contribute to optimizing patient stratification and provide the rationale for combinatorial approaches with immunotherapy. METHODS We sought to uncover processes enriched in NK cell-infiltrated tumors as compared to NK cell-desert tumors by microarray analysis. Findings were validated in clinical trial-derived transcriptomic data. In vitro and in vivo preclinical models were used for mechanistic studies. Findings were analysed in clinical samples (tumor and serum) from breast cancer patients. RESULTS NK cell-infiltrated tumors were enriched in CCL5/IFNG-CXCL9/10 transcripts. In multivariate logistic regression analysis, IFNG levels underlie the association between TI-NK cells and pathological complete response to neoadjuvant treatment with trastuzumab. Mechanistically, the production of IFN-ɣ by CD16+ NK cells triggered the secretion of CXCL9/10 from cancer cells. This effect was associated to tumor growth control and the conversion of CD16 into CD16-CD103+ NK cells in humanized in vivo models. In human breast tumors, the CD16 and CD103 markers identified lineage-related NK cell subpopulations capable of producing CCL5 and IFN-ɣ, which correlated with tissue-resident CD8+ T cells. Finally, an early increase in serum CCL5/CXCL9 levels identified patients with NK cell-rich tumors showing good responses to anti-HER2 antibody-based neoadjuvant treatment. CONCLUSIONS This study identifies specialized NK cell subsets as the source of IFN-ɣ influencing the clinical efficacy of anti-HER2 antibodies. It also reveals the potential of serum CCL5/CXCL9 as biomarkers for identifying patients with NK cell-rich tumors and favorable responses to anti-HER2 antibody-based neoadjuvant treatment.
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Affiliation(s)
| | | | - Sonia Servitja
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Oncology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERonc), Madrid, Spain
| | | | | | - Laura Comerma
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERonc), Madrid, Spain
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | - Anna Rea
- University Pompeu Fabra, Barcelona, Spain
| | - Julia Perera-Bel
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Silvia Menendez
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Oriol Arpí
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Begoña Bermejo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERonc), Madrid, Spain
- Department of Oncology, Hospital Clínico de Valencia, Valencia, Spain
| | | | | | - Iñaki Comino-Méndez
- Centro de Investigación Biomédica en Red de Cáncer (CIBERonc), Madrid, Spain
- Hospitales Universitarios Regional y Virgen de La Victoria, Málaga, Spain
- The Biomedical Research Institute of Málaga, Málaga, Spain
| | - Javier Pascual
- Centro de Investigación Biomédica en Red de Cáncer (CIBERonc), Madrid, Spain
- Hospitales Universitarios Regional y Virgen de La Victoria, Málaga, Spain
- The Biomedical Research Institute of Málaga, Málaga, Spain
| | - Emilio Alba
- Centro de Investigación Biomédica en Red de Cáncer (CIBERonc), Madrid, Spain
- Hospitales Universitarios Regional y Virgen de La Victoria, Málaga, Spain
- The Biomedical Research Institute of Málaga, Málaga, Spain
| | - Miguel López-Botet
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- University Pompeu Fabra, Barcelona, Spain
| | - Federico Rojo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERonc), Madrid, Spain
- Department of Pathology, IIS 'Fundación Jimenez Díaz University Hospital', Madrid, Spain
| | - Ana Rovira
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Oncology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERonc), Madrid, Spain
| | - Joan Albanell
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Oncology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERonc), Madrid, Spain
- University Pompeu Fabra, Barcelona, Spain
| | - Aura Muntasell
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERonc), Madrid, Spain.
- Universitat Autònoma de Barcelona, Hospital del Mar Research Institute (IMIM), Doctor Aiguader, 88, 08003, Barcelona, Spain.
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8
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Zhang Y, Hu L, Ren G, Zeng Y, Zhao X, Zhong C. Distinct regulatory machineries underlying divergent chromatin landscapes distinguish innate lymphoid cells from T helper cells. Front Immunol 2023; 14:1271879. [PMID: 38106414 PMCID: PMC10722145 DOI: 10.3389/fimmu.2023.1271879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Innate lymphoid cells (ILCs), as the innate counterpart of CD4+ T helper (Th) cells, play crucial roles in maintaining tissue homeostasis. While the ILC subsets and their corresponding Th subsets demonstrate significant similarities in core programming related to effector function and regulatory mechanisms, their principal distinctions, given their innate and adaptive lymphocyte nature, remain largely unknown. In this study, we have employed an integrative analysis of 294 bulk RNA-sequencing results across all ILC and Th subsets, using scRNA-seq algorithms. Consequently, we identify two genesets that predominantly differentiate ILCs from Th cells, as well as three genesets that distinguish various immune responses. Furthermore, through chromatin accessibility analysis, we find that the ILC geneset tends to rely on specific transcriptional regulation at promoter regions compared with the Th geneset. Additionally, we observe that ILCs and Th cells are under differential transcriptional regulation. For example, ILCs are under stronger regulation by multiple transcription factors, including RORα, GATA3, and NF-κB. Otherwise, Th cells are under stronger regulation by AP-1. Thus, our findings suggest that, despite the acknowledged similarities in effector functions between ILC subsets and corresponding Th subsets, the underlying regulatory machineries still exhibit substantial distinctions. These insights provide a comprehensive understanding of the unique roles played by each cell type during immune responses.
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Affiliation(s)
- Yime Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Luni Hu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing, China
| | - Guanqun Ren
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing, China
| | - Yanyu Zeng
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xingyu Zhao
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Chao Zhong
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing, China
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9
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Scarno G, Mazej J, Laffranchi M, Di Censo C, Mattiola I, Candelotti AM, Pietropaolo G, Stabile H, Fionda C, Peruzzi G, Brooks SR, Tsai WL, Mikami Y, Bernardini G, Gismondi A, Sozzani S, Di Santo JP, Vosshenrich CAJ, Diefenbach A, Gadina M, Santoni A, Sciumè G. Divergent roles for STAT4 in shaping differentiation of cytotoxic ILC1 and NK cells during gut inflammation. Proc Natl Acad Sci U S A 2023; 120:e2306761120. [PMID: 37756335 PMCID: PMC10556635 DOI: 10.1073/pnas.2306761120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/10/2023] [Indexed: 09/29/2023] Open
Abstract
Natural killer (NK) cells and type 1 innate lymphoid cells (ILC1) require signal transducer and activator of transcription 4 (STAT4) to elicit rapid effector responses and protect against pathogens. By combining genetic and transcriptomic approaches, we uncovered divergent roles for STAT4 in regulating effector differentiation of these functionally related cell types. Stat4 deletion in Ncr1-expressing cells led to impaired NK cell terminal differentiation as well as to an unexpected increased generation of cytotoxic ILC1 during intestinal inflammation. Mechanistically, Stat4-deficient ILC1 exhibited upregulation of gene modules regulated by STAT5 in vivo and an aberrant effector differentiation upon in vitro stimulation with IL-2, used as a prototypical STAT5 activator. Moreover, STAT4 expression in NCR+ innate lymphocytes restrained gut inflammation in the dextran sulfate sodium-induced colitis model limiting pathogenic production of IL-13 from adaptive CD4+ T cells in the large intestine. Collectively, our data shed light on shared and distinctive mechanisms of STAT4-regulated transcriptional control in NK cells and ILC1 required for intestinal inflammatory responses.
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Affiliation(s)
- Gianluca Scarno
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
| | - Julija Mazej
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
| | - Mattia Laffranchi
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
| | - Chiara Di Censo
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
| | - Irene Mattiola
- Laboratory of Innate Immunity, Institute of Microbiology, Infectious Diseases and Immunology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt–Universität zu Berlin, Campus Benjamin Franklin, Berlin12203, Germany
- Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Association, Berlin10117, Germany
| | - Arianna M. Candelotti
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
| | - Giuseppe Pietropaolo
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
| | - Helena Stabile
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
| | - Cinzia Fionda
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Rome00161, Italy
| | - Stephen R. Brooks
- Biodata Mining and Discovery Section, Office of Science and Technology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
| | - Wanxia Li Tsai
- Translational Immunology Section, Office of Science and Technology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo1608582, Japan
| | - Giovanni Bernardini
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
| | - Angela Gismondi
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
| | - Silvano Sozzani
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
- Istituti di Ricovero e Cura a Carattere Scientifico Neuromed, Isernia86077, Italy
| | - James P. Di Santo
- Innate Immunity Unit, Institut Pasteur, Université Paris Cité, INSERM U1223, Paris75724, France
| | | | - Andreas Diefenbach
- Laboratory of Innate Immunity, Institute of Microbiology, Infectious Diseases and Immunology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt–Universität zu Berlin, Campus Benjamin Franklin, Berlin12203, Germany
- Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Association, Berlin10117, Germany
| | - Massimo Gadina
- Translational Immunology Section, Office of Science and Technology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
| | - Angela Santoni
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
- Istituti di Ricovero e Cura a Carattere Scientifico Neuromed, Isernia86077, Italy
| | - Giuseppe Sciumè
- Department of Molecular Medicine, Sapienza University of Rome, Rome00161, Italy
- Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Rome00161, Italy
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10
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Falquet M, Su Z, Wyss T, Ercolano G, Trabanelli S, Jandus C. Dynamic single-cell regulomes characterize human peripheral blood innate lymphoid cell subpopulations. iScience 2023; 26:107728. [PMID: 37694139 PMCID: PMC10483052 DOI: 10.1016/j.isci.2023.107728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/25/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
Innate lymphoid cells (ILCs) are plastic immune cells divided into 3 main subsets, characterized by distinct phenotypic and functional profiles. Using single cell approaches, heightened heterogeneity of mouse ILCs has been appreciated, imprinted by tissue signals that shape their transcriptome and epigenome. Intra-subset diversity has also been observed in human ILCs. However, combined transcriptomic and epigenetic analyses of single ILCs in humans are lacking. Here, we show high transcriptional and epigenetic heterogeneity among human circulating ILCs in healthy individuals. We describe phenotypically distinct subclusters and diverse chromatin accessibility within main ILC populations, compatible with differentially poised states. We validate the use of this healthy donor-based analysis as resource dataset to help inferring ILC changes occurring in disease conditions. Overall, our work provides insights in the complex human ILC biology. We anticipate it to facilitate hypothesis-driven studies in patients, without the need to perform single cell OMICs using precious patients' material.
