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Liu Z, Liang Q, Ren Y, Guo C, Ge X, Wang L, Cheng Q, Luo P, Zhang Y, Han X. Immunosenescence: molecular mechanisms and diseases. Signal Transduct Target Ther 2023; 8:200. [PMID: 37179335 PMCID: PMC10182360 DOI: 10.1038/s41392-023-01451-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/24/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Infection susceptibility, poor vaccination efficacy, age-related disease onset, and neoplasms are linked to innate and adaptive immune dysfunction that accompanies aging (known as immunosenescence). During aging, organisms tend to develop a characteristic inflammatory state that expresses high levels of pro-inflammatory markers, termed inflammaging. This chronic inflammation is a typical phenomenon linked to immunosenescence and it is considered the major risk factor for age-related diseases. Thymic involution, naïve/memory cell ratio imbalance, dysregulated metabolism, and epigenetic alterations are striking features of immunosenescence. Disturbed T-cell pools and chronic antigen stimulation mediate premature senescence of immune cells, and senescent immune cells develop a proinflammatory senescence-associated secretory phenotype that exacerbates inflammaging. Although the underlying molecular mechanisms remain to be addressed, it is well documented that senescent T cells and inflammaging might be major driving forces in immunosenescence. Potential counteractive measures will be discussed, including intervention of cellular senescence and metabolic-epigenetic axes to mitigate immunosenescence. In recent years, immunosenescence has attracted increasing attention for its role in tumor development. As a result of the limited participation of elderly patients, the impact of immunosenescence on cancer immunotherapy is unclear. Despite some surprising results from clinical trials and drugs, it is necessary to investigate the role of immunosenescence in cancer and other age-related diseases.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China
| | - Qimeng Liang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 4500052, Henan, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Xiaoyong Ge
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China.
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Mathews J, Chang A(J, Devlin L, Levin M. Cellular signaling pathways as plastic, proto-cognitive systems: Implications for biomedicine. PATTERNS (NEW YORK, N.Y.) 2023; 4:100737. [PMID: 37223267 PMCID: PMC10201306 DOI: 10.1016/j.patter.2023.100737] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Many aspects of health and disease are modeled using the abstraction of a "pathway"-a set of protein or other subcellular activities with specified functional linkages between them. This metaphor is a paradigmatic case of a deterministic, mechanistic framework that focuses biomedical intervention strategies on altering the members of this network or the up-/down-regulation links between them-rewiring the molecular hardware. However, protein pathways and transcriptional networks exhibit interesting and unexpected capabilities such as trainability (memory) and information processing in a context-sensitive manner. Specifically, they may be amenable to manipulation via their history of stimuli (equivalent to experiences in behavioral science). If true, this would enable a new class of biomedical interventions that target aspects of the dynamic physiological "software" implemented by pathways and gene-regulatory networks. Here, we briefly review clinical and laboratory data that show how high-level cognitive inputs and mechanistic pathway modulation interact to determine outcomes in vivo. Further, we propose an expanded view of pathways from the perspective of basal cognition and argue that a broader understanding of pathways and how they process contextual information across scales will catalyze progress in many areas of physiology and neurobiology. We argue that this fuller understanding of the functionality and tractability of pathways must go beyond a focus on the mechanistic details of protein and drug structure to encompass their physiological history as well as their embedding within higher levels of organization in the organism, with numerous implications for data science addressing health and disease. Exploiting tools and concepts from behavioral and cognitive sciences to explore a proto-cognitive metaphor for the pathways underlying health and disease is more than a philosophical stance on biochemical processes; at stake is a new roadmap for overcoming the limitations of today's pharmacological strategies and for inferring future therapeutic interventions for a wide range of disease states.
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Affiliation(s)
- Juanita Mathews
- Allen Discovery Center at Tufts University, Medford, MA, USA
| | | | - Liam Devlin
- Allen Discovery Center at Tufts University, Medford, MA, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
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Biswas S, Clawson W, Levin M. Learning in Transcriptional Network Models: Computational Discovery of Pathway-Level Memory and Effective Interventions. Int J Mol Sci 2022; 24:285. [PMID: 36613729 PMCID: PMC9820177 DOI: 10.3390/ijms24010285] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/23/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Trainability, in any substrate, refers to the ability to change future behavior based on past experiences. An understanding of such capacity within biological cells and tissues would enable a particularly powerful set of methods for prediction and control of their behavior through specific patterns of stimuli. This top-down mode of control (as an alternative to bottom-up modification of hardware) has been extensively exploited by computer science and the behavioral sciences; in biology however, it is usually reserved for organism-level behavior in animals with brains, such as training animals towards a desired response. Exciting work in the field of basal cognition has begun to reveal degrees and forms of unconventional memory in non-neural tissues and even in subcellular biochemical dynamics. Here, we characterize biological gene regulatory circuit models and protein pathways and find them capable of several different kinds of memory. We extend prior results on learning in binary transcriptional networks to continuous models and identify specific interventions (regimes of stimulation, as opposed to network rewiring) that abolish undesirable network behavior such as drug pharmacoresistance and drug sensitization. We also explore the stability of created memories by assessing their long-term behavior and find that most memories do not decay over long time periods. Additionally, we find that the memory properties are quite robust to noise; surprisingly, in many cases noise actually increases memory potential. We examine various network properties associated with these behaviors and find that no one network property is indicative of memory. Random networks do not show similar memory behavior as models of biological processes, indicating that generic network dynamics are not solely responsible for trainability. Rational control of dynamic pathway function using stimuli derived from computational models opens the door to empirical studies of proto-cognitive capacities in unconventional embodiments and suggests numerous possible applications in biomedicine, where behavior shaping of pathway responses stand as a potential alternative to gene therapy.
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Affiliation(s)
- Surama Biswas
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA
- Department of Computer Science & Engineering and Information Technology, Meghnad Saha Institute of Technology, Kolkata 700150, India
| | - Wesley Clawson
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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4
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Epigenetic Regulation of Cancer Immune Cells. Semin Cancer Biol 2021; 83:377-383. [PMID: 34182142 DOI: 10.1016/j.semcancer.2021.06.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 05/06/2021] [Accepted: 06/23/2021] [Indexed: 12/17/2022]
Abstract
The epigenetic regulation of immune response involves reversible and heritable changes that do not alter the DNA sequence. Though there have been extensive studies accomplished relating to epigenetic changes in cancer cells, recent focus has been shifted on epigenetic-mediated changes in the immune cells including T cells, Macrophages, Natural Killer cells and anti-tumor immune responses. This review compiles the most relevant and recent literature related to the role of epigenetic mechanisms including DNA methylation and histone modifications in immune cells of wide range of cancers. We also include recent research with respect to role of the most relevant transcription factors that epigenetically control the anti-tumor immune response. Finally, a statement of future direction that promises to look forward for strategies to improve immunotherapy in cancer.
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Gene regulatory networks exhibit several kinds of memory: quantification of memory in biological and random transcriptional networks. iScience 2021; 24:102131. [PMID: 33748699 PMCID: PMC7970124 DOI: 10.1016/j.isci.2021.102131] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/09/2020] [Accepted: 01/26/2021] [Indexed: 02/08/2023] Open
Abstract
Gene regulatory networks (GRNs) process important information in developmental biology and biomedicine. A key knowledge gap concerns how their responses change over time. Hypothesizing long-term changes of dynamics induced by transient prior events, we created a computational framework for defining and identifying diverse types of memory in candidate GRNs. We show that GRNs from a wide range of model systems are predicted to possess several types of memory, including Pavlovian conditioning. Associative memory offers an alternative strategy for the biomedical use of powerful drugs with undesirable side effects, and a novel approach to understanding the variability and time-dependent changes of drug action. We find evidence of natural selection favoring GRN memory. Vertebrate GRNs overall exhibit more memory than invertebrate GRNs, and memory is most prevalent in differentiated metazoan cell networks compared with undifferentiated cells. Timed stimuli are a powerful alternative for biomedical control of complex in vivo dynamics without genomic editing or transgenes. Gene regulatory networks' dynamics are modified by transient stimuli GRNs have several different types of memory, including associative conditioning Evolution favored GRN memory, and differentiated cells have the most memory capacity Training GRNs offers a novel biomedical strategy not dependent on genetic rewiring
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Sui Y, Berzofsky JA. Myeloid Cell-Mediated Trained Innate Immunity in Mucosal AIDS Vaccine Development. Front Immunol 2020; 11:315. [PMID: 32184782 PMCID: PMC7058986 DOI: 10.3389/fimmu.2020.00315] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/07/2020] [Indexed: 12/12/2022] Open
Abstract
Trained innate immunity has recently emerged as a novel concept of innate immune cells, such as myeloid cells, exhibiting immune memory, and nonspecific heterologous immunity to protect against infections. The memory and specificity are mediated by epigenetic, metabolic, and functional reprogramming of the myeloid cells and myeloid progenitors (and/or NK cells) in the bone marrow and peripheral tissues such as gut and lung mucosa. A variety of agents, such as BCG, viruses, and their components, as well as TLR agonists, and cytokines have been shown to be involved in the induction of trained immunity. Since these agents have been widely used in AIDS vaccine development as antigen delivery vectors or adjuvants, myeloid cell mediated trained immunity might also play an important role in protecting against mucosal AIDS virus transmission or in control of virus replication in the major gut mucosal reservoir. Here we review the trained innate immunity induced by these vectors/adjuvants that have been used in AIDS vaccine studies and discuss their role in mucosal vaccine efficacy and possible utilization in AIDS vaccine development. Delineating the protective effect of the trained innate immunity mediated by myeloid cells will guide the design of novel AIDS vaccines.
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Affiliation(s)
- Yongjun Sui
- Vaccine Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Jay A Berzofsky
- Vaccine Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States
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Yamada T, Nabe S, Toriyama K, Suzuki J, Inoue K, Imai Y, Shiraishi A, Takenaka K, Yasukawa M, Yamashita M. Histone H3K27 Demethylase Negatively Controls the Memory Formation of Antigen-Stimulated CD8 + T Cells. THE JOURNAL OF IMMUNOLOGY 2019; 202:1088-1098. [PMID: 30626691 DOI: 10.4049/jimmunol.1801083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/08/2018] [Indexed: 12/11/2022]
Abstract
Although the methylation status of histone H3K27 plays a critical role in CD4+ T cell differentiation and its function, the role of Utx histone H3K27 demethylase in the CD8+ T cell-dependent immune response remains unclear. We therefore generated T cell-specific Utx flox/flox Cd4-Cre Tg (Utx KO) mice to determine the role of Utx in CD8+ T cells. Wild-type (WT) and Utx KO mice were infected with Listeria monocytogenes expressing OVA to analyze the immune response of Ag-specific CD8+ T cells. There was no significant difference in the number of Ag-specific CD8+ T cells upon primary infection between WT and Utx KO mice. However, Utx deficiency resulted in more Ag-specific CD8+ T cells upon secondary infection. Adoptive transfer of Utx KO CD8+ T cells resulted in a larger number of memory cells in the primary response than in WT. We observed a decreased gene expression of effector-associated transcription factors, including Prdm1 encoding Blimp1, in Utx KO CD8+ T cells. We confirmed that the trimethylation level of histone H3K27 in the Prdm1 gene loci in the Utx KO cells was higher than in the WT cells. The treatment of CD8+ T cells with Utx-cofactor α-ketoglutarate hampered the memory formation, whereas Utx inhibitor GSK-J4 enhanced the memory formation in WT CD8+ T cells. These data suggest that Utx negatively controls the memory formation of Ag-stimulated CD8+ T cells by epigenetically regulating the gene expression. Based on these findings, we identified a critical link between Utx and the differentiation of Ag-stimulated CD8+ T cells.
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Affiliation(s)
- Takeshi Yamada
- Department of Medical Technology, Ehime Prefectural University of Health Sciences, Tobe, Ehime 791-2101, Japan; .,Department of Infection and Host Defenses, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Shogo Nabe
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Koji Toriyama
- Department of Ophthalmology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Junpei Suzuki
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan.,Department of Translational Immunology, Translational Research Center, Ehime University Hospital, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Kazuki Inoue
- Division of Integrative Pathophysiology, Department of Proteo-Inovation, Proteo-Science Center, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan; and
| | - Yuuki Imai
- Division of Integrative Pathophysiology, Department of Proteo-Inovation, Proteo-Science Center, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan; and
| | - Atsushi Shiraishi
- Department of Ophthalmology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Katsuto Takenaka
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Masaki Yasukawa
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan.,Division of Immune Regulation, Department of Proteo-Innovation, Proteo-Science Center, Graduate School of Medicine, Ehime University, Toon, Ehime 791-0295, Japan
| | - Masakatsu Yamashita
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan; .,Department of Translational Immunology, Translational Research Center, Ehime University Hospital, Shitsukawa, Toon, Ehime 791-0295, Japan.,Division of Immune Regulation, Department of Proteo-Innovation, Proteo-Science Center, Graduate School of Medicine, Ehime University, Toon, Ehime 791-0295, Japan
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8
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Leopold Wager CM, Hole CR, Campuzano A, Castro-Lopez N, Cai H, Caballero Van Dyke MC, Wozniak KL, Wang Y, Wormley FL. IFN-γ immune priming of macrophages in vivo induces prolonged STAT1 binding and protection against Cryptococcus neoformans. PLoS Pathog 2018; 14:e1007358. [PMID: 30304063 PMCID: PMC6197699 DOI: 10.1371/journal.ppat.1007358] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 10/22/2018] [Accepted: 09/26/2018] [Indexed: 12/30/2022] Open
Abstract
Development of vaccines against opportunistic infections is difficult as patients most at risk of developing disease are deficient in aspects of the adaptive immune system. Here, we utilized an experimental immunization strategy to induce innate memory in macrophages in vivo. Unlike current trained immunity models, we present an innate memory-like phenotype in macrophages that is maintained for at least 70 days post-immunization and results in complete protection against secondary challenge in the absence of adaptