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Meng M, Zhong Z, Song L, Zhang Z, Yin X, Xie X, Tian L, Wu W, Yang Y, Deng Y, Peng H, Wu S, Ran G, Lin Y, Lai Q, Bi Q, Yan F, Ji Y, Wang Y, Li X, Yi P, Yu J, Deng Y. mTOR Signaling Promotes Rapid m6A mRNA Methylation to Regulate NK-Cell Activation and Effector Functions. Cancer Immunol Res 2024; 12:1039-1057. [PMID: 38640466 DOI: 10.1158/2326-6066.cir-23-0339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 01/13/2024] [Accepted: 04/18/2024] [Indexed: 04/21/2024]
Abstract
NK cells can be rapidly activated in response to cytokines during host defense against malignant cells or viral infection. However, it remains unclear what mechanisms precisely and rapidly regulate the expression of a large number of genes involved in activating NK cells. In this study, we discovered that NK-cell N6-methyladenosine (m6A) methylation levels were rapidly upregulated upon short-term NK-cell activation and were repressed in the tumor microenvironment (TME). Deficiency of methyltransferase-like 3 (METTL3) or METTL14 moderately influenced NK-cell homeostasis, while double-knockout of METTL3/14 more significantly impacted NK-cell homeostasis, maturation, and antitumor immunity. This suggests a cooperative role of METTL3 and METTL14 in regulating NK-cell development and effector functions. Using methylated RNA immunoprecipitation sequencing, we demonstrated that genes involved in NK-cell effector functions, such as Prf1 and Gzmb, were directly modified by m6A methylation. Furthermore, inhibiting mTOR complex 1 activation prevented m6A methylation levels from increasing when NK cells were activated, and this could be restored by S-adenosylmethionine supplementation. Collectively, we have unraveled crucial roles for rapid m6A mRNA methylation downstream of the mTOR complex 1-S-adenosylmethionine signal axis in regulating NK-cell activation and effector functions.
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Affiliation(s)
- Meng Meng
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
- School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Zhaoyang Zhong
- The Fifth People's Hospital of Chongqing, Chongqing, China
| | - Liang Song
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China
| | - Zhaohui Zhang
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Xiaofeng Yin
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Xiqiang Xie
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Lei Tian
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, California
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, California
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, China
| | - Yao Yang
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Yafei Deng
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, China
| | - Hongyan Peng
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, China
| | - Shuting Wu
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, China
| | - Guanghe Ran
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Yuqing Lin
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Qiangqiang Lai
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Qinghua Bi
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Fulin Yan
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Yan Ji
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Yang Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaohui Li
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, California
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, California
| | - Youcai Deng
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
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2
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Fan C, Xing X, Murphy SJH, Poursine-Laurent J, Schmidt H, Parikh BA, Yoon J, Choudhary MNK, Saligrama N, Piersma SJ, Yokoyama WM, Wang T. Cis-regulatory evolution of the recently expanded Ly49 gene family. Nat Commun 2024; 15:4839. [PMID: 38844462 PMCID: PMC11156856 DOI: 10.1038/s41467-024-48990-y] [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: 11/13/2023] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Comparative genomics has revealed the rapid expansion of multiple gene families involved in immunity. Members within each gene family often evolved distinct roles in immunity. However, less is known about the evolution of their epigenome and cis-regulation. Here we systematically profile the epigenome of the recently expanded murine Ly49 gene family that mainly encode either inhibitory or activating surface receptors on natural killer cells. We identify a set of cis-regulatory elements (CREs) for activating Ly49 genes. In addition, we show that in mice, inhibitory and activating Ly49 genes are regulated by two separate sets of proximal CREs, likely resulting from lineage-specific losses of CRE activity. Furthermore, we find that some Ly49 genes are cross-regulated by the CREs of other Ly49 genes, suggesting that the Ly49 family has begun to evolve a concerted cis-regulatory mechanism. Collectively, we demonstrate the different modes of cis-regulatory evolution for a rapidly expanding gene family.
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Affiliation(s)
- Changxu Fan
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Samuel J H Murphy
- Department of Neurology, Washington University School of Medicine, St. Louis, 63110, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, 63110, USA
| | - Jennifer Poursine-Laurent
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA
| | - Heather Schmidt
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Bijal A Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Jeesang Yoon
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA
| | - Mayank N K Choudhary
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Naresha Saligrama
- Department of Neurology, Washington University School of Medicine, St. Louis, 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, 63110, USA
| | - Sytse J Piersma
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, 63110, USA.
| | - Wayne M Yokoyama
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA.
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA.
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63110, USA.
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3
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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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4
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Hermans L, O’Sullivan TE. No time to die: Epigenetic regulation of natural killer cell survival. Immunol Rev 2024; 323:61-79. [PMID: 38426615 PMCID: PMC11102341 DOI: 10.1111/imr.13314] [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] [Indexed: 03/02/2024]
Abstract
NK cells are short-lived innate lymphocytes that can mediate antigen-independent responses to infection and cancer. However, studies from the past two decades have shown that NK cells can acquire transcriptional and epigenetic modifications during inflammation that result in increased survival and lifespan. These findings blur the lines between the innate and adaptive arms of the immune system, and suggest that the homeostatic mechanisms that govern the persistence of innate immune cells are malleable. Indeed, recent studies have shown that NK cells undergo continuous and strictly regulated adaptations controlling their survival during development, tissue residency, and following inflammation. In this review, we summarize our current understanding of the critical factors regulating NK cell survival throughout their lifespan, with a specific emphasis on the epigenetic modifications that regulate the survival of NK cells in various contexts. A precise understanding of the molecular mechanisms that govern NK cell survival will be important to enhance therapies for cancer and infectious diseases.
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Affiliation(s)
- Leen Hermans
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095
| | - Timothy E. O’Sullivan
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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5
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Fortelny N, Farlik M, Fife V, Gorki AD, Lassnig C, Maurer B, Meissl K, Dolezal M, Boccuni L, Ravi Sundar Jose Geetha A, Akagha MJ, Karjalainen A, Shoebridge S, Farhat A, Mann U, Jain R, Tikoo S, Zila N, Esser-Skala W, Krausgruber T, Sitnik K, Penz T, Hladik A, Suske T, Zahalka S, Senekowitsch M, Barreca D, Halbritter F, Macho-Maschler S, Weninger W, Neubauer HA, Moriggl R, Knapp S, Sexl V, Strobl B, Decker T, Müller M, Bock C. JAK-STAT signaling maintains homeostasis in T cells and macrophages. Nat Immunol 2024; 25:847-859. [PMID: 38658806 PMCID: PMC11065702 DOI: 10.1038/s41590-024-01804-1] [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: 07/22/2022] [Accepted: 03/07/2024] [Indexed: 04/26/2024]
Abstract
Immune cells need to sustain a state of constant alertness over a lifetime. Yet, little is known about the regulatory processes that control the fluent and fragile balance that is called homeostasis. Here we demonstrate that JAK-STAT signaling, beyond its role in immune responses, is a major regulator of immune cell homeostasis. We investigated JAK-STAT-mediated transcription and chromatin accessibility across 12 mouse models, including knockouts of all STAT transcription factors and of the TYK2 kinase. Baseline JAK-STAT signaling was detected in CD8+ T cells and macrophages of unperturbed mice-but abrogated in the knockouts and in unstimulated immune cells deprived of their normal tissue context. We observed diverse gene-regulatory programs, including effects of STAT2 and IRF9 that were independent of STAT1. In summary, our large-scale dataset and integrative analysis of JAK-STAT mutant and wild-type mice uncovered a crucial role of JAK-STAT signaling in unstimulated immune cells, where it contributes to a poised epigenetic and transcriptional state and helps prepare these cells for rapid response to immune stimuli.
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Affiliation(s)
- Nikolaus Fortelny
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Tumor Biology and Immunology, Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, Salzburg, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.
| | - Victoria Fife
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna-Dorothea Gorki
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Caroline Lassnig
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Barbara Maurer
- Pharmacology and Toxicology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Katrin Meissl
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Marlies Dolezal
- Platform for Bioinformatics and Biostatistics, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Laura Boccuni
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | | | - Mojoyinola Joanna Akagha
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Anzhelika Karjalainen
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Stephen Shoebridge
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Asma Farhat
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Ulrike Mann
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Rohit Jain
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Shweta Tikoo
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Nina Zila
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Esser-Skala
- Center for Tumor Biology and Immunology, Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, Salzburg, Austria
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence, Center for Medical Data Science, Medical University of Vienna, Vienna, Austria
| | - Katarzyna Sitnik
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anastasiya Hladik
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Tobias Suske
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Sophie Zahalka
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Martin Senekowitsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniele Barreca
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Florian Halbritter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sabine Macho-Maschler
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Heidi A Neubauer
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Richard Moriggl
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Sylvia Knapp
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Veronika Sexl
- Pharmacology and Toxicology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
- University of Innsbruck, Innsbruck, Austria
| | - Birgit Strobl
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Decker
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Mathias Müller
- Animal Breeding and Genetics and VetBiomodels, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Institute of Artificial Intelligence, Center for Medical Data Science, Medical University of Vienna, Vienna, Austria.
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6
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Watson NB, Patel RK, Kean C, Veazey J, Oyesola OO, Laniewski N, Grenier JK, Wang J, Tabilas C, Yee Mon KJ, McNairn AJ, Peng SA, Wesnak SP, Nzingha K, Davenport MP, Tait Wojno ED, Scheible KM, Smith NL, Grimson A, Rudd BD. The gene regulatory basis of bystander activation in CD8 + T cells. Sci Immunol 2024; 9:eadf8776. [PMID: 38394230 DOI: 10.1126/sciimmunol.adf8776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/26/2024] [Indexed: 02/25/2024]
Abstract
CD8+ T cells are classically recognized as adaptive lymphocytes based on their ability to recognize specific foreign antigens and mount memory responses. However, recent studies indicate that some antigen-inexperienced CD8+ T cells can respond to innate cytokines alone in the absence of cognate T cell receptor stimulation, a phenomenon referred to as bystander activation. Here, we demonstrate that neonatal CD8+ T cells undergo a robust and diverse program of bystander activation, which corresponds to enhanced innate-like protection against unrelated pathogens. Using a multi-omics approach, we found that the ability of neonatal CD8+ T cells to respond to innate cytokines derives from their capacity to undergo rapid chromatin remodeling, resulting in the usage of a distinct set of enhancers and transcription factors typically found in innate-like T cells. We observed that the switch between innate and adaptive functions in the CD8+ T cell compartment is mediated by changes in the abundance of distinct subsets of cells. The innate CD8+ T cell subset that predominates in early life was also present in adult mice and humans. Our findings provide support for the layered immune hypothesis and indicate that the CD8+ T cell compartment is more functionally diverse than previously thought.
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Affiliation(s)
- Neva B Watson
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Ravi K Patel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Connor Kean
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Janelle Veazey
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Oyebola O Oyesola
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Nathan Laniewski
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jennifer K Grenier
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Jocelyn Wang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Cybelle Tabilas
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Kristel J Yee Mon
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Adrian J McNairn
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Seth A Peng
- Department of Clinical Science, Cornell University, Ithaca, NY 14853, USA
| | - Samantha P Wesnak
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Kito Nzingha
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Miles P Davenport
- Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW 2052, Australia
| | - Elia D Tait Wojno
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Kristin M Scheible
- Department of Pediatrics, University of Rochester, Rochester, NY 14642, USA
| | - Norah L Smith
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
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7
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Di Giorgio E, Cortolezzis Y, Gualandi N, Agostini F, Rapozzi V, Xodo LE. NRF2 interacts with distal enhancer and inhibits nitric oxide synthase 2 expression in KRAS-driven pancreatic cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119606. [PMID: 37852325 DOI: 10.1016/j.bbamcr.2023.119606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Nitric oxide is a pleiotropic free radical produced by three nitric oxide synthases (NOS1-3), of which inducible NOS2 is involved in tumor initiation and progression. In this study, RNA-seq, ChIP-seq and qRT-PCR experiments combined with bioinformatic analyses showed that NRF2 is a repressor of NOS2 gene by maintaining a distal enhancer located 22 kb downstream of TSS in an inactive state. Deletion of NRF2 leads to activation of the enhancer, which exerts a pioneering function before it is fully activated. Specifically, NRF2 controls the expression of NOS2 in response to intracellular oxidative stress and extracellular oxygen pressure. We found that abrogation of NOS2 expression by siRNAs partially reduced the ability of WT Panc-1 cells to form 3D spheroids, but strongly reduced the formation of 3D spheroids by NRF2-depleted Panc-1 cells. Mechanistically, this effect correlates with the finding that NOS2 and nitric oxide stimulate epithelial-to-mesenchymal transition in NRF2-depleted Panc-1 and MIA PaCa-2 cells. We also found that knockdown of NOS2 leads to blockade of 3D matrigel invasion of NRF2-depleted PDAC cells, demonstrating that a short-circuit in the reciprocal regulation of NOS2 and NRF2 attenuates the malignancy of PDAC cells. In summary, we show for the first time that: (i) NRF2 is a suppressor of NOS2 in pancreatic cancer cells; (ii) NRF2 binds to and inactivates an enhancer located 22 kb downstream of TSS of the NOS2 gene; (iii) activation of NOS2 requires suppression of NRF2; (iv) NOS2 is required for NRF2-depleted Panc-1 cells to maintain their malignancy and invasiveness.
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Affiliation(s)
- Eros Di Giorgio
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy.
| | - Ylenia Cortolezzis
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Nicolò Gualandi
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Francesca Agostini
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Valentina Rapozzi
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Luigi E Xodo
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy.
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8
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Hartana CA, Lancien M, Gao C, Rassadkina Y, Lichterfeld M, Yu XG. IL-15-dependent immune crosstalk between natural killer cells and dendritic cells in HIV-1 elite controllers. Cell Rep 2023; 42:113530. [PMID: 38048223 PMCID: PMC10765318 DOI: 10.1016/j.celrep.2023.113530] [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: 03/17/2023] [Revised: 10/04/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
As the principal effector cell population of the innate immune system, natural killer (NK) cells may make critical contributions to natural, immune-mediated control of HIV-1 replication. Using genome-wide assessments of activating and inhibitory chromatin features, we demonstrate here that cytotoxic NK (cNK) cells from elite controllers (ECs) display elevated activating histone modifications at the interleukin 2 (IL-2)/IL-15 receptor β chain and the BCL2 gene loci. These histone changes translate into increased responsiveness of cNK cells to paracrine IL-15 secretion, which coincides with higher levels of IL-15 transcription by myeloid dendritic cells in ECs. The distinct immune crosstalk between these innate immune cell populations results in improved IL-15-dependent cNK cell survival and cytotoxicity, paired with a metabolic profile biased toward IL-15-mediated glycolytic activities. Together, these results suggest that cNK cells from ECs display a programmed IL-15 response signature and support the emerging role of innate immune pathways in natural, drug-free control of HIV-1.
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Affiliation(s)
| | - Melanie Lancien
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA.
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9
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Schnoegl D, Hiesinger A, Huntington ND, Gotthardt D. AP-1 transcription factors in cytotoxic lymphocyte development and antitumor immunity. Curr Opin Immunol 2023; 85:102397. [PMID: 37931499 DOI: 10.1016/j.coi.2023.102397] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 11/08/2023]
Abstract
The proper functioning of cytotoxic lymphocytes, such as natural killer and CD8+ T cells, is essential for effective cancer-immunity and immunotherapy responses. The differentiation of these cells is controlled by several transcription factors (TFs), including members of the activator protein (AP)-1 family. The activity of AP-1 family members is regulated by various immune signaling pathways, which can be triggered by activating or inhibitory receptors as well as cytokines. The target genes controlled by AP-1 TFs are central to generate immunity to pathogens or malignancies. Here, we provide an overview of the current understanding of how AP-1 TFs regulate cytotoxic lymphocytes.
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Affiliation(s)
- Diana Schnoegl
- Institute for Rheumatology and Immunology, Medical University of Graz, Austria; Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Angela Hiesinger
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | | | - Dagmar Gotthardt
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria.
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10
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Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ. Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. eLife 2023; 12:RP89993. [PMID: 37938195 PMCID: PMC10631760 DOI: 10.7554/elife.89993] [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] [Indexed: 11/09/2023] Open
Abstract
Neuronal and behavioral adaptations to novel stimuli are regulated by temporally dynamic waves of transcriptional activity, which shape neuronal function and guide enduring plasticity. Neuronal activation promotes expression of an immediate early gene (IEG) program comprised primarily of activity-dependent transcription factors, which are thought to regulate a second set of late response genes (LRGs). However, while the mechanisms governing IEG activation have been well studied, the molecular interplay between IEGs and LRGs remain poorly characterized. Here, we used transcriptomic and chromatin accessibility profiling to define activity-driven responses in rat striatal neurons. As expected, neuronal depolarization generated robust changes in gene expression, with early changes (1 hr) enriched for inducible transcription factors and later changes (4 hr) enriched for neuropeptides, synaptic proteins, and ion channels. Remarkably, while depolarization did not induce chromatin remodeling after 1 hr, we found broad increases in chromatin accessibility at thousands of sites in the genome at 4 hr after neuronal stimulation. These putative regulatory elements were found almost exclusively at non-coding regions of the genome, and harbored consensus motifs for numerous activity-dependent transcription factors such as AP-1. Furthermore, blocking protein synthesis prevented activity-dependent chromatin remodeling, suggesting that IEG proteins are required for this process. Targeted analysis of LRG loci identified a putative enhancer upstream of Pdyn (prodynorphin), a gene encoding an opioid neuropeptide implicated in motivated behavior and neuropsychiatric disease states. CRISPR-based functional assays demonstrated that this enhancer is both necessary and sufficient for Pdyn transcription. This regulatory element is also conserved at the human PDYN locus, where its activation is sufficient to drive PDYN transcription in human cells. These results suggest that IEGs participate in chromatin remodeling at enhancers and identify a conserved enhancer that may act as a therapeutic target for brain disorders involving dysregulation of Pdyn.
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Affiliation(s)
- Robert A Phillips
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Ethan Wan
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Jennifer J Tuscher
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - David Reid
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Olivia R Drake
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Lara Ianov
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
- Civitan International Research Center, University of Alabama at BirminghamBirminghamUnited States
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
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11
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Santosa EK, Sun JC. Cardinal features of immune memory in innate lymphocytes. Nat Immunol 2023; 24:1803-1812. [PMID: 37828377 PMCID: PMC10998651 DOI: 10.1038/s41590-023-01607-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/28/2023] [Indexed: 10/14/2023]
Abstract
The ability of vertebrates to 'remember' previous infections had once been attributed exclusively to adaptive immunity. We now appreciate that innate lymphocytes also possess memory properties akin to those of adaptive immune cells. In this Review, we draw parallels from T cell biology to explore the key features of immune memory in innate lymphocytes, including quantity, quality, and location. We discuss the signals that trigger clonal or clonal-like expansion in innate lymphocytes, and highlight recent studies that shed light on the complex cellular and molecular crosstalk between metabolism, epigenetics, and transcription responsible for differentiating innate lymphocyte responses towards a memory fate. Additionally, we explore emerging evidence that activated innate lymphocytes relocate and establish themselves in specific peripheral tissues during infection, which may facilitate an accelerated response program akin to those of tissue-resident memory T cells.
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Affiliation(s)
- Endi K Santosa
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA.
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12
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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: 1] [Impact Index Per Article: 1.0] [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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13
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Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ. Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543489. [PMID: 37333110 PMCID: PMC10274686 DOI: 10.1101/2023.06.02.543489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Neuronal and behavioral adaptations to novel stimuli are regulated by temporally dynamic waves of transcriptional activity, which shape neuronal function and guide enduring plasticity. Neuronal activation promotes expression of an immediate early gene (IEG) program comprised primarily of activity-dependent transcription factors, which are thought to regulate a second set of late response genes (LRGs). However, while the mechanisms governing IEG activation have been well studied, the molecular interplay between IEGs and LRGs remain poorly characterized. Here, we used transcriptomic and chromatin accessibility profiling to define activity-driven responses in rat striatal neurons. As expected, neuronal depolarization generated robust changes in gene expression, with early changes (1 h) enriched for inducible transcription factors and later changes (4 h) enriched for neuropeptides, synaptic proteins, and ion channels. Remarkably, while depolarization did not induce chromatin remodeling after 1 h, we found broad increases in chromatin accessibility at thousands of sites in the genome at 4 h after neuronal stimulation. These putative regulatory elements were found almost exclusively at non-coding regions of the genome, and harbored consensus motifs for numerous activity-dependent transcription factors such as AP-1. Furthermore, blocking protein synthesis prevented activity-dependent chromatin remodeling, suggesting that IEG proteins are required for this process. Targeted analysis of LRG loci identified a putative enhancer upstream of Pdyn (prodynorphin), a gene encoding an opioid neuropeptide implicated in motivated behavior and neuropsychiatric disease states. CRISPR-based functional assays demonstrated that this enhancer is both necessary and sufficient for Pdyn transcription. This regulatory element is also conserved at the human PDYN locus, where its activation is sufficient to drive PDYN transcription in human cells. These results suggest that IEGs participate in chromatin remodeling at enhancers and identify a conserved enhancer that may act as a therapeutic target for brain disorders involving dysregulation of Pdyn.
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Affiliation(s)
- Robert A. Phillips
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ethan Wan
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jennifer J. Tuscher
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David Reid
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Olivia R. Drake
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lara Ianov
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jeremy J. Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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14
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Chowdhary K, Benoist C. A variegated model of transcription factor function in the immune system. Trends Immunol 2023; 44:530-541. [PMID: 37258360 PMCID: PMC10332489 DOI: 10.1016/j.it.2023.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 06/02/2023]
Abstract
Specific combinations of transcription factors (TFs) control the gene expression programs that underlie specialized immune responses. Previous models of TF function in immunocytes had restricted each TF to a single functional categorization [e.g., lineage-defining (LDTFs) vs. signal-dependent TFs (SDTFs)] within one cell type. Synthesizing recent results, we instead propose a variegated model of immunological TF function, whereby many TFs have flexible and different roles across distinct cell states, contributing to cell phenotypic diversity. We discuss evidence in support of this variegated model, describe contextual inputs that enable TF diversification, and look to the future to imagine warranted experimental and computational tools to build quantitative and predictive models of immunocyte gene regulatory networks.
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15
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Lee EC, Kim K, Jung WJ, Kim HP. Vorinostat-induced acetylation of RUNX3 reshapes transcriptional profile through long-range enhancer-promoter interactions in natural killer cells. BMB Rep 2023; 56:398-403. [PMID: 37220907 PMCID: PMC10390292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/07/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Natural killer (NK) cells are an essential part of the innate immune system that helps control infections and tumors. Recent studies have shown that Vorinostat, a histone deacetylase (HDAC) inhibitor, can cause significant changes in gene expression and signaling pathways in NK cells. Since gene expression in eukaryotic cells is closely linked to the complex three-dimensional (3D) chromatin architecture, an integrative analysis of the transcriptome, histone profiling, chromatin accessibility, and 3D genome organization is needed to gain a more comprehensive understanding of how Vorinostat impacts transcription regulation of NK cells from a chromatin-based perspective. The results demonstrate that Vorinostat treatment reprograms the enhancer landscapes of the human NK-92 NK cell line while overall 3D genome organization remains largely stable. Moreover, we identified that the Vorinostat-induced RUNX3 acetylation is linked to the increased enhancer activity, leading to elevated expression of immune response-related genes via long-range enhancerpromoter chromatin interactions. In summary, these findings have important implications in the development of new therapies for cancer and immune-related diseases by shedding light on the mechanisms underlying Vorinostat's impact on transcriptional regulation in NK cells within the context of 3D enhancer network. [BMB Reports 2023; 56(7): 398-403].
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Affiliation(s)
- Eun-Chong Lee
- Department of Tropical Medicine, Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Kyungwoo Kim
- Department of Tropical Medicine, Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Woong-Jae Jung
- Department of Tropical Medicine, Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hyoung-Pyo Kim
- Department of Tropical Medicine, Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
- Yonsei Genome Center, Yonsei University College of Medicine, Seoul 03722, Korea
- Division of Biology, Pohang University of Science and Technology, Pohang 37673, Korea
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16
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Foo YY, Tiah A, Aung SW. Harnessing the power of memory-like NK cells to fight cancer. Clin Exp Immunol 2023; 212:212-223. [PMID: 36866467 PMCID: PMC10243875 DOI: 10.1093/cei/uxad030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/16/2023] [Accepted: 03/01/2023] [Indexed: 03/04/2023] Open
Abstract
Natural killer (NK) cells possess the innate ability to eliminate cancerous cells effectively. Their crucial role in immunosurveillance has been widely recognized and exploited for therapeutic intervention. Despite the fast-acting nature of NK cells, NK adoptive cell transfer lacks favorable response in some patients. Patient NK cells often display diminished phenotype in preventing cancer progression resulting in poor prognosis. Tumor microenvironment plays a significant role in causing the downfall of NK cells in patients. The release of inhibitory factors by tumor microenvironment hinders normal function of NK cells against tumor. To overcome this challenge, therapeutic strategies such as cytokine stimulation and genetic manipulation are being investigated to improve NK tumor-killing capacity. One of the promising approaches includes generation of more competent NK cells via ex vivo cytokines activation and proliferation. Cytokine-induced ML-NK demonstrated phenotypic alterations such as enhanced expression of activating receptors which help elevate their antitumor response. Previous preclinical studies showed enhanced cytotoxicity and IFNγ production in ML-NK cells compared to normal NK cells against malignant cells. Similar effects are shown in clinical studies in which MK-NK demonstrated encouraging results in treating hematological cancer. However, there is still a lack of in-depth studies using ML-NK in treating different types of tumors and cancers. With convincing preliminary response, this cell-based approach could be used to complement other therapeutic modalities to achieve better clinical outcomes.
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Affiliation(s)
- Yun Yan Foo
- Department of Research and Development, CELLAAX Sdn Bhd, Block D & E, No. 3, Jalan Tasik, Mines Wellness City, Seri Kembangan, 43300 Selangor, Malaysia
| | - Angelina Tiah
- Department of Research and Development, CELLAAX Sdn Bhd, Block D & E, No. 3, Jalan Tasik, Mines Wellness City, Seri Kembangan, 43300 Selangor, Malaysia
- Beike 23 Century Laboratory, 23 Century International Life Science Centre, Block D & E, No. 3, Jalan Tasik, Mines Wellness City, Seri Kembangan, 43300 Selangor, Malaysia
| | - Shuh Wen Aung
- Beike 23 Century Laboratory, 23 Century International Life Science Centre, Block D & E, No. 3, Jalan Tasik, Mines Wellness City, Seri Kembangan, 43300 Selangor, Malaysia
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17
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Abstract
Inflammatory bowel diseases (IBD) are currently recognized to involve chronic intestinal inflammation in genetically susceptible individuals. Patients with IBD mainly develop gastrointestinal inflammation, but it is sometimes accompanied by extraintestinal manifestations such as arthritis, erythema nodosum, episcleritis, pyoderma gangrenosum, uveitis, and primary sclerosing cholangitis. These clinical aspects imply the importance of interorgan networks in IBD. In the gastrointestinal tract, immune cells are influenced by multiple local environmental factors including microbiota, dietary environment, and intercellular networks, which further alter molecular networks in immune cells. Therefore, deciphering networks at interorgan, intercellular, and intracellular levels should help to obtain a comprehensive understanding of IBD. This review focuses on the intestinal immune system, which governs the physiological and pathological functions of the digestive system in harmony with the other organs.
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18
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Brandão YDO, Molento MB. A Systematic Review of Apicomplexa Looking into Epigenetic Pathways and the Opportunity for Novel Therapies. Pathogens 2023; 12:pathogens12020299. [PMID: 36839571 PMCID: PMC9963874 DOI: 10.3390/pathogens12020299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Interest in host epigenetic changes during apicomplexan infections increased in the last decade, mainly due to the emergence of new therapies directed to these alterations. This review aims to carry out a bibliometric analysis of the publications related to host epigenetic changes during apicomplexan infections and to summarize the main studied pathways in this context, pointing out those that represent putative drug targets. We used four databases for the article search. After screening, 116 studies were included. The bibliometric analysis revealed that the USA and China had the highest number of relevant publications. The evaluation of the selected studies revealed that Toxoplasma gondii was considered in most of the studies, non-coding RNA was the most frequently reported epigenetic event, and host defense was the most explored pathway. These findings were reinforced by an analysis of the co-occurrence of keywords. Even though we present putative targets for repurposing epidrugs and ncRNA-based drugs in apicomplexan infections, we understand that more detailed knowledge of the hosts' epigenetic pathways is still needed before establishing a definitive drug target.
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19
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Santosa EK, Lau CM, Sahin M, Leslie CS, Sun JC. 3D Chromatin Dynamics during Innate and Adaptive Immune Memory Acquisition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524322. [PMID: 36711541 PMCID: PMC9882143 DOI: 10.1101/2023.01.16.524322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Immune cells responding to pathogens undergo molecular changes that are intimately linked to genome organization. Recent work has demonstrated that natural killer (NK) and CD8 + T cells experience substantial transcriptomic and epigenetic rewiring during their differentiation from naïve to effector to memory cells. Whether these molecular adaptations are accompanied by changes in three-dimensional (3D) chromatin architecture is unknown. In this study, we combine histone profiling, ATAC-seq, RNA-seq and high-throughput chromatin capture (HiC) assay to investigate the dynamics of one-dimensional (1D) and 3D chromatin during the differentiation of innate and adaptive lymphocytes. To this end, we discovered a coordinated 1D and 3D epigenetic remodeling during innate immune memory differentiation, and demonstrate that effector CD8 + T cells adopt an NK-like architectural program that is maintained in memory cells. Altogether, our study reveals the dynamic nature of the 1D and 3D genome during the formation of innate and adaptive immunological memory.
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20
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Chopp L, Redmond C, O'Shea JJ, Schwartz DM. From thymus to tissues and tumors: A review of T-cell biology. J Allergy Clin Immunol 2023; 151:81-97. [PMID: 36272581 PMCID: PMC9825672 DOI: 10.1016/j.jaci.2022.10.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
Abstract
T cells are critical orchestrators of the adaptive immune response that optimally eliminate a specific pathogen. Aberrant T-cell development and function are implicated in a broad range of human disease including immunodeficiencies, autoimmune diseases, and allergic diseases. Accordingly, therapies targeting T cells and their effector cytokines have markedly improved the care of patients with immune dysregulatory diseases. Newer discoveries concerning T-cell-mediated antitumor immunity and T-cell exhaustion have further prompted development of highly effective and novel treatment modalities for malignancies, including checkpoint inhibitors and antigen-reactive T cells. Recent discoveries are also uncovering the depth and variability of T-cell phenotypes: while T cells have long been described using a subset-based classification system, next-generation sequencing technologies suggest an astounding degree of complexity and heterogeneity at the single-cell level.
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Affiliation(s)
- Laura Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda
| | - Christopher Redmond
- Clinical Fellowship Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda
| | - Daniella M Schwartz
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda; Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh.
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21
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The JAK-STAT pathway at 30: Much learned, much more to do. Cell 2022; 185:3857-3876. [PMID: 36240739 PMCID: PMC9815833 DOI: 10.1016/j.cell.2022.09.023] [Citation(s) in RCA: 219] [Impact Index Per Article: 109.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/01/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022]
Abstract
The discovery of the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway arose from investigations of how cells respond to interferons (IFNs), revealing a paradigm in cell signaling conserved from slime molds to mammals. These discoveries revealed mechanisms underlying rapid gene expression mediated by a wide variety of extracellular polypeptides including cytokines, interleukins, and related factors. This knowledge has provided numerous insights into human disease, from immune deficiencies to cancer, and was rapidly translated to new drugs for autoimmune, allergic, and infectious diseases, including COVID-19. Despite these advances, major challenges and opportunities remain.
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22
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Abdi K, Laky K, Abshari M, Hill EM, Lantz L, Singh NJ, Long EO. Dendritic cells Trigger IFN-γ secretion by NK cells independent of IL-12 and IL-18. Eur J Immunol 2022; 52:1431-1440. [PMID: 35816444 PMCID: PMC10608798 DOI: 10.1002/eji.202149733] [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: 11/16/2021] [Revised: 06/09/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022]
Abstract
It is commonly believed that IL-12 produced by DCs in response to pathogens is the first signal that stimulates the production of IFN-γ by NK cells. However, IL-12 production by DCs in response to bacterial LPS depends on either engagement of CD40 by CD40L on activated T cells or IFN-γ from NK cells. This suggests that during the primary immune response, NK cells produce IFN-γ before IL-12 production by DCs. Here, using single-cell measurements, cell sorting and mouse lines deficient in IL-12, IL-23, type I IFN receptor and the IL-18 receptor, we show that a subset of BM-derived DCs characterized by low expression of MHC class II (MHCIIlow ) stimulates IFN-γ production by NK cells. The expression of Toll-like Receptor (TLR) 4 on DCs but not NK cells was required for such NK-derived IFN-γ. In addition, soluble factor(s) produced by LPS-activated MHCIIlow DCs were sufficient to induce IFN-γ production by NK cells independent of IL-12, IL-23, and IL-18. This response was enhanced in the presence of a low dose of IL-2. These results delineate a previously unknown pathway of DC-mediated IFN-γ production by NK cells, which is independent of commonly known cytokines.
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Affiliation(s)
- Kaveh Abdi
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - Karen Laky
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - Mehrnoosh Abshari
- National Institute of Dental and Craniofacial Research, National Institute of Health, Bethesda, MD, USA
| | - Elizabeth M. Hill
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Larry Lantz
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - Nevil J. Singh
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eric O. Long
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
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23
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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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24
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Kissiov DU, Ethell A, Chen S, Wolf NK, Zhang C, Dang SM, Jo Y, Madsen KN, Paranjpe I, Lee AY, Chim B, Muljo SA, Raulet DH. Binary outcomes of enhancer activity underlie stable random monoallelic expression. eLife 2022; 11:e74204. [PMID: 35617021 PMCID: PMC9135403 DOI: 10.7554/elife.74204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Mitotically stable random monoallelic gene expression (RME) is documented for a small percentage of autosomal genes. We developed an in vivo genetic model to study the role of enhancers in RME using high-resolution single-cell analysis of natural killer (NK) cell receptor gene expression and enhancer deletions in the mouse germline. Enhancers of the RME NK receptor genes were accessible and enriched in H3K27ac on silent and active alleles alike in cells sorted according to allelic expression status, suggesting enhancer activation and gene expression status can be decoupled. In genes with multiple enhancers, enhancer deletion reduced gene expression frequency, in one instance converting the universally expressed gene encoding NKG2D into an RME gene, recapitulating all aspects of natural RME including mitotic stability of both the active and silent states. The results support the binary model of enhancer action, and suggest that RME is a consequence of general properties of gene regulation by enhancers rather than an RME-specific epigenetic program. Therefore, many and perhaps all genes may be subject to some degree of RME. Surprisingly, this was borne out by analysis of several genes that define different major hematopoietic lineages, that were previously thought to be universally expressed within those lineages: the genes encoding NKG2D, CD45, CD8α, and Thy-1. We propose that intrinsically probabilistic gene allele regulation is a general property of enhancer-controlled gene expression, with previously documented RME representing an extreme on a broad continuum.
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Affiliation(s)
- Djem U Kissiov
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Alexander Ethell
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Sean Chen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Natalie K Wolf
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Chenyu Zhang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Susanna M Dang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Yeara Jo
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Katrine N Madsen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Ishan Paranjpe
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Angus Y Lee
- Cancer Research Laboratory, University of California, BerkeleyBerkeleyUnited States
| | - Bryan Chim
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Stefan A Muljo
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - David H Raulet
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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25
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Hasim MS, Marotel M, Hodgins JJ, Vulpis E, Makinson OJ, Asif S, Shih HY, Scheer AK, MacMillan O, Alonso FG, Burke KP, Cook DP, Li R, Petrucci MT, Santoni A, Fallon PG, Sharpe AH, Sciumè G, Veillette A, Zingoni A, Gray DA, McCurdy A, Ardolino M. When killers become thieves: Trogocytosed PD-1 inhibits NK cells in cancer. SCIENCE ADVANCES 2022; 8:eabj3286. [PMID: 35417234 PMCID: PMC9007500 DOI: 10.1126/sciadv.abj3286] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 02/23/2022] [Indexed: 05/12/2023]
Abstract
Trogocytosis modulates immune responses, with still unclear underlying molecular mechanisms. Using leukemia mouse models, we found that lymphocytes perform trogocytosis at high rates with tumor cells. While performing trogocytosis, both Natural Killer (NK) and CD8+ T cells acquire the checkpoint receptor PD-1 from leukemia cells. In vitro and in vivo investigation revealed that PD-1 on the surface of NK cells, rather than being endogenously expressed, was derived entirely from leukemia cells in a SLAM receptor-dependent fashion. PD-1 acquired via trogocytosis actively suppressed NK cell antitumor immunity. PD-1 trogocytosis was corroborated in patients with clonal plasma cell disorders, where NK cells that stained for PD-1 also stained for tumor cell markers. Our results, in addition to shedding light on a previously unappreciated mechanism underlying the presence of PD-1 on NK and cytotoxic T cells, reveal the immunoregulatory effect of membrane transfer occurring when immune cells contact tumor cells.
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Affiliation(s)
- Mohamed S. Hasim
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- CI3, University of Ottawa, Ottawa, ON, Canada
| | - Marie Marotel
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- CI3, University of Ottawa, Ottawa, ON, Canada
| | - Jonathan J. Hodgins
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- CI3, University of Ottawa, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Elisabetta Vulpis
- Department of Molecular Medicine, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia—Fondazione Cenci-Bolognetti, Rome, Italy
| | - Olivia J. Makinson
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- CI3, University of Ottawa, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Sara Asif
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- CI3, University of Ottawa, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Han-Yun Shih
- Neuro-Immune Regulome Unit, National Eye Institute, NIH, Bethesda, MD, USA
| | - Amit K. Scheer
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Olivia MacMillan
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- CI3, University of Ottawa, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Felipe G. Alonso
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Kelly P. Burke
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - David P. Cook
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Rui Li
- Department of Medicine, McGill University, Montréal, QC, Canada
- Laboratory of Molecular Oncology, Institut de recherches cliniques de Montréal, Montréal, QC, Canada
| | - Maria Teresa Petrucci
- Department of Cellular Biotechnology and Hematology, “Sapienza” University of Rome, Rome, Italy
| | - Angela Santoni
- Department of Molecular Medicine, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia—Fondazione Cenci-Bolognetti, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Padraic G. Fallon
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Arlene H. Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
| | - Giuseppe Sciumè
- Department of Molecular Medicine, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia—Fondazione Cenci-Bolognetti, Rome, Italy
| | - André Veillette
- Department of Medicine, McGill University, Montréal, QC, Canada
- Laboratory of Molecular Oncology, Institut de recherches cliniques de Montréal, Montréal, QC, Canada
- Department of Medicine, University of Montréal, Montréal, QC, Canada
| | - Alessandra Zingoni
- Department of Molecular Medicine, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia—Fondazione Cenci-Bolognetti, Rome, Italy
| | - Douglas A. Gray
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Arleigh McCurdy
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Division of Hematology, Department of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Michele Ardolino
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- CI3, University of Ottawa, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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26
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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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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: 17] [Impact Index Per Article: 8.5] [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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Millrine D, Jenkins RH, Hughes STO, Jones SA. Making sense of IL-6 signalling cues in pathophysiology. FEBS Lett 2022; 596:567-588. [PMID: 34618359 PMCID: PMC9673051 DOI: 10.1002/1873-3468.14201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 12/15/2022]
Abstract
Unravelling the molecular mechanisms that account for functional pleiotropy is a major challenge for researchers in cytokine biology. Cytokine-receptor cross-reactivity and shared signalling pathways are considered primary drivers of cytokine pleiotropy. However, reports epitomized by studies of Jak-STAT cytokine signalling identify interesting biochemical and epigenetic determinants of transcription factor regulation that affect the delivery of signal-dependent cytokine responses. Here, a regulatory interplay between STAT transcription factors and their convergence to specific genomic enhancers support the fine-tuning of cytokine responses controlling host immunity, functional identity, and tissue homeostasis and repair. In this review, we provide an overview of the signalling networks that shape the way cells sense and interpret cytokine cues. With an emphasis on the biology of interleukin-6, we highlight the importance of these mechanisms to both physiological processes and pathophysiological outcomes.
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Affiliation(s)
- David Millrine
- Division of Infection & ImmunitySchool of MedicineCardiff UniversityUK
- Systems Immunity University Research InstituteCardiff UniversityUK
- Present address:
Medical Research Council Protein Phosphorylation and Ubiquitylation UnitSir James Black CentreSchool of Life SciencesUniversity of Dundee3rd FloorDundeeUK
| | - Robert H. Jenkins
- Division of Infection & ImmunitySchool of MedicineCardiff UniversityUK
- Systems Immunity University Research InstituteCardiff UniversityUK
| | - Stuart T. O. Hughes
- Division of Infection & ImmunitySchool of MedicineCardiff UniversityUK
- Systems Immunity University Research InstituteCardiff UniversityUK
| | - Simon A. Jones
- Division of Infection & ImmunitySchool of MedicineCardiff UniversityUK
- Systems Immunity University Research InstituteCardiff UniversityUK
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29
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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: 7] [Impact Index Per Article: 3.5] [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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30
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Abstract
Natural killer (NK) cells play an important role in innate immune responses to viral infections. Here, we review recent insights into the role of NK cells in viral infections, with particular emphasis on human studies. We first discuss NK cells in the context of acute viral infections, with flavivirus and influenza virus infections as examples. Questions related to activation of NK cells, homing to infected tissues and the role of tissue-resident NK cells in acute viral infections are also addressed. Next, we discuss NK cells in the context of chronic viral infections with hepatitis C virus and HIV-1. Also covered is the role of adaptive-like NK cell expansions as well as the appearance of CD56- NK cells in the course of chronic infection. Specific emphasis is then placed in viral infections in patients with primary immunodeficiencies affecting NK cells. Not least, studies in this area have revealed an important role for NK cells in controlling several herpesvirus infections. Finally, we address new data with respect to the activation of NK cells and NK cell function in humans infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) giving rise to coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
| | - Benedikt Strunz
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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31
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Zhang J, Rousseaux N, Walzer T. Eomes and T‐bet, a dynamic duo regulating NK cell differentiation. Bioessays 2022; 44:e2100281. [DOI: 10.1002/bies.202100281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Jiang Zhang
- Department of Dermatology Brigham and Women's Hospital Harvard Medical School Boston Massachusetts USA
| | - Noémi Rousseaux
- CIRI Centre International de Recherche en Infectiologie CNRS, UMR5308, ENS de Lyon Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1 Lyon France
| | - Thierry Walzer
- CIRI Centre International de Recherche en Infectiologie CNRS, UMR5308, ENS de Lyon Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1 Lyon France
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32
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Morrison TA, Hudson WH, Chisolm DA, Kanno Y, Shih HY, Ahmed R, Henao-Mejia J, Hafner M, O'Shea JJ. Evolving Views of Long Noncoding RNAs and Epigenomic Control of Lymphocyte State and Memory. Cold Spring Harb Perspect Biol 2022; 14:a037952. [PMID: 34001528 PMCID: PMC8725624 DOI: 10.1101/cshperspect.a037952] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Not simply an attribute of the adaptive immune system, immunological memory can be viewed on multiple levels. Accordingly, the molecular basis of memory comprises multiple mechanisms. The advent of new sequencing technologies has greatly enhanced the understanding of gene regulation and lymphocyte specification, and improved measurement of chromatin states affords new insights into the epigenomic and transcriptomic programs that underlie memory. Beyond canonical genes, the involvement of long noncoding RNAs (lncRNAs) is becoming increasingly apparent, and it appears that there are more than two to three times as many lncRNAs as protein-coding genes. lncRNAs can directly interact with DNA, RNA, and proteins, and a single lncRNA can contain multiple modular domains and thus interact with different classes of molecules. Yet, most lncRNAs have not been tested for function, and even fewer knockout mice have been generated. It is therefore timely to consider new potential mechanisms that may contribute to immune memory.
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Affiliation(s)
- Tasha A Morrison
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - William H Hudson
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Danielle A Chisolm
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yuka Kanno
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Han-Yu Shih
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Rafi Ahmed
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Jorge Henao-Mejia
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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33
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Lau CM, Wiedemann GM, Sun JC. Epigenetic regulation of natural killer cell memory. Immunol Rev 2022; 305:90-110. [PMID: 34908173 PMCID: PMC8955591 DOI: 10.1111/imr.13031] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/20/2021] [Accepted: 09/29/2021] [Indexed: 01/03/2023]
Abstract
Immunological memory is the underlying mechanism by which the immune system remembers previous encounters with pathogens to produce an enhanced secondary response upon re-encounter. It stands as the hallmark feature of the adaptive immune system and the cornerstone of vaccine development. Classic recall responses are executed by conventional T and B cells, which undergo somatic recombination and modify their receptor repertoire to ensure recognition of a vast number of antigens. However, recent evidence has challenged the dogma that memory responses are restricted to the adaptive immune system, which has prompted a reevaluation of what delineates "immune memory." Natural killer (NK) cells of the innate immune system have been at the forefront of these pushed boundaries, and have proved to be more "adaptable" than previously thought. Like T cells, we now appreciate that their "natural" abilities actually require a myriad of signals for optimal responses. In this review, we discuss the many signals required for effector and memory NK cell responses and the epigenetic mechanisms that ultimately endow their enhanced features.
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Affiliation(s)
- Colleen M. Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gabriela M. Wiedemann
- Department of Internal Medicine II, School of Medicine, Technical University of Munich, Munich, Germany
| | - Joseph C. Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, New York, USA
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34
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Clayton SA, Daley KK, MacDonald L, Fernandez-Vizarra E, Bottegoni G, O’Neil JD, Major T, Griffin D, Zhuang Q, Adewoye AB, Woolcock K, Jones SW, Goodyear C, Elmesmari A, Filer A, Tennant DA, Alivernini S, Buckley CD, Pitceathly RDS, Kurowska-Stolarska M, Clark AR. Inflammation causes remodeling of mitochondrial cytochrome c oxidase mediated by the bifunctional gene C15orf48. SCIENCE ADVANCES 2021; 7:eabl5182. [PMID: 34878835 PMCID: PMC8654286 DOI: 10.1126/sciadv.abl5182] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/18/2021] [Indexed: 05/10/2023]
Abstract
Dysregulated mitochondrial function is a hallmark of immune-mediated inflammatory diseases. Cytochrome c oxidase (CcO), which mediates the rate-limiting step in mitochondrial respiration, is remodeled during development and in response to changes of oxygen availability, but there has been little study of CcO remodeling during inflammation. Here, we describe an elegant molecular switch mediated by the bifunctional transcript C15orf48, which orchestrates the substitution of the CcO subunit NDUFA4 by its paralog C15ORF48 in primary macrophages. Expression of C15orf48 is a conserved response to inflammatory signals and occurs in many immune-related pathologies. In rheumatoid arthritis, C15orf48 mRNA is elevated in peripheral monocytes and proinflammatory synovial tissue macrophages, and its expression positively correlates with disease severity and declines in remission. C15orf48 is also expressed by pathogenic macrophages in severe coronavirus disease 2019 (COVID-19). Study of a rare metabolic disease syndrome provides evidence that loss of the NDUFA4 subunit supports proinflammatory macrophage functions.
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Affiliation(s)
- Sally A. Clayton
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Kalbinder K. Daley
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Lucy MacDonald
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | | | - Giovanni Bottegoni
- Dipartimento di Scienze Biomolecolari, University of Urbino, Urbino, Italy
- School of Pharmacy, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - John D. O’Neil
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Triin Major
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Daniel Griffin
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Qinqin Zhuang
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Adeolu B. Adewoye
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Kieran Woolcock
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Simon W. Jones
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Carl Goodyear
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Aziza Elmesmari
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Andrew Filer
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Daniel A. Tennant
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Stefano Alivernini
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Division of Rheumatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Christopher D. Buckley
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Robert D. S. Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Mariola Kurowska-Stolarska
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Andrew R. Clark
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Universities of Glasgow, Birmingham, Newcastle, Oxford, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
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35
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Tuong ZK, Stewart BJ, Guo SA, Clatworthy MR. Epigenetics and tissue immunity-Translating environmental cues into functional adaptations. Immunol Rev 2021; 305:111-136. [PMID: 34821397 DOI: 10.1111/imr.13036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/21/2022]
Abstract
There is an increasing appreciation that many innate and adaptive immune cell subsets permanently reside within non-lymphoid organs, playing a critical role in tissue homeostasis and defense. The best characterized are macrophages and tissue-resident T lymphocytes that work in concert with organ structural cells to generate appropriate immune responses and are functionally shaped by organ-specific environmental cues. The interaction of tissue epithelial, endothelial and stromal cells is also required to attract, differentiate, polarize and maintain organ immune cells in their tissue niche. All of these processes require dynamic regulation of cellular transcriptional programmes, with epigenetic mechanisms playing a critical role, including DNA methylation and post-translational histone modifications. A failure to appropriately regulate immune cell transcription inevitably results in inadequate or inappropriate immune responses and organ pathology. Here, with a focus on the mammalian kidney, an organ which generates differing regional environmental cues (including hypersalinity and hypoxia) due to its physiological functions, we will review the basic concepts of tissue immunity, discuss the technologies available to profile epigenetic modifications in tissue immune cells, including those that enable single-cell profiling, and consider how these mechanisms influence the development, phenotype, activation and function of different tissue immune cell subsets, as well as the immunological function of structural cells.
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Affiliation(s)
- Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Shuang Andrew Guo
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
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36
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Yu M, Su Z, Huang X, Wang X. Single-Cell Sequencing Reveals the Novel Role of Ezh2 in NK Cell Maturation and Function. Front Immunol 2021; 12:724276. [PMID: 34764950 PMCID: PMC8576367 DOI: 10.3389/fimmu.2021.724276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
Natural killer (NK) cells are lymphocytes primarily involved in innate immunity and exhibit important functional properties in antimicrobial and antitumoral responses. Our previous work indicated that the enhancer of zeste homolog 2 (Ezh2) is a negative regulator of early NK cell differentiation and function through trimethylation of histone H3 lysine 27 (H3K27me3). Here, we deleted Ezh2 from immature NK cells and downstream progeny to explore its role in NK cell maturation by single-cell RNA sequencing (scRNA-seq). We identified six distinct NK stages based on the transcriptional signature during NK cell maturation. Conditional deletion of Ezh2 in NK cells resulted in a maturation trajectory toward NK cell arrest in CD11b SP stage 5, which was clustered with genes related to the activating function of NK cells. Mechanistically, we speculated that Ezh2 plays a critical role in NK development by activating AP-1 family gene expression independent of PRC2 function. Our results implied a novel role for the Ezh2-AP-1-Klrg1 axis in altering the NK cell maturation trajectory and NK cell-mediated cytotoxicity.
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Affiliation(s)
- Minghang Yu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Immunology, School of Basic Medical Sciences; Advanced Innovation Center for Human Brain Protection, Beijing Key Laboratory for Cancer Invasion and Metastasis, Department of Oncology, Capital Medical University, Beijing, China
| | - Ziyang Su
- Department of Immunology, School of Basic Medical Sciences; Advanced Innovation Center for Human Brain Protection, Beijing Key Laboratory for Cancer Invasion and Metastasis, Department of Oncology, Capital Medical University, Beijing, China
| | - Xuefeng Huang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Immunology, School of Basic Medical Sciences; Advanced Innovation Center for Human Brain Protection, Beijing Key Laboratory for Cancer Invasion and Metastasis, Department of Oncology, Capital Medical University, Beijing, China
| | - Xi Wang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Immunology, School of Basic Medical Sciences; Advanced Innovation Center for Human Brain Protection, Beijing Key Laboratory for Cancer Invasion and Metastasis, Department of Oncology, Capital Medical University, Beijing, China
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37
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Roma S, Carpen L, Raveane A, Bertolini F. The Dual Role of Innate Lymphoid and Natural Killer Cells in Cancer. from Phenotype to Single-Cell Transcriptomics, Functions and Clinical Uses. Cancers (Basel) 2021; 13:cancers13205042. [PMID: 34680190 PMCID: PMC8533946 DOI: 10.3390/cancers13205042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Innate lymphoid cells (ILCs), a family of innate immune cells including natural killers (NKs), play a multitude of roles in first-line cancer control, in escape from immunity and in cancer progression. In this review, we summarize preclinical and clinical data on ILCs and NK cells concerning their phenotype, function and clinical applications in cellular therapy trials. We also describe how single-cell transcriptome sequencing has been used and forecast how it will be used to better understand ILC and NK involvement in cancer control and progression as well as their therapeutic potential. Abstract The role of innate lymphoid cells (ILCs), including natural killer (NK) cells, is pivotal in inflammatory modulation and cancer. Natural killer cell activity and count have been demonstrated to be regulated by the expression of activating and inhibitory receptors together with and as a consequence of different stimuli. The great majority of NK cell populations have an anti-tumor activity due to their cytotoxicity, and for this reason have been used for cellular therapies in cancer patients. On the other hand, the recently classified helper ILCs are fundamentally involved in inflammation and they can be either helpful or harmful in cancer development and progression. Tissue niche seems to play an important role in modulating ILC function and conversion, as observed at the transcriptional level. In the past, these cell populations have been classified by the presence of specific cellular receptor markers; more recently, due to the advent of single-cell RNA sequencing (scRNA-seq), it has been possible to also explore them at the transcriptomic level. In this article we review studies on ILC (and NK cell) classification, function and their involvement in cancer. We also summarize the potential application of NK cells in cancer therapy and give an overview of the most recent studies involving ILCs and NKs at scRNA-seq, focusing on cancer. Finally, we provide a resource for those who wish to start single-cell transcriptomic analysis on the context of these innate lymphoid cell populations.
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38
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George TB, Strawn NK, Leviyang S. Tree-Based Co-Clustering Identifies Chromatin Accessibility Patterns Associated With Hematopoietic Lineage Structure. Front Genet 2021; 12:707117. [PMID: 34659332 PMCID: PMC8517275 DOI: 10.3389/fgene.2021.707117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/14/2021] [Indexed: 01/21/2023] Open
Abstract
Chromatin accessibility, as measured by ATACseq, varies between hematopoietic cell types in different lineages of the hematopoietic differentiation tree, e.g. T cells vs. B cells, but methods that associate variation in chromatin accessibility to the lineage structure of the differentiation tree are lacking. Using an ATACseq dataset recently published by the ImmGen consortium, we construct associations between chromatin accessibility and hematopoietic cell types using a novel co-clustering approach that accounts for the structure of the hematopoietic, differentiation tree. Under a model in which all loci and cell types within a co-cluster have a shared accessibility state, we show that roughly 80% of cell type associated accessibility variation can be captured through 12 cell type clusters and 20 genomic locus clusters, with the cell type clusters reflecting coherent components of the differentiation tree. Using publicly available ChIPseq datasets, we show that our clustering reflects transcription factor binding patterns with implications for regulation across cell types. We show that traditional methods such as hierarchical and kmeans clusterings lead to cell type clusters that are more dispersed on the tree than our tree-based algorithm. We provide a python package, chromcocluster, that implements the algorithms presented.
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Affiliation(s)
| | | | - Sivan Leviyang
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, United States
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39
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Mikelez-Alonso I, Magadán S, González-Fernández Á, Borrego F. Natural killer (NK) cell-based immunotherapies and the many faces of NK cell memory: A look into how nanoparticles enhance NK cell activity. Adv Drug Deliv Rev 2021; 176:113860. [PMID: 34237404 DOI: 10.1016/j.addr.2021.113860] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/21/2021] [Accepted: 07/01/2021] [Indexed: 12/16/2022]
Abstract
Natural killer (NK) cells are lymphocytes able to exert potent antitumor and antiviral functions by different means. Besides their classification as innate lymphoid cells (ILCs), NK cells exhibit memory-like and memory responses after cytokine preactivation, viral infections and hapten exposure. Multiple NK cell-based immunotherapies have been developed and are currently being tested, including the possibility to translate the NK cell memory responses into the clinic. Nevertheless, still there is a need to improve these therapies, especially for the treatment of solid tumors, and nanotechnology represents an attractive option to increase NK cell effector functions against transformed cells. In this article, we review the basis of NK cell activity, the diversity of the NK cell memory responses and the current NK cell-based immunotherapies that are being used in the clinic. Furthermore, we take a look into nanotechnology-based strategies targeting NK cells to modulate their responses for effective immunotherapy.
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Affiliation(s)
- Idoia Mikelez-Alonso
- Biocruces Bizkaia Health Research Institute, Immunopathology Group, Barakaldo, Spain; Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia - San Sebastián, Spain
| | - Susana Magadán
- CINBIO, Universidade de Vigo, Immunology Group, Vigo, Spain; Galicia Sur Health Research Institute (IIS-GS), Hospital Alvaro Cunqueiro, Vigo, Spain
| | - África González-Fernández
- CINBIO, Universidade de Vigo, Immunology Group, Vigo, Spain; Galicia Sur Health Research Institute (IIS-GS), Hospital Alvaro Cunqueiro, Vigo, Spain
| | - Francisco Borrego
- Biocruces Bizkaia Health Research Institute, Immunopathology Group, Barakaldo, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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40
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Abstract
PURPOSE OF REVIEW HIV-1 elite controllers encompass small populations of people infected with HIV-1 who can spontaneously control plasma viral loads below the limit of detection, in the absence of antiretroviral treatment. Antiviral immune responses are likely to contribute to such an impressive HIV-1 disease outcome. In this review, we discuss recent novel findings regarding antiviral innate and adaptive immune responses in elite controllers. RECENT FINDINGS Elite controllers maintain a pool of infected cells in which intact HIV-1 proviruses are more frequently integrated into noncoding regions of the host genome, likely conferring a state of deep latency. This atypical viral reservoir configuration is best explained by potent antiviral immune responses that can successfully eliminate virally infected cells in which proviruses are integrated into permissive chromatin. However, identifying the specific type and nature of this immune selection pressure represents a formidable challenge. Recent studies continue to support the role of HIV-1-specific CD8+ T cells as the main driver of elite immune control of HIV-1, however, increasing evidence suggests that their role is complemented by a fine-tuned interplay with innate immune cell subsets. Therefore, the combination of different immune effector mechanisms may shape antiviral immunity in elite controllers. SUMMARY Understanding the complex immune mechanisms responsible for natural, drug-free HIV-1 control represents a premier avenue to find and develop interventions for a cure of HIV-1 infection. Future single-cell assays designed to uncover the full genetic, epigenetic, transcriptional and functional complexity of antiviral immune responses in elite controllers may allow us to define correlates of antiviral immune protection in greater detail.
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Affiliation(s)
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA; 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA, USA
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41
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Higashijima Y, Kanki Y. Potential roles of super enhancers in inflammatory gene transcription. FEBS J 2021; 289:5762-5775. [PMID: 34173323 DOI: 10.1111/febs.16089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/26/2021] [Accepted: 06/24/2021] [Indexed: 12/15/2022]
Abstract
Acute and chronic inflammation is a basic pathological event that contributes to atherosclerosis, cancer, infectious diseases, and immune disorders. Inflammation is an adaptive process to both external and internal stimuli experienced by the human body. Although the mechanism of gene transcription is highly complicated and orchestrated in a timely and spatial manner, recent developments in next-generation sequencing, genome-editing, cryo-electron microscopy, and single cell-based technologies could provide us with insights into the roles of super enhancers (SEs). Initially, SEs were implicated in determining cell fate; subsequent studies have clarified that SEs are associated with various pathological conditions, including cancer and inflammatory diseases. Recent technological advances have unveiled the molecular mechanisms of SEs, which involve epigenetic histone modifications, chromatin three-dimensional structures, and phase-separated condensates. In this review, we discuss the relationship between inflammation and SEs and the therapeutic potential of SEs for inflammatory diseases.
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Affiliation(s)
- Yoshiki Higashijima
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Yasuharu Kanki
- Isotope Science Center, The University of Tokyo, Japan.,Laboratory of Laboratory/Sports Medicine, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Japan
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42
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NK cell and ILC heterogeneity in colorectal cancer. New perspectives from high dimensional data. Mol Aspects Med 2021; 80:100967. [PMID: 33941383 DOI: 10.1016/j.mam.2021.100967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 12/14/2022]
Abstract
Innate lymphoid cells (ILCs) and tissue-resident natural killer (NK) cells ensure immunity at environmental interfaces and help maintain barrier integrity of the intestinal tract. This wide range of innate lymphocytes is able to provide fast and potent inflammatory responses that, when deregulated, have been associated with pathogenesis of inflammatory bowel disease (IBD) and colorectal cancer (CRC). While the presence of tumor-infiltrating NK cells is generally associated with a favorable outcome in CRC patients, emerging evidence reveals distinct roles for ILCs in regulating CRC pathogenesis and progression. Advances in next generation sequencing technology, and in particular of single-cell RNA-seq approaches, along with multidimensional flow cytometry analysis, have helped to deconvolute the complexity and heterogeneity of the ILC system both in homeostatic and pathological contexts. In this review, we discuss the protective and detrimental roles of NK cells and ILCs in the pathogenesis of CRC, focusing on the phenotypic and transcriptional modifications these cells undergo during CRC development and progression.
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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: 10] [Impact Index Per Article: 3.3] [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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Beaulieu AM. Transcriptional and epigenetic regulation of memory NK cell responses. Immunol Rev 2021; 300:125-133. [PMID: 33491231 DOI: 10.1111/imr.12947] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/28/2020] [Accepted: 12/31/2020] [Indexed: 12/14/2022]
Abstract
Natural killer (NK) cells are cytotoxic innate lymphocytes with key roles in host protection against viruses and malignancy. Notwithstanding their historical classification as innate immune cells, NK cells are now understood to have some capacity to mount memory or memory-like immune responses in which effector cells undergo antigen-driven expansion and give rise to long-lived memory cells with enhanced functionality. Understanding how antigen-specific effector and memory NK responses are regulated is an important and active area of research in the field. Here, we discuss key transcription factors and epigenetic processes involved in antigen-specific effector and memory NK cell differentiation.
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Affiliation(s)
- Aimee M Beaulieu
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers - The State University of New Jersey, Newark, NJ, USA.,Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers - The State University of New Jersey, Newark, NJ, USA
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