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Affiliation(s)
- Maryline Falquet
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ziyang Su
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Tania Wyss
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Data Science Facility, AGORA Cancer Research Center, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Giuseppe Ercolano
- Department of Experimental Pharmacology, University of Naples Federico II, Naples, Italy
| | - Sara Trabanelli
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Camilla Jandus
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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11
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Smith KJ, Sciumè G, Amarnath S. Twenty-One Flavors of Type 1 Innate Lymphoid Cells with PD-1 (Programmed Cell Death-1 Receptor) Sprinkles. DISCOVERY IMMUNOLOGY 2023; 2:kyad003. [PMID: 38567059 PMCID: PMC10917210 DOI: 10.1093/discim/kyad003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/16/2023] [Accepted: 02/06/2023] [Indexed: 04/04/2024]
Abstract
Innate lymphoid cells (ILCs) are tissue-resident immune cells that have been recently implicated in initiating and driving anti-tumor responses. ILCs are classified into three main groups, namely type 1 ILCs (ILC1), type 2 ILCs, and type 3 ILCs. All three groups have been implicated in either eliciting pro or anti-tumor immune responses in different cancer subtypes with the consensus that ILCs cannot be overlooked within the field of anti-tumor immune responses. In this review, we will specifically expand on the knowledge on ILC1, their characterization, function, and plasticity in anti-cancer immune responses. Within this premise, we will discuss caveats of ILC1 characterization, and expand on the expression and function of immune checkpoint receptors within ILC1 subsets, specifically focusing on the role of programmed cell death-1 receptor in controlling specific ILC1 responses. We summarize that ILC1s are a vital component in initiating anti-tumor responses and can be boosted by checkpoint receptors.
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Affiliation(s)
- Katie J Smith
- The Biosciences Institute, Newcastle University Biosciences Institute, Newcastle upon Tyne, UK
- The Centre for Cancer, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
- Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Giuseppe Sciumè
- Department of Molecular Medicine, Laboratory affiliated to Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | - Shoba Amarnath
- The Biosciences Institute, Newcastle University Biosciences Institute, Newcastle upon Tyne, UK
- The Centre for Cancer, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
- Medical School, Newcastle University, Newcastle upon Tyne, UK
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12
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Taggenbrock RLRE, van Gisbergen KPJM. ILC1: Development, maturation, and transcriptional regulation. Eur J Immunol 2023; 53:e2149435. [PMID: 36408791 PMCID: PMC10099236 DOI: 10.1002/eji.202149435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
Type 1 Innate Lymphoid cells (ILC1s) are tissue-resident cells that partake in the regulation of inflammation and homeostasis. A major feature of ILC1s is their ability to rapidly respond after infections. The effector repertoire of ILC1s includes the pro-inflammatory cytokines IFN-γ and TNF-α and cytotoxic mediators such as granzymes, which enable ILC1s to establish immune responses and to directly kill target cells. Recent advances in the characterization of ILC1s have considerably furthered our understanding of ILC1 development and maintenance in tissues. In particular, it has become clear how ILC1s operate independently from conventional natural killer cells, with which they share many characteristics. In this review, we discuss recent developments with regards to the differentiation, polarization, and effector maturation of ILC1s. These processes may underlie the observed heterogeneity in ILC1 populations within and between different tissues. Next, we highlight transcriptional programs that control each of the separate steps in the differentiation of ILC1s. These transcriptional programs are shared with other tissue-resident type-1 lymphocytes, such as tissue-resident memory T cells (TRM ) and invariant natural killer T cells (iNKT), highlighting that ILC1s utilize networks of transcriptional regulation that are conserved between lymphocyte lineages to respond effectively to tissue-invading pathogens.
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Affiliation(s)
- Renske L R E Taggenbrock
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Klaas P J M van Gisbergen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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13
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van de Pavert SA. Layered origins of lymphoid tissue inducer cells. Immunol Rev 2023; 315:71-78. [PMID: 36705244 DOI: 10.1111/imr.13189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The Innate Lymphoid Cell (ILC) family is a relatively recently described immune cell family involved in innate immune responses and tissue homeostasis. Lymphoid Tissue Inducer (LTi) cells are part of the type 3 (ILC3) family. The ILC3 family is the main ILC population within the embryo, in which the LTi cells are critically associated with embryonic lymph node formation. Recent studies have shown more insights in ILC origin and residency from local embryonic and tissue resident precursors. Embryonic LTi cells originating from a different hemogenic endothelial source were shown to be replaced by HSC derived progenitors in adult. This review will discuss the layered origin of the ILC3 family with an emphasis on the LTi cell lineage.
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Affiliation(s)
- Serge A van de Pavert
- Aix-Marseille Univ, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy (CIML), Marseille, France
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14
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Abstract
The pleiotropic actions of the Farnesoid X Receptor (FXR) are required for gut health, and reciprocally, reduced intestinal FXR signaling is seen in inflammatory bowel diseases (IBDs). Here, we show that activation of FXR selectively in the intestine is protective in inflammation-driven models of IBD. Prophylactic activation of FXR restored homeostatic levels of pro-inflammatory cytokines, most notably IL17. Importantly, these changes were attributed to FXR regulation of innate lymphoid cells (ILCs), with both the inflammation-driven increases in ILCs, and ILC3s in particular, and the induction of Il17a and Il17f in ILC3s blocked by FXR activation. Moreover, a population of ILC precursor-like cells increased with treatment, implicating FXR in the maturation/differentiation of ILC precursors. These findings identify FXR as an intrinsic regulator of intestinal ILCs and a potential therapeutic target in inflammatory intestinal diseases.
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15
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Beckstette M, Lu CW, Herppich S, Diem EC, Ntalli A, Ochel A, Kruse F, Pietzsch B, Neumann K, Huehn J, Floess S, Lochner M. Profiling of epigenetic marker regions in murine ILCs under homeostatic and inflammatory conditions. J Exp Med 2022; 219:213389. [PMID: 35938981 PMCID: PMC9386974 DOI: 10.1084/jem.20210663] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/26/2022] [Accepted: 07/14/2022] [Indexed: 12/03/2022] Open
Abstract
Epigenetic modifications such as DNA methylation play an essential role in imprinting specific transcriptional patterns in cells. We performed genome-wide DNA methylation profiling of murine lymph node–derived ILCs, which led to the identification of differentially methylated regions (DMRs) and the definition of epigenetic marker regions in ILCs. Marker regions were located in genes with a described function for ILCs, such as Tbx21, Gata3, or Il23r, but also in genes that have not been related to ILC biology. Methylation levels of the marker regions and expression of the associated genes were strongly correlated, indicating their functional relevance. Comparison with T helper cell methylomes revealed clear lineage differences, despite partial similarities in the methylation of specific ILC marker regions. IL-33–mediated challenge affected methylation of ILC2 epigenetic marker regions in the liver, while remaining relatively stable in the lung. In our study, we identified a set of epigenetic markers that can serve as a tool to study phenotypic and functional properties of ILCs.
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Affiliation(s)
- Michael Beckstette
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Bielefeld Institute for Bioinformatics Infrastructure, Department of Technology, Bielefeld University, Bielefeld, Germany
| | - Chia-Wen Lu
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.,Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research; a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Susanne Herppich
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Elia C Diem
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Anna Ntalli
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Aaron Ochel
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friederike Kruse
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research; a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Beate Pietzsch
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Katrin Neumann
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jochen Huehn
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Floess
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Matthias Lochner
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.,Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research; a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany
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16
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NK Cells and Other Cytotoxic Innate Lymphocytes in Colorectal Cancer Progression and Metastasis. Int J Mol Sci 2022; 23:ijms23147859. [PMID: 35887206 PMCID: PMC9322916 DOI: 10.3390/ijms23147859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 12/16/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies and leading causes of cancer-related deaths worldwide. Despite its complex pathogenesis and progression, CRC represents a well-fitting example of how the immune contexture can dictate the disease outcome. The presence of cytotoxic lymphocytes, both CD8+ T cells and natural killer (NK) cells, represents a relevant prognostic factor in CRC and is associated with a better overall survival. Together with NK cells, other innate lymphocytes, namely, innate lymphoid cells (ILCs), have been found both in biopsies of CRC patients and in murine models of intestinal cancer, playing both pro- and anti-tumor activities. In particular, several type 1 innate lymphoid cells (ILC1) with cytotoxic functions have been recently described, and evidence in mice shows a role for both NK cells and ILC1 in controlling CRC metastasis. In this review, we provide an overview of the features of NK cells and the expanding spectrum of innate lymphocytes with cytotoxic functions. We also comment on both the described and the potential roles these innate lymphocytes can play during the progression of intestinal cancer leading to metastasis. Finally, we discuss recent advances in the molecular mechanisms underlying the functional regulation of cytotoxic innate lymphocytes in CRC.
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17
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Morgan RC, Kee BL. Genomic and Transcriptional Mechanisms Governing Innate-like T Lymphocyte Development. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:208-216. [PMID: 35821098 DOI: 10.4049/jimmunol.2200141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 12/16/2022]
Abstract
Innate-like lymphocytes are a subset of lymphoid cells that function as a first line of defense against microbial infection. These cells are activated by proinflammatory cytokines or broadly expressed receptors and are able to rapidly perform their effector functions owing to a uniquely primed chromatin state that is acquired as a part of their developmental program. These cells function in many organs to protect against disease, but they release cytokines and cytotoxic mediators that can also lead to severe tissue pathologies. Therefore, harnessing the capabilities of these cells for therapeutic interventions will require a deep understanding of how these cells develop and regulate their effector functions. In this review we discuss recent advances in the identification of the transcription factors and the genomic regions that guide the development and function of invariant NKT cells and we highlight related mechanisms in other innate-like lymphocytes.
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Affiliation(s)
- Roxroy C Morgan
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL; and
| | - Barbara L Kee
- Cancer Biology and Immunology, Department of Pathology, University of Chicago, Chicago, IL
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18
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Wahlen S, Matthijssens F, Van Loocke W, Taveirne S, Kiekens L, Persyn E, Van Ammel E, De Vos Z, De Munter S, Matthys P, Van Nieuwerburgh F, Taghon T, Vandekerckhove B, Van Vlierberghe P, Leclercq G. The transcription factor RUNX2 drives the generation of human NK cells and promotes tissue residency. eLife 2022; 11:e80320. [PMID: 35793229 PMCID: PMC9259014 DOI: 10.7554/elife.80320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/26/2022] [Indexed: 12/16/2022] Open
Abstract
Natural killer (NK) cells are innate lymphocytes that eliminate virus-infected and cancer cells by cytotoxicity and cytokine secretion. In addition to circulating NK cells, distinct tissue-resident NK subsets have been identified in various organs. Although transcription factors regulating NK cell development and function have been extensively studied in mice, the role of RUNX2 in these processes has not been investigated, neither in mice nor in human. Here, by manipulating RUNX2 expression with either knockdown or overexpression in human haematopoietic stem cell-based NK cell differentiation cultures, combined with transcriptomic and ChIP-sequencing analyses, we established that RUNX2 drives the generation of NK cells, possibly through induction of IL-2Rβ expression in NK progenitor cells. Importantly, RUNX2 promotes tissue residency in human NK cells. Our findings have the potential to improve existing NK cell-based cancer therapies and can impact research fields beyond NK cell biology, since tissue-resident subsets have also been described in other lymphocyte subpopulations.
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Affiliation(s)
- Sigrid Wahlen
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Filip Matthijssens
- Cancer Research Institute GhentGhentBelgium
- Department of Biomolecular Medicine, Ghent UniversityGhentBelgium
| | - Wouter Van Loocke
- Cancer Research Institute GhentGhentBelgium
- Department of Biomolecular Medicine, Ghent UniversityGhentBelgium
| | - Sylvie Taveirne
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Laura Kiekens
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Eva Persyn
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Els Van Ammel
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Zenzi De Vos
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Stijn De Munter
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Patrick Matthys
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU LeuvenLeuvenBelgium
| | | | - Tom Taghon
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute GhentGhentBelgium
- Department of Biomolecular Medicine, Ghent UniversityGhentBelgium
| | - Georges Leclercq
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
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19
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Paldor M, Levkovitch-Siany O, Eidelshtein D, Adar R, Enk CD, Marmary Y, Elgavish S, Nevo Y, Benyamini H, Plaschkes I, Klein S, Mali A, Rose-John S, Peled A, Galun E, Axelrod JH. Single-cell transcriptomics reveals a senescence-associated IL-6/CCR6 axis driving radiodermatitis. EMBO Mol Med 2022; 14:e15653. [PMID: 35785521 PMCID: PMC9358397 DOI: 10.15252/emmm.202115653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 12/22/2022] Open
Abstract
Irradiation‐induced alopecia and dermatitis (IRIAD) are two of the most visually recognized complications of radiotherapy, of which the molecular and cellular basis remains largely unclear. By combining scRNA‐seq analysis of whole skin‐derived irradiated cells with genetic ablation and molecular inhibition studies, we show that senescence‐associated IL‐6 and IL‐1 signaling, together with IL‐17 upregulation and CCR6+‐mediated immune cell migration, are crucial drivers of IRIAD. Bioinformatics analysis colocalized irradiation‐induced IL‐6 signaling with senescence pathway upregulation largely within epidermal hair follicles, basal keratinocytes, and dermal fibroblasts. Loss of cytokine signaling by genetic ablation in IL‐6−/− or IL‐1R−/− mice, or by molecular blockade, strongly ameliorated IRIAD, as did deficiency of CCL20/CCR6‐mediated immune cell migration in CCR6−/− mice. Moreover, IL‐6 deficiency strongly reduced IL‐17, IL‐22, CCL20, and CCR6 upregulation, whereas CCR6 deficiency reciprocally diminished IL‐6, IL‐17, CCL3, and MHC upregulation, suggesting that proximity‐dependent cellular cross talk promotes IRIAD. Therapeutically, topical application of Janus kinase blockers or inhibition of T‐cell activation by cyclosporine effectively reduced IRIAD, suggesting the potential of targeted approaches for the treatment of dermal side effects in radiotherapy patients.
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Affiliation(s)
- Mor Paldor
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Orr Levkovitch-Siany
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Dana Eidelshtein
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Revital Adar
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Claes D Enk
- Department of Dermatology, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Yitzhak Marmary
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Sharona Elgavish
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Nevo
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hadar Benyamini
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Inbar Plaschkes
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shiri Klein
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Alex Mali
- Department of Pathology, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Stefan Rose-John
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Amnon Peled
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Eithan Galun
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Jonathan H Axelrod
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
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20
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Coman D, Coales I, Roberts LB, Neves JF. Helper-Like Type-1 Innate Lymphoid Cells in Inflammatory Bowel Disease. Front Immunol 2022; 13:903688. [PMID: 35844597 PMCID: PMC9285720 DOI: 10.3389/fimmu.2022.903688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/17/2022] [Indexed: 12/17/2022] Open
Abstract
Inflammatory bowel disease (IBD) is an idiopathic condition characterized by chronic relapsing inflammation in the intestine. While the precise etiology of IBD remains unknown, genetics, the gut microbiome, environmental factors, and the immune system have all been shown to contribute to the disease pathophysiology. In recent years, attention has shifted towards the role that innate lymphoid cells (ILCs) may play in the dysregulation of intestinal immunity observed in IBD. ILCs are a group of heterogenous immune cells which can be found at mucosal barriers. They act as critical mediators of the regulation of intestinal homeostasis and the orchestration of its inflammatory response. Despite helper-like type 1 ILCs (ILC1s) constituting a particularly rare ILC population in the intestine, recent work has suggested that an accumulation of intestinal ILC1s in individuals with IBD may act to exacerbate its pathology. In this review, we summarize existing knowledge on helper-like ILC1 plasticity and their classification in murine and human settings. Moreover, we discuss what is currently understood about the roles that ILC1s may play in the progression of IBD pathogenesis.
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Affiliation(s)
- Diana Coman
- Centre for Host Microbiome Interactions, King’s College London, London, United Kingdom
| | - Isabelle Coales
- Centre for Host Microbiome Interactions, King’s College London, London, United Kingdom
| | - Luke B. Roberts
- School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Joana F. Neves
- Centre for Host Microbiome Interactions, King’s College London, London, United Kingdom
- *Correspondence: Joana F. Neves,
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21
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Wiedemann GM. Localization Matters: Epigenetic Regulation of Natural Killer Cells in Different Tissue Microenvironments. Front Immunol 2022; 13:913054. [PMID: 35707540 PMCID: PMC9191276 DOI: 10.3389/fimmu.2022.913054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/29/2022] [Indexed: 11/24/2022] Open
Abstract
Natural Killer cells (NK cells) are cytotoxic innate lymphoid cells (ILCs), which play a key role in the early protection against viral infection and cancer. In addition to mounting rapid effector responses, NK cells possess the capacity to generate long-lived memory cells in response to certain stimuli, thus blurring the lines between innate and adaptive immunity and making NK cells an ideal candidate for tumor immunotherapy. NK cell development, activation and memory formation are regulated by epigenetic alterations driven by a complex interplay of external and internal signals. These epigenetic modifications can convey long-lasting functional and phenotypic changes and critically modify their response to stimulation. Here, we review how NK cell functionality and plasticity are regulated at the epigenetic level in different tissue microenvironments and within tumor microenvironments. An in-depth understanding of the epigenetic modifications underlying NK cell functional diversity in different environments is an essential step in the development of NK cell-based cancer therapies.
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22
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Schroeder JH, Howard JK, Lord GM. Transcription factor-driven regulation of ILC1 and ILC3. Trends Immunol 2022; 43:564-579. [PMID: 35618586 PMCID: PMC10166716 DOI: 10.1016/j.it.2022.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
Abstract
Mammalian innate lymphoid cells (ILCs) have functional relevance under both homeostatic and disease settings, such as inflammatory bowel disease (IBD), particularly in the context of maintaining the integrity of mucosal surfaces. Early reports highlighted group 1 and 3 ILC regulatory transcription factors (TFs), T-box expressed in T cells (T-bet; Tbx21) and RAR-related orphan nuclear receptor γt (RORγt; Rorc), as key regulators of ILC biology. Since then, other canonical TFs have been shown to have a role in the development and function of ILC subsets. In this review, we focus on recent insights into the balance between mature ILC1 and ILC3 based on these TFs and how they interact with other key cell-intrinsic molecular pathways. We outline how this TF interplay might be explored to identify novel candidate therapeutic avenues for human diseases.
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23
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Kokkinou E, Pandey RV, Mazzurana L, Gutierrez-Perez I, Tibbitt CA, Weigel W, Soini T, Carrasco A, Rao A, Nagasawa M, Bal SM, Jangard M, Friberg D, Lindforss U, Nordenvall C, Ljunggren M, Haapaniemi S, Keita ÅV, Söderholm J, Hedin C, Spits H, Bryceson YT, Mjösberg J. CD45RA +CD62L - ILCs in human tissues represent a quiescent local reservoir for the generation of differentiated ILCs. Sci Immunol 2022; 7:eabj8301. [PMID: 35427178 DOI: 10.1126/sciimmunol.abj8301] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Innate lymphoid cells (ILCs) are highly plastic and predominantly mucosal tissue-resident cells that contribute to both homeostasis and inflammation depending on the microenvironment. The discovery of naïve-like ILCs suggests an ILC differentiation process that is akin to naïve T cell differentiation. Delineating the mechanisms that underlie ILC differentiation in tissues is crucial for understanding ILC biology in health and disease. Here, we showed that tonsillar ILCs expressing CD45RA lacked proliferative activity, indicative of cellular quiescence. CD62L distinguished two subsets of CD45RA+ ILCs. CD45RA+CD62L+ ILCs (CD62L+ ILCs) resembled circulating naïve ILCs because they lacked the transcriptional, metabolic, epigenetic, and cytokine production signatures of differentiated ILCs. CD45RA+CD62L- ILCs (CD62L- ILCs) were epigenetically similar to CD62L+ ILCs but showed a transcriptional, metabolic, and cytokine production signature that was more akin to differentiated ILCs. CD62L+ and CD62L- ILCs contained uni- and multipotent precursors of ILC1s/NK cells and ILC3s. Differentiation of CD62L+ and CD62L- ILCs led to metabolic reprogramming including up-regulation of genes associated with glycolysis, which was needed for their effector functions after differentiation. CD62L- ILCs with preferential differentiation capacity toward IL-22-producing ILC3s accumulated in the inflamed mucosa of patients with inflammatory bowel disease. These data suggested distinct differentiation potential of CD62L+ and CD62L- ILCs between tissue microenvironments and identified that manipulation of these cells is a possible approach to restore tissue-immune homeostasis.
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Affiliation(s)
- Efthymia Kokkinou
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Ram Vinay Pandey
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Luca Mazzurana
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Irene Gutierrez-Perez
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Christopher Andrew Tibbitt
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Whitney Weigel
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Tea Soini
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Anna Carrasco
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Anna Rao
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Maho Nagasawa
- Department of Experimental Immunology, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Suzanne M Bal
- Department of Experimental Immunology, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Mattias Jangard
- ENT Unit, Sophiahemmet University Research Laboratory and Sophiahemmet Hospital, Stockholm, Sweden
| | - Danielle Friberg
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Ulrik Lindforss
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Pelvic Cancer, GI Oncology and Colorectal Surgery Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Nordenvall
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Pelvic Cancer, GI Oncology and Colorectal Surgery Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Ljunggren
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Pelvic Cancer, GI Oncology and Colorectal Surgery Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Staffan Haapaniemi
- Department of Surgery, Vrinnevi Hospital, Norrköping, Sweden.,Department of Surgery, Linköping University, Linköping, Sweden
| | - Åsa V Keita
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johan Söderholm
- Department of Surgery, Linköping University, Linköping, Sweden.,Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Charlotte Hedin
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.,Gastroenterology Unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Hergen Spits
- Department of Experimental Immunology, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Yenan T Bryceson
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
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24
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Fang D, Cui K, Cao Y, Zheng M, Kawabe T, Hu G, Khillan JS, Li D, Zhong C, Jankovic D, Sher A, Zhao K, Zhu J. Differential regulation of transcription factor T-bet induction during NK cell development and T helper-1 cell differentiation. Immunity 2022; 55:639-655.e7. [PMID: 35381213 PMCID: PMC9059963 DOI: 10.1016/j.immuni.2022.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 01/04/2022] [Accepted: 03/08/2022] [Indexed: 12/11/2022]
Abstract
Adaptive CD4+ T helper cells and their innate counterparts, innate lymphoid cells, utilize an identical set of transcription factors (TFs) for their differentiation and functions. However, similarities and differences in the induction of these TFs in related lymphocytes are still elusive. Here, we show that T helper-1 (Th1) cells and natural killer (NK) cells displayed distinct epigenomes at the Tbx21 locus, which encodes T-bet, a critical TF for regulating type 1 immune responses. The initial induction of T-bet in NK precursors was dependent on the NK-specific DNase I hypersensitive site Tbx21-CNS-3, and the expression of the interleukin-18 (IL-18) receptor; IL-18 induced T-bet expression through the transcription factor RUNX3, which bound to Tbx21-CNS-3. By contrast, signal transducer and activator of transcription (STAT)-binding motifs within Tbx21-CNS-12 were critical for IL-12-induced T-bet expression during Th1 cell differentiation both in vitro and in vivo. Thus, type 1 innate and adaptive lymphocytes utilize distinct enhancer elements for their development and differentiation.
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Affiliation(s)
- Difeng Fang
- Molecular and Cellular Immunoregulation Section, 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, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mingzhu Zheng
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Microbiology and Immunology School of Medicine, Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Takeshi Kawabe
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Microbiology and Immunology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Gangqing Hu
- Laboratory of Epigenome Biology, 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
| | - Jaspal S Khillan
- Mouse Genetics and Gene Modification Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dan Li
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Clinical Laboratory, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Chao Zhong
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Dragana Jankovic
- Immunoparasitology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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25
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de Sousa TR, Sgnotto FDR, Fagundes BO, Duarte AJDS, Victor JR. Non-atopic Neonatal Thymic Innate Lymphoid Cell Subsets (ILC1, ILC2, and ILC3) Identification and the Modulatory Effect of IgG From Dermatophagoides Pteronyssinus (Derp)-Atopic Individuals. FRONTIERS IN ALLERGY 2022; 2:650235. [PMID: 35387031 PMCID: PMC8974683 DOI: 10.3389/falgy.2021.650235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/29/2021] [Indexed: 12/17/2022] Open
Abstract
Innate lymphoid cells (ILCs) are classified into distinct subsets termed ILC1, ILC2, and ILC3 cells. The existing literature lacks evidence identifying ILCs and their subsets in the human thymus but already demonstrates that they can exert several functions in regulating immune responses. Furthermore, it was already described that IgG's repertoires could modulate lymphocytes' maturation in the human thymus. Here we aimed to identify ILCs subsets in the human thymus and provide insight into the possible modulatory effect of purified IgG on these cells. Thymic tissues were obtained from 12 infants without an allergic background (non-atopic), and a literature-based peripheral ILCs staining protocol was used. Purified IgG was obtained from non-atopic individuals (n-At), atopic individuals reactive to allergens non-related to dust mites (nr-At), and atopic individuals reactive to the mite Dermatophagoides pteronyssinus (Derp-At). As with all tissues in which they have already been detected, thymic ILCs are rare, but we could detect viable ILCs in all tested tissues, which did not occur with the ILC1 subset. ILC2 and ILC3 NKp44+ subsets could be detected in all evaluated thymus, but ILC3 NKp44- subset could not. Next, we observed that Derp-At IgG could induce the expression of ILC2 phenotype, higher levels of IL-13, and lower levels of IL-4 when compared to IgG purified from non-atopic or non-related atopic (atopic to allergens excluding dust mites) individuals. These results contribute to the elucidation of human thymic ILCs and corroborate emerging evidence about IgG's premature effect on allergy development-related human lymphocytes' modulation.
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Affiliation(s)
- Thamires Rodrigues de Sousa
- Laboratory of Medical Investigation LIM-56, Division of Clinical Dermatology, Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Beatriz Oliveira Fagundes
- Laboratory of Medical Investigation LIM-56, Division of Clinical Dermatology, Medical School, University of São Paulo, São Paulo, Brazil
| | - Alberto José da Silva Duarte
- Laboratory of Medical Investigation LIM-56, Division of Clinical Dermatology, Medical School, University of São Paulo, São Paulo, Brazil.,Division of Pathology, Medical School, University of São Paulo, São Paulo, Brazil
| | - Jefferson Russo Victor
- Laboratory of Medical Investigation LIM-56, Division of Clinical Dermatology, Medical School, University of São Paulo, São Paulo, Brazil.,Medical School, Universidade Santo Amaro (Unisa), São Paulo, Brazil.,Faculdades Metropolitanas Unidas (FMU), São Paulo, Brazil
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26
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Shi S, Ye L, Jin K, Xiao Z, Yu X, Wu W. Innate Lymphoid Cells: Emerging Players in Pancreatic Disease. Int J Mol Sci 2022; 23:ijms23073748. [PMID: 35409105 PMCID: PMC8998564 DOI: 10.3390/ijms23073748] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/19/2022] [Accepted: 03/27/2022] [Indexed: 02/07/2023] Open
Abstract
Common pancreatic diseases have caused significant economic and social burdens worldwide. The interstitial microenvironment is involved in and plays a crucial part in the occurrence and progression of pancreatic diseases. Innate lymphoid cells (ILCs), an innate population of immune cells which have only gradually entered our visual field in the last 10 years, play an important role in maintaining tissue homeostasis, regulating metabolism, and participating in regeneration and repair. Recent evidence indicates that ILCs in the pancreas, as well as in other tissues, are also key players in pancreatic disease and health. Herein, we examined the possible functions of different ILC subsets in common pancreatic diseases, including diabetes mellitus, pancreatitis and pancreatic cancer, and discussed the potential practical implications of the relevant findings for future further treatment of these pancreatic diseases.
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Affiliation(s)
- Saimeng Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (S.S.); (L.Y.); (K.J.); (Z.X.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
- Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Longyun Ye
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (S.S.); (L.Y.); (K.J.); (Z.X.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
- Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Kaizhou Jin
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (S.S.); (L.Y.); (K.J.); (Z.X.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
- Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Zhiwen Xiao
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (S.S.); (L.Y.); (K.J.); (Z.X.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
- Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (S.S.); (L.Y.); (K.J.); (Z.X.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
- Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
- Correspondence: (X.Y.); (W.W.); Tel.: +86-21-6403-1446 (X.Y. & W.W.)
| | - Weiding Wu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (S.S.); (L.Y.); (K.J.); (Z.X.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
- Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
- Correspondence: (X.Y.); (W.W.); Tel.: +86-21-6403-1446 (X.Y. & W.W.)
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27
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Whole-genome profiling of DNA methylation and hydroxymethylation identifies distinct regulatory programs among innate lymphocytes. Nat Immunol 2022; 23:619-631. [PMID: 35332328 PMCID: PMC8989654 DOI: 10.1038/s41590-022-01164-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 02/18/2022] [Indexed: 12/11/2022]
Abstract
Innate lymphocytes encompass a diverse array of phenotypic identities with specialized functions. DNA methylation and hydroxymethylation are essential for epigenetic fidelity and fate commitment. The landscapes of these modifications are unknown in innate lymphocytes. Here, we characterized the whole-genome distribution of methyl-CpG and 5-hydroxymethylcytosine in mouse ILC3, ILC2, and NK cells. We identified differentially methylated and hydroxymethylated DNA regions between ILC-NK subsets and correlated them with transcriptional signatures. We associated lineage-determining transcription factors with demethylation and demonstrated unique patterns of DNA methylation/hydroxymethylation in relationship to open chromatin regions, histone modifications, and transcription factor binding sites. We further discovered a novel association between hydroxymethylation and NK cell super-enhancers. Using mice lacking DNA hydroxymethylase TET2, we showed its requirement for optimal production of hallmark cytokines by ILC3 and IL-17A by inflammatory ILC2. These findings provide a powerful resource for studying innate lymphocyte epigenetic regulation and decode the regulatory logic governing their identity.
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28
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Saini A, Ghoneim HE, Lio CWJ, Collins PL, Oltz EM. Gene Regulatory Circuits in Innate and Adaptive Immune Cells. Annu Rev Immunol 2022; 40:387-411. [PMID: 35119910 DOI: 10.1146/annurev-immunol-101320-025949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell identity and function largely rely on the programming of transcriptomes during development and differentiation. Signature gene expression programs are orchestrated by regulatory circuits consisting of cis-acting promoters and enhancers, which respond to a plethora of cues via the action of transcription factors. In turn, transcription factors direct epigenetic modifications to revise chromatin landscapes, and drive contacts between distal promoter-enhancer combinations. In immune cells, regulatory circuits for effector genes are especially complex and flexible, utilizing distinct sets of transcription factors and enhancers, depending on the cues each cell type receives during an infection, after sensing cellular damage, or upon encountering a tumor. Here, we review major players in the coordination of gene regulatory programs within innate and adaptive immune cells, as well as integrative omics approaches that can be leveraged to decipher their underlying circuitry. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ankita Saini
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Chan-Wang Jerry Lio
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Patrick L Collins
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
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29
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Coordination of Mucosal Immunity by Innate Lymphoid Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1365:113-134. [DOI: 10.1007/978-981-16-8387-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Chu TH, Khairallah C, Shieh J, Cho R, Qiu Z, Zhang Y, Eskiocak O, Thanassi DG, Kaplan MH, Beyaz S, Yang VW, Bliska JB, Sheridan BS. γδ T cell IFNγ production is directly subverted by Yersinia pseudotuberculosis outer protein YopJ in mice and humans. PLoS Pathog 2021; 17:e1010103. [PMID: 34871329 PMCID: PMC8648121 DOI: 10.1371/journal.ppat.1010103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/09/2021] [Indexed: 12/31/2022] Open
Abstract
Yersinia pseudotuberculosis is a foodborne pathogen that subverts immune function by translocation of Yersinia outer protein (Yop) effectors into host cells. As adaptive γδ T cells protect the intestinal mucosa from pathogen invasion, we assessed whether Y. pseudotuberculosis subverts these cells in mice and humans. Tracking Yop translocation revealed that the preferential delivery of Yop effectors directly into murine Vγ4 and human Vδ2+ T cells inhibited anti-microbial IFNγ production. Subversion was mediated by the adhesin YadA, injectisome component YopB, and translocated YopJ effector. A broad anti-pathogen gene signature and STAT4 phosphorylation levels were inhibited by translocated YopJ. Thus, Y. pseudotuberculosis attachment and translocation of YopJ directly into adaptive γδ T cells is a major mechanism of immune subversion in mice and humans. This study uncovered a conserved Y. pseudotuberculosis pathway that subverts adaptive γδ T cell function to promote pathogenicity. Unconventional γδ T cells are a dynamic immune population important for mucosal protection of the intestine against invading pathogens. We determined that the foodborne pathogen Y. pseudotuberculosis preferentially targets an adaptive subset of these cells to subvert immune function. We found that direct injection of Yersinia outer proteins (Yop) into adaptive γδ T cells inhibited their anti-pathogen functions. We screened all Yop effectors and identified YopJ as the sole effector to inhibit adaptive γδ T cell production of IFNγ. We determined that adaptive γδ T cell subversion occurred by limiting activation of the transcription factor STAT4. When we infected mice with Y. pseudotuberculosis expressing an inactive YopJ, this enhanced the adaptive γδ T cell response and led to greater cytokine production from this subset of cells to aid mouse recovery. This mechanism of immune evasion appears conserved in humans as direct injection of Y. pseudotuberculosis YopJ into human γδ T cells inhibited cytokine production. This suggested to us that Y. pseudotuberculosis actively inhibits the adaptive γδ T cell response through YopJ as a mechanism to evade immune surveillance at the site of pathogen invasion.
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Affiliation(s)
- Timothy H. Chu
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Camille Khairallah
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Jason Shieh
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Rhea Cho
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Zhijuan Qiu
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Yue Zhang
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Onur Eskiocak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - David G. Thanassi
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Mark H. Kaplan
- Department of Microbiology and Immunology, School of Medicine, Indiana University, Indianapolis, Indiana, United States of America
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Vincent W. Yang
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - James B. Bliska
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Dartmouth, New Hampshire, United States of America
| | - Brian S. Sheridan
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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31
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Jegatheeswaran S, Mathews JA, Crome SQ. Searching for the Elusive Regulatory Innate Lymphoid Cell. THE JOURNAL OF IMMUNOLOGY 2021; 207:1949-1957. [PMID: 34607908 DOI: 10.4049/jimmunol.2100661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/06/2021] [Indexed: 12/26/2022]
Abstract
The complex nature of the innate lymphoid cell (ILC) family and wide range of ILC effector functions has been the focus of intense research. In addition to important roles in host defense, ILCs have central roles in maintaining tissue homeostasis and can promote immune tolerance. Alterations within the microenvironment can impart new functions on ILCs, and can even induce conversion to a distinct ILC family member. Complicating current definitions of ILCs are recent findings of distinct regulatory ILC populations that limit inflammatory responses or recruit other immunosuppressive cells such as regulatory T cells. Whether these populations are distinct ILC family members or rather canonical ILCs that exhibit immunoregulatory functions due to microenvironment signals has been the subject of much debate. In this review, we highlight studies identifying regulatory populations of ILCs that span regulatory NK-like cells, regulatory ILCs, and IL-10-producing ILC2s.
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Affiliation(s)
- Sinthuja Jegatheeswaran
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; and.,Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, Ontario, Canada
| | - Jessica A Mathews
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, Ontario, Canada
| | - Sarah Q Crome
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; and .,Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, Ontario, Canada
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32
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Kiekens L, Van Loocke W, Taveirne S, Wahlen S, Persyn E, Van Ammel E, De Vos Z, Matthys P, Van Nieuwerburgh F, Taghon T, Van Vlierberghe P, Vandekerckhove B, Leclercq G. T-BET and EOMES Accelerate and Enhance Functional Differentiation of Human Natural Killer Cells. Front Immunol 2021; 12:732511. [PMID: 34630413 PMCID: PMC8497824 DOI: 10.3389/fimmu.2021.732511] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
T-bet and Eomes are transcription factors that are known to be important in maturation and function of murine natural killer (NK) cells. Reduced T-BET and EOMES expression results in dysfunctional NK cells and failure to control tumor growth. In contrast to mice, the current knowledge on the role of T-BET and EOMES in human NK cells is rudimentary. Here, we ectopically expressed either T-BET or EOMES in human hematopoietic progenitor cells. Combined transcriptome, chromatin accessibility and protein expression analyses revealed that T-BET or EOMES epigenetically represses hematopoietic stem cell quiescence and non-NK lineage differentiation genes, while activating an NK cell-specific transcriptome and thereby drastically accelerating NK cell differentiation. In this model, the effects of T-BET and EOMES are largely overlapping, yet EOMES shows a superior role in early NK cell maturation and induces faster NK receptor and enhanced CD16 expression. T-BET particularly controls transcription of terminal maturation markers and epigenetically controls strong induction of KIR expression. Finally, NK cells generated upon T-BET or EOMES overexpression display improved functionality, including increased IFN-γ production and killing, and especially EOMES overexpression NK cells have enhanced antibody-dependent cellular cytotoxicity. Our findings reveal novel insights on the regulatory role of T-BET and EOMES in human NK cell maturation and function, which is essential to further understand human NK cell biology and to optimize adoptive NK cell therapies.
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Affiliation(s)
- Laura Kiekens
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Wouter Van Loocke
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sylvie Taveirne
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Sigrid Wahlen
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Eva Persyn
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Els Van Ammel
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Zenzi De Vos
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Patrick Matthys
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, K.U. Leuven, Leuven, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bart Vandekerckhove
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Georges Leclercq
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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33
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Fiancette R, Finlay CM, Willis C, Bevington SL, Soley J, Ng STH, Baker SM, Andrews S, Hepworth MR, Withers DR. Reciprocal transcription factor networks govern tissue-resident ILC3 subset function and identity. Nat Immunol 2021; 22:1245-1255. [PMID: 34556884 PMCID: PMC7611981 DOI: 10.1038/s41590-021-01024-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 08/05/2021] [Indexed: 12/13/2022]
Abstract
Innate lymphoid cells (ILCs) are guardians of mucosal immunity, yet the transcriptional networks that support their function remain poorly understood. We used inducible combinatorial deletion of key transcription factors (TFs) required for ILC development (RORγt, RORα and T-bet) to determine their necessity in maintaining ILC3 identity and function. Both RORγt and RORα were required to preserve optimum effector functions; however, RORα was sufficient to support robust interleukin-22 production among the lymphoid tissue inducer (LTi)-like ILC3 subset, but not natural cytotoxicity receptor (NCR)+ ILC3s. Lymphoid tissue inducer-like ILC3s persisted with only selective loss of phenotype and effector functions even after the loss of both TFs. In contrast, continued RORγt expression was essential to restrain transcriptional networks associated with type 1 immunity within NCR+ ILC3s, which coexpress T-bet. Full differentiation to an ILC1-like population required the additional loss of RORα. Together, these data demonstrate how TF networks integrate within mature ILCs after development to sustain effector functions, imprint phenotype and restrict alternative differentiation programs.
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Affiliation(s)
- Rémi Fiancette
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Conor M Finlay
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Claire Willis
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sarah L Bevington
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jake Soley
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sky T H Ng
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Syed Murtuza Baker
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Division of Informatics, Imaging & Data Science, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, UK
| | - Matthew R Hepworth
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
| | - David R Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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34
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Zhang J, Le Gras S, Pouxvielh K, Faure F, Fallone L, Kern N, Moreews M, Mathieu AL, Schneider R, Marliac Q, Jung M, Berton A, Hayek S, Vidalain PO, Marçais A, Dodard G, Dejean A, Brossay L, Ghavi-Helm Y, Walzer T. Sequential actions of EOMES and T-BET promote stepwise maturation of natural killer cells. Nat Commun 2021; 12:5446. [PMID: 34521844 PMCID: PMC8440589 DOI: 10.1038/s41467-021-25758-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/06/2021] [Indexed: 02/08/2023] Open
Abstract
EOMES and T-BET are related T-box transcription factors that control natural killer (NK) cell development. Here we demonstrate that EOMES and T-BET regulate largely distinct gene sets during this process. EOMES is dominantly expressed in immature NK cells and drives early lineage specification by inducing hallmark receptors and functions. By contrast, T-BET is dominant in mature NK cells, where it induces responsiveness to IL-12 and represses the cell cycle, likely through transcriptional repressors. Regardless, many genes with distinct functions are co-regulated by the two transcription factors. By generating two gene-modified mice facilitating chromatin immunoprecipitation of endogenous EOMES and T-BET, we show a strong overlap in their DNA binding targets, as well as extensive epigenetic changes during NK cell differentiation. Our data thus suggest that EOMES and T-BET may distinctly govern, via differential expression and co-factors recruitment, NK cell maturation by inserting partially overlapping epigenetic regulations.
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MESH Headings
- Animals
- Base Sequence
- Bone Marrow Cells/cytology
- Bone Marrow Cells/immunology
- CD11b Antigen/genetics
- CD11b Antigen/immunology
- Cell Cycle/drug effects
- Cell Cycle/genetics
- Cell Cycle/immunology
- Cell Differentiation
- Cell Lineage/drug effects
- Cell Lineage/genetics
- Cell Lineage/immunology
- Epigenesis, Genetic/immunology
- Interleukin-12/pharmacology
- Killer Cells, Natural/cytology
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/immunology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Promoter Regions, Genetic
- Protein Binding
- Spleen/cytology
- Spleen/immunology
- T-Box Domain Proteins/deficiency
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/immunology
- Transcription, Genetic
- Tumor Necrosis Factor Receptor Superfamily, Member 7/genetics
- Tumor Necrosis Factor Receptor Superfamily, Member 7/immunology
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Affiliation(s)
- Jiang Zhang
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Stéphanie Le Gras
- IGBMC, CNRS UMR7104, Inserm U1258, Université de Strasbourg, Illkirch, France
- Plateforme GenomEast, infrastructure France Génomique, Illkirch, France
| | - Kevin Pouxvielh
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Fabrice Faure
- Institut NeuroMyoGène, INSERM U1217/CNRS UMR5310, Université de Lyon, Université Claude Bernard, Lyon 1, Lyon, France
| | - Lucie Fallone
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Nicolas Kern
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Marion Moreews
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Anne-Laure Mathieu
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Raphaël Schneider
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon Université Claude Bernard Lyon 1, 46 allée d'Italie, F-69364, Lyon, France
| | - Quentin Marliac
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Mathieu Jung
- IGBMC, CNRS UMR7104, Inserm U1258, Université de Strasbourg, Illkirch, France
- Plateforme GenomEast, infrastructure France Génomique, Illkirch, France
| | - Aurore Berton
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Simon Hayek
- Equipe Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Université Paris Descartes, CNRS UMR 8601, 75006, Paris, France
| | - Pierre-Olivier Vidalain
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
- Equipe Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Université Paris Descartes, CNRS UMR 8601, 75006, Paris, France
| | - Antoine Marçais
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Garvin Dodard
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University Alpert Medical School, Providence, RI, 02912, USA
| | - Anne Dejean
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051 - Université Toulouse III, Toulouse, France
| | - Laurent Brossay
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University Alpert Medical School, Providence, RI, 02912, USA
| | - Yad Ghavi-Helm
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon Université Claude Bernard Lyon 1, 46 allée d'Italie, F-69364, Lyon, France
| | - Thierry Walzer
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.
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35
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Zablon HA, Ko CI, Puga A. Converging Roles of the Aryl Hydrocarbon Receptor in Early Embryonic Development, Maintenance of Stemness, and Tissue Repair. Toxicol Sci 2021; 182:1-9. [PMID: 34009372 PMCID: PMC8285021 DOI: 10.1093/toxsci/kfab050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor well-known for its adaptive role as a sensor of environmental toxicants and mediator of the metabolic detoxification of xenobiotic ligands. In addition, a growing body of experimental data has provided indisputable evidence that the AHR regulates critical functions of cell physiology and embryonic development. Recent studies have shown that the naïve AHR-that is, unliganded to xenobiotics but activated endogenously-has a crucial role in maintenance of embryonic stem cell pluripotency, tissue repair, and regulation of cancer stem cell stemness. Depending on the cellular context, AHR silences the expression of pluripotency genes Oct4 and Nanog and potentiates differentiation, whereas curtailing cellular plasticity and stemness. In these processes, AHR-mediated contextual responses and outcomes are dictated by changes of interacting partners in signaling pathways, gene networks, and cell-type-specific genomic structures. In this review, we focus on AHR-mediated changes of genomic architecture as an emerging mechanism for the AHR to regulate gene expression at the transcriptional level. Collective evidence places this receptor as a physiological hub connecting multiple biological processes whose disruption impacts on embryonic development, tissue repair, and maintenance or loss of stemness.
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Affiliation(s)
| | | | - Alvaro Puga
- Department of Environmental and Public Health Sciences, Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, USA
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36
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Castleman MJ, Dillon SM, Thompson TA, Santiago ML, McCarter MD, Barker E, Wilson CC. Gut Bacteria Induce Granzyme B Expression in Human Colonic ILC3s In Vitro in an IL-15-Dependent Manner. THE JOURNAL OF IMMUNOLOGY 2021; 206:3043-3052. [PMID: 34117105 DOI: 10.4049/jimmunol.2000239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/13/2021] [Indexed: 12/13/2022]
Abstract
Group 3 innate lymphoid cells (ILC3s) in the gut mucosa have long been thought to be noncytotoxic lymphocytes that are critical for homeostasis of intestinal epithelial cells through secretion of IL-22. Recent work using human tonsillar cells demonstrated that ILC3s exposed to exogenous inflammatory cytokines for a long period of time acquired expression of granzyme B, suggesting that under pathological conditions ILC3s may become cytotoxic. We hypothesized that inflammation associated with bacterial exposure might trigger granzyme B expression in gut ILC3s. To test this, we exposed human colon lamina propria mononuclear cells to a panel of enteric bacteria. We found that the Gram-negative commensal and pathogenic bacteria induced granzyme B expression in a subset of ILC3s that were distinct from IL-22-producing ILC3s. A fraction of granzyme B+ ILC3s coexpressed the cytolytic protein perforin. Granzyme B expression was mediated, in part, by IL-15 produced upon exposure to bacteria. ILC3s coexpressing all three IL-15R subunits (IL15Rα/β/γ) increased following bacterial stimulation, potentially allowing for cis presentation of IL-15 during bacterial exposure. Additionally, a large frequency of colonic myeloid dendritic cells expressed IL-15Rα, implicating myeloid dendritic cells in trans presentation of IL-15 to ILC3s. Tonsillar ILC3s minimally expressed granzyme B when exposed to the same bacteria or to rIL-15. Overall, these data establish the novel, to our knowledge, finding that human colonic ILC3s can express granzyme B in response to a subset of enteric bacteria through a process mediated by IL-15. These observations raise new questions about the multifunctional role of human gut ILC3s.
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Affiliation(s)
- Moriah J Castleman
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Stephanie M Dillon
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Tezha A Thompson
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Mario L Santiago
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Martin D McCarter
- Department of Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO; and
| | - Edward Barker
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL
| | - Cara C Wilson
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO;
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37
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Dynamic regulation of innate lymphoid cells in the mucosal immune system. Cell Mol Immunol 2021; 18:1387-1394. [PMID: 33980994 PMCID: PMC8167116 DOI: 10.1038/s41423-021-00689-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/18/2021] [Indexed: 02/03/2023] Open
Abstract
The mucosal immune system is considered a local immune system, a term that implies regional restriction. Mucosal tissues are continually exposed to a wide range of antigens. The regulation of mucosal immune cells is tightly associated with the progression of mucosal diseases. Innate lymphoid cells (ILCs) are abundant in mucosal barriers and serve as first-line defenses against pathogens. The subtype changes and translocation of ILCs are accompanied by the pathologic processes of mucosal diseases. Here, we review the plasticity and circulation of ILCs in the mucosal immune system under physiological and pathological conditions. We also discuss the signaling pathways involved in dynamic ILC changes and the related targets in mucosal diseases.
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38
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Ghaedi M, Takei F. Innate lymphoid cell development. J Allergy Clin Immunol 2021; 147:1549-1560. [PMID: 33965092 DOI: 10.1016/j.jaci.2021.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/25/2022]
Abstract
Innate lymphoid cells (ILCs) mainly reside at barrier surfaces and regulate tissue homeostasis and immunity. ILCs are divided into 3 groups, group 1 ILCs, group 2 ILCs, and group 3 ILC3, on the basis of their similar effector programs to T cells. The development of ILCs from lymphoid progenitors in adult mouse bone marrow has been studied in detail, and multiple ILC progenitors have been characterized. ILCs are mostly tissue-resident cells that develop in the perinatal period. More recently, ILC progenitors have also been identified in peripheral tissues. In this review, we discuss the stepwise transcription factor-directed differentiation of mouse ILC progenitors into mature ILCs, the critical time windows in ILC development, and the contribution of bone marrow versus tissue ILC progenitors to the pool of mature ILCs in tissues.
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Affiliation(s)
- Maryam Ghaedi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fumio Takei
- the Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada; Terry Fox Laboratory, B.C. Cancer, Vancouver, British Columbia, Canada.
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39
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Belver L, Albero R, Ferrando AA. Deregulation of enhancer structure, function, and dynamics in acute lymphoblastic leukemia. Trends Immunol 2021; 42:418-431. [PMID: 33858773 PMCID: PMC8091164 DOI: 10.1016/j.it.2021.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/25/2022]
Abstract
Enhancers control dynamic changes in gene expression and orchestrate the tightly controlled transcriptional circuitries that direct and coordinate cell growth, proliferation, survival, lineage commitment, and differentiation during lymphoid development. Enhancer hijacking and neoenhancer formation at oncogene loci, as well as aberrant activation of oncogene-associated enhancers, can induce constitutive activation of self-perpetuating oncogenic transcriptional circuitries, and contribute to the malignant transformation of immature lymphoid progenitors in acute lymphoblastic leukemia (ALL). In this review, we present recent discoveries of the role of enhancer dynamics in mouse and human lymphoid development, and discuss how genetic and epigenetic alterations of enhancer function can promote leukemogenesis, and potential strategies for targeting the enhancer machinery in the treatment of ALL.
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Affiliation(s)
- Laura Belver
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA; Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, 08916, Spain
| | - Robert Albero
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA; Department of Systems Biology, Columbia University, New York, NY, 10032, USA; Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA; Department of Pathology, Columbia University Medical Center, New York, NY, 10032, USA.
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40
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Farini A, Sitzia C, Villa C, Cassani B, Tripodi L, Legato M, Belicchi M, Bella P, Lonati C, Gatti S, Cerletti M, Torrente Y. Defective dystrophic thymus determines degenerative changes in skeletal muscle. Nat Commun 2021; 12:2099. [PMID: 33833239 PMCID: PMC8032677 DOI: 10.1038/s41467-021-22305-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 02/24/2021] [Indexed: 02/02/2023] Open
Abstract
In Duchenne muscular dystrophy (DMD), sarcolemma fragility and myofiber necrosis produce cellular debris that attract inflammatory cells. Macrophages and T-lymphocytes infiltrate muscles in response to damage-associated molecular pattern signalling and the release of TNF-α, TGF-β and interleukins prevent skeletal muscle improvement from the inflammation. This immunological scenario was extended by the discovery of a specific response to muscle antigens and a role for regulatory T cells (Tregs) in muscle regeneration. Normally, autoimmunity is avoided by autoreactive T-lymphocyte deletion within thymus, while in the periphery Tregs monitor effector T-cells escaping from central regulatory control. Here, we report impairment of thymus architecture of mdx mice together with decreased expression of ghrelin, autophagy dysfunction and AIRE down-regulation. Transplantation of dystrophic thymus in recipient nude mice determine the up-regulation of inflammatory/fibrotic markers, marked metabolic breakdown that leads to muscle atrophy and loss of force. These results indicate that involution of dystrophic thymus exacerbates muscular dystrophy by altering central immune tolerance.
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Affiliation(s)
- Andrea Farini
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Unit of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Milan, Italy
| | - Clementina Sitzia
- Residency Program in Clinical Pathology and Clinical Biochemistry, Università degli Studi di Milano, Milan, Italy
| | - Chiara Villa
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Unit of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Milan, Italy
| | - Barbara Cassani
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan Unit, Milan, Italy
- IRCCS Humanitas clinical and research center, Rozzano, 20089, Milan, Italy
| | - Luana Tripodi
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Unit of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Milan, Italy
| | - Mariella Legato
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Unit of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Milan, Italy
| | - Marzia Belicchi
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Unit of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Milan, Italy
| | - Pamela Bella
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Unit of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Milan, Italy
| | - Caterina Lonati
- Center for Surgical Research, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Gatti
- Center for Surgical Research, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Massimiliano Cerletti
- UCL Research Department for Surgical Biotechnology, University College London, London, UK
- UCL Institute for Immunity and Transplantation, University College London, London, UK
| | - Yvan Torrente
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Unit of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Milan, Italy.
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41
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Ebihara T, Tatematsu M, Fuchimukai A, Yamada T, Yamagata K, Takasuga S, Yamada T. Trained innate lymphoid cells in allergic diseases. Allergol Int 2021; 70:174-180. [PMID: 33328130 DOI: 10.1016/j.alit.2020.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Group 2 innate lymphoid cells (ILC2s) reside in peripheral tissues such as the lungs, skin, nasal cavity, and gut and provoke innate type 2 immunity against allergen exposure, parasitic worm infection, and respiratory virus infection by producing TH2 cytokines. Recent advances in understanding ILC2 biology revealed that ILC2s can be trained by IL-33 or allergic inflammation, are long-lived, and mount memory-like type 2 immune responses to any other allergens afterwards. In contrast, IL-33, together with retinoic acid, induces IL-10-producing immunosuppressive ILC2s. In this review, we discuss how the allergic cytokine milieu and other immune cells direct the generation of trained ILC2s with immunostimulatory or immunosuppressive recall capability in allergic diseases and infections associated with type 2 immunity. The molecular mechanisms of trained immunity by ILCs and the physiological relevance of trained ILC2s are also discussed.
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Affiliation(s)
- Takashi Ebihara
- Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan.
| | - Megumi Tatematsu
- Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan
| | - Akane Fuchimukai
- Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan
| | - Toshiki Yamada
- Department of Otorhinolaryngology, Head & Neck Surgery, Akita University Graduate School of Medicine, Akita, Japan
| | - Kenki Yamagata
- Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan
| | - Shunsuke Takasuga
- Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan
| | - Takechiyo Yamada
- Department of Otorhinolaryngology, Head & Neck Surgery, Akita University Graduate School of Medicine, Akita, Japan
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42
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Fernando N, Sciumè G, O'Shea JJ, Shih HY. Multi-Dimensional Gene Regulation in Innate and Adaptive Lymphocytes: A View From Regulomes. Front Immunol 2021; 12:655590. [PMID: 33841440 PMCID: PMC8034253 DOI: 10.3389/fimmu.2021.655590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/09/2021] [Indexed: 12/24/2022] Open
Abstract
The precise control of cytokine production by innate lymphoid cells (ILCs) and their T cell adaptive system counterparts is critical to mounting a proper host defense immune response without inducing collateral damage and autoimmunity. Unlike T cells that differentiate into functionally divergent subsets upon antigen recognition, ILCs are developmentally programmed to rapidly respond to environmental signals in a polarized manner, without the need of T cell receptor (TCR) signaling. The specification of cytokine production relies on dynamic regulation of cis-regulatory elements that involve multi-dimensional epigenetic mechanisms, including DNA methylation, transcription factor binding, histone modification and DNA-DNA interactions that form chromatin loops. How these different layers of gene regulation coordinate with each other to fine tune cytokine production, and whether ILCs and their T cell analogs utilize the same regulatory strategy, remain largely unknown. Herein, we review the molecular mechanisms that underlie cell identity and functionality of helper T cells and ILCs, focusing on networks of transcription factors and cis-regulatory elements. We discuss how higher-order chromatin architecture orchestrates these components to construct lineage- and state-specific regulomes that support ordered immunoregulation.
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Affiliation(s)
- Nilisha Fernando
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Giuseppe Sciumè
- Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci-Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Han-Yu Shih
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States.,National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
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43
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Holmes TD, Pandey RV, Helm EY, Schlums H, Han H, Campbell TM, Drashansky TT, Chiang S, Wu CY, Tao C, Shoukier M, Tolosa E, Von Hardenberg S, Sun M, Klemann C, Marsh RA, Lau CM, Lin Y, Sun JC, Månsson R, Cichocki F, Avram D, Bryceson YT. The transcription factor Bcl11b promotes both canonical and adaptive NK cell differentiation. Sci Immunol 2021; 6:6/57/eabc9801. [PMID: 33712472 DOI: 10.1126/sciimmunol.abc9801] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
Epigenetic landscapes can provide insight into regulation of gene expression and cellular diversity. Here, we examined the transcriptional and epigenetic profiles of seven human blood natural killer (NK) cell populations, including adaptive NK cells. The BCL11B gene, encoding a transcription factor (TF) essential for T cell development and function, was the most extensively regulated, with expression increasing throughout NK cell differentiation. Several Bcl11b-regulated genes associated with T cell signaling were specifically expressed in adaptive NK cell subsets. Regulatory networks revealed reciprocal regulation at distinct stages of NK cell differentiation, with Bcl11b repressing RUNX2 and ZBTB16 in canonical and adaptive NK cells, respectively. A critical role for Bcl11b in driving NK cell differentiation was corroborated in BCL11B-mutated patients and by ectopic Bcl11b expression. Moreover, Bcl11b was required for adaptive NK cell responses in a murine cytomegalovirus model, supporting expansion of these cells. Together, we define the TF regulatory circuitry of human NK cells and uncover a critical role for Bcl11b in promoting NK cell differentiation and function.
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Affiliation(s)
- Tim D Holmes
- Broegelmann Research Laboratory, Department of Clinical Sciences, University of Bergen, N-5021 Bergen, Norway. .,Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-14186 Stockholm, Sweden
| | - Ram Vinay Pandey
- Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-14186 Stockholm, Sweden
| | - Eric Y Helm
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Heinrich Schlums
- Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-14186 Stockholm, Sweden
| | - Hongya Han
- Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-14186 Stockholm, Sweden
| | - Tessa M Campbell
- Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-14186 Stockholm, Sweden
| | - Theodore T Drashansky
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Samuel Chiang
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Cheng-Ying Wu
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota Cancer Center, Minneapolis, MN 55455, USA
| | - Christine Tao
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | | | - Eva Tolosa
- Department of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Miao Sun
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Christian Klemann
- Department of Pediatric Pneumology, Allergy and Neonatology, Hannover Medical School, Hannover, Germany
| | - Rebecca A Marsh
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Colleen M Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yin Lin
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75246, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert Månsson
- Centre for Hematology and Regenerative Medicine, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-14186 Stockholm, Sweden
| | - Frank Cichocki
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota Cancer Center, Minneapolis, MN 55455, USA
| | - Dorina Avram
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Yenan T Bryceson
- Broegelmann Research Laboratory, Department of Clinical Sciences, University of Bergen, N-5021 Bergen, Norway. .,Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-14186 Stockholm, Sweden
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44
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Hosokawa H, Rothenberg EV. How transcription factors drive choice of the T cell fate. Nat Rev Immunol 2021; 21:162-176. [PMID: 32918063 PMCID: PMC7933071 DOI: 10.1038/s41577-020-00426-6] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 12/21/2022]
Abstract
Recent evidence has elucidated how multipotent blood progenitors transform their identities in the thymus and undergo commitment to become T cells. Together with environmental signals, a core group of transcription factors have essential roles in this process by directly activating and repressing specific genes. Many of these transcription factors also function in later T cell development, but control different genes. Here, we review how these transcription factors work to change the activities of specific genomic loci during early intrathymic development to establish T cell lineage identity. We introduce the key regulators and highlight newly emergent insights into the rules that govern their actions. Whole-genome deep sequencing-based analysis has revealed unexpectedly rich relationships between inherited epigenetic states, transcription factor-DNA binding affinity thresholds and influences of given transcription factors on the activities of other factors in the same cells. Together, these mechanisms determine T cell identity and make the lineage choice irreversible.
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Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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45
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Hosokawa H, Masuhara K, Koizumi M. Transcription factors regulate early T cell development via redeployment of other factors: Functional dynamics of constitutively required factors in cell fate decisions. Bioessays 2021; 43:e2000345. [PMID: 33624856 DOI: 10.1002/bies.202000345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/30/2021] [Accepted: 02/08/2021] [Indexed: 01/02/2023]
Abstract
Establishment of cell lineage identity from multipotent progenitors is controlled by cooperative actions of lineage-specific and stably expressed transcription factors, combined with input from environmental signals. Lineage-specific master transcription factors activate and repress gene expression by recruiting consistently expressed transcription factors and chromatin modifiers to their target loci. Recent technical advances in genome-wide and multi-omics analysis have shed light on unexpected mechanisms that underlie more complicated actions of transcription factors in cell fate decisions. In this review, we discuss functional dynamics of stably expressed and continuously required factors, Notch and Runx family members, throughout developmental stages of early T cell development in the thymus. Pre- and post-commitment stage-specific transcription factors induce dynamic redeployment of Notch and Runx binding genomic regions. Thus, together with stage-specific transcription factors, shared transcription factors across distinct developmental stages regulate acquisition of T lineage identity.
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Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan.,Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
| | - Kaori Masuhara
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Maria Koizumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
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46
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Congras A, Hoareau-Aveilla C, Caillet N, Tosolini M, Villarese P, Cieslak A, Rodriguez L, Asnafi V, Macintyre E, Egger G, Brousset P, Lamant L, Meggetto F. ALK-transformed mature T lymphocytes restore early thymus progenitor features. J Clin Invest 2021; 130:6395-6408. [PMID: 33141118 DOI: 10.1172/jci134990] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Anaplastic large cell lymphoma (ALCL) is a mature T cell neoplasm that often expresses the CD4+ T cell surface marker. It usually harbors the t(2;5) (p23;q35) translocation, leading to the ectopic expression of NPM-ALK, a chimeric tyrosine kinase. We demonstrated that in vitro transduction of normal human CD4+ T lymphocytes with NPM-ALK results in their immortalization and malignant transformation. The tumor cells displayed morphological and immunophenotypical characteristics of primary patient-derived anaplastic large cell lymphomas. Cell growth, proliferation, and survival were strictly dependent on NPM-ALK activity and include activation of the key factors STAT3 and DNMT1 and expression of CD30 (the hallmark of anaplastic large-cell lymphoma). Implantation of NPM-ALK-transformed CD4+ T lymphocytes into immunodeficient mice resulted in the formation of tumors indistinguishable from patients' anaplastic large cell lymphomas. Integration of "Omic" data revealed that NPM-ALK-transformed CD4+ T lymphocytes and primary NPM-ALK+ ALCL biopsies share similarities with early T cell precursors. Of note, these NPM-ALK+ lymphoma cells overexpress stem cell regulators (OCT4, SOX2, and NANOG) and HIF2A, which is known to affect hematopoietic precursor differentiation and NPM-ALK+ cell growth. Altogether, for the first time our findings suggest that NPM-ALK could restore progenitor-like features in mature CD30+ peripheral CD4+ T cells, in keeping with a thymic progenitor-like pattern.
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Affiliation(s)
- Annabelle Congras
- INSERM, UMR1037 CRCT, F-31000, Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000, Toulouse, France.,CNRS, ERL5294 UMR1037 CRCT, F-31000, Toulouse, France.,Equipe Labellisée LIGUE 2017, Toulouse, France
| | - Coralie Hoareau-Aveilla
- INSERM, UMR1037 CRCT, F-31000, Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000, Toulouse, France.,CNRS, ERL5294 UMR1037 CRCT, F-31000, Toulouse, France.,Equipe Labellisée LIGUE 2017, Toulouse, France
| | - Nina Caillet
- INSERM, UMR1037 CRCT, F-31000, Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000, Toulouse, France.,CNRS, ERL5294 UMR1037 CRCT, F-31000, Toulouse, France.,Equipe Labellisée LIGUE 2017, Toulouse, France
| | - Marie Tosolini
- INSERM, UMR1037 CRCT, F-31000, Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000, Toulouse, France.,CNRS, ERL5294 UMR1037 CRCT, F-31000, Toulouse, France.,Pôle Technologique du CRCT, Plateau Bioinformatique, Toulouse, France
| | - Patrick Villarese
- Hematology and INSERM1151, Institut Necker-Enfants Malades, University Sorbonne Paris Cité at Descartes and Assistance Publique-Hopitaux de Paris, Paris, France
| | - Agata Cieslak
- Hematology and INSERM1151, Institut Necker-Enfants Malades, University Sorbonne Paris Cité at Descartes and Assistance Publique-Hopitaux de Paris, Paris, France
| | - Laura Rodriguez
- Etablissement Français du Sang, Nouvelle Aquitaine, INSERM U1035, Université de Bordeaux, Bordeaux, France
| | - Vahid Asnafi
- Hematology and INSERM1151, Institut Necker-Enfants Malades, University Sorbonne Paris Cité at Descartes and Assistance Publique-Hopitaux de Paris, Paris, France
| | - Elisabeth Macintyre
- Hematology and INSERM1151, Institut Necker-Enfants Malades, University Sorbonne Paris Cité at Descartes and Assistance Publique-Hopitaux de Paris, Paris, France
| | - Gerda Egger
- Department of Pathology, Medical University Vienna, Vienna, Austria.,Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria
| | - Pierre Brousset
- INSERM, UMR1037 CRCT, F-31000, Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000, Toulouse, France.,CNRS, ERL5294 UMR1037 CRCT, F-31000, Toulouse, France.,Equipe Labellisée LIGUE 2017, Toulouse, France.,Institut Carnot Lymphome, Toulouse, France.,Laboratoire d'Excellence Toulouse Cancer and after Cancer (Labex TOUCAN), Toulouse, France
| | - Laurence Lamant
- INSERM, UMR1037 CRCT, F-31000, Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000, Toulouse, France.,CNRS, ERL5294 UMR1037 CRCT, F-31000, Toulouse, France.,Equipe Labellisée LIGUE 2017, Toulouse, France.,Institut Carnot Lymphome, Toulouse, France.,Laboratoire d'Excellence Toulouse Cancer and after Cancer (Labex TOUCAN), Toulouse, France.,European Research Initiative on ALK-Related Malignancies, Cambridge, United Kingdom, Vienna, Austria, and Toulouse, France
| | - Fabienne Meggetto
- INSERM, UMR1037 CRCT, F-31000, Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000, Toulouse, France.,CNRS, ERL5294 UMR1037 CRCT, F-31000, Toulouse, France.,Equipe Labellisée LIGUE 2017, Toulouse, France.,Hematology and INSERM1151, Institut Necker-Enfants Malades, University Sorbonne Paris Cité at Descartes and Assistance Publique-Hopitaux de Paris, Paris, France.,Institut Carnot Lymphome, Toulouse, France.,Laboratoire d'Excellence Toulouse Cancer and after Cancer (Labex TOUCAN), Toulouse, France.,European Research Initiative on ALK-Related Malignancies, Cambridge, United Kingdom, Vienna, Austria, and Toulouse, France
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47
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Abstract
The innate immune response is a rapid response to pathogens or danger signals. It is precisely activated not only to efficiently eliminate pathogens but also to avoid excessive inflammation and tissue damage. cis-Regulatory element-associated chromatin architecture shaped by epigenetic factors, which we define as the epiregulome, endows innate immune cells with specialized phenotypes and unique functions by establishing cell-specific gene expression patterns, and it also contributes to resolution of the inflammatory response. In this review, we focus on two aspects: (a) how niche signals during lineage commitment or following infection and pathogenic stress program epiregulomes by regulating gene expression levels, enzymatic activities, or gene-specific targeting of chromatin modifiers and (b) how the programed epiregulomes in turn mediate regulation of gene-specific expression, which contributes to controlling the development of innate cells, or the response to infection and inflammation, in a timely manner. We also discuss the effects of innate immunometabolic rewiring on epiregulomes and speculate on several future challenges to be encountered during the exploration of the master regulators of epiregulomes in innate immunity and inflammation.
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Affiliation(s)
- Qian Zhang
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; , .,National Key Laboratory of Medical Immunology, Institute of Immunology, Navy Military Medical University, Shanghai 200433, China
| | - Xuetao Cao
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; , .,National Key Laboratory of Medical Immunology, Institute of Immunology, Navy Military Medical University, Shanghai 200433, China.,Laboratory of Immunity and Inflammation, College of Life Sciences, Nankai University, Tianjin 300071, China
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48
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Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S. Chromatin accessibility profiling methods. NATURE REVIEWS. METHODS PRIMERS 2021; 1:10. [PMID: 38410680 PMCID: PMC10895463 DOI: 10.1038/s43586-020-00008-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 02/06/2023]
Abstract
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied characteristic of the eukaryotic genome. As active regulatory DNA elements are generally 'accessible', the genome-wide profiling of chromatin accessibility can be used to identify candidate regulatory genomic regions in a tissue or cell type. Multiple biochemical methods have been developed to profile chromatin accessibility, both in bulk and at the single-cell level. Depending on the method, enzymatic cleavage, transposition or DNA methyltransferases are used, followed by high-throughput sequencing, providing a view of genome-wide chromatin accessibility. In this Primer, we discuss these biochemical methods, as well as bioinformatics tools for analysing and interpreting the generated data, and insights into the key regulators underlying developmental, evolutionary and disease processes. We outline standards for data quality, reproducibility and deposition used by the genomics community. Although chromatin accessibility profiling is invaluable to study gene regulation, alone it provides only a partial view of this complex process. Orthogonal assays facilitate the interpretation of accessible regions with respect to enhancer-promoter proximity, functional transcription factor binding and regulatory function. We envision that technological improvements including single-molecule, multi-omics and spatial methods will bring further insight into the secrets of genome regulation.
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Affiliation(s)
- Liesbeth Minnoye
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lixia Pan
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | | | - Stefano Secchia
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | | | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | | | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Stein Aerts
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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49
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de Carvalho MV, Gonçalves-de-Albuquerque CF, Silva AR. PPAR Gamma: From Definition to Molecular Targets and Therapy of Lung Diseases. Int J Mol Sci 2021; 22:ijms22020805. [PMID: 33467433 PMCID: PMC7830538 DOI: 10.3390/ijms22020805] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily that regulate the expression of genes related to lipid and glucose metabolism and inflammation. There are three members: PPARα, PPARβ or PPARγ. PPARγ have several ligands. The natural agonists are omega 9, curcumin, eicosanoids and others. Among the synthetic ligands, we highlight the thiazolidinediones, clinically used as an antidiabetic. Many of these studies involve natural or synthetic products in different pathologies. The mechanisms that regulate PPARγ involve post-translational modifications, such as phosphorylation, sumoylation and ubiquitination, among others. It is known that anti-inflammatory mechanisms involve the inhibition of other transcription factors, such as nuclear factor kB(NFκB), signal transducer and activator of transcription (STAT) or activator protein 1 (AP-1), or intracellular signaling proteins such as mitogen-activated protein (MAP) kinases. PPARγ transrepresses other transcription factors and consequently inhibits gene expression of inflammatory mediators, known as biomarkers for morbidity and mortality, leading to control of the exacerbated inflammation that occurs, for instance, in lung injury/acute respiratory distress. Many studies have shown the therapeutic potentials of PPARγ on pulmonary diseases. Herein, we describe activities of the PPARγ as a modulator of inflammation, focusing on lung injury and including definition and mechanisms of regulation, biological effects and molecular targets, and its role in lung diseases caused by inflammatory stimuli, bacteria and virus, and molecular-based therapy.
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Affiliation(s)
- Márcia V. de Carvalho
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil;
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Cassiano F. Gonçalves-de-Albuquerque
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil;
- Laboratório de Imunofarmacologia, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro 20211-010, Brazil
- Programa de Pós-Graduação em Biologia Molecular e Celular, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro 20211-010, Brazil
- Correspondence: (C.F.G.-d.-A.); (A.R.S.)
| | - Adriana R. Silva
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil;
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
- Correspondence: (C.F.G.-d.-A.); (A.R.S.)
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50
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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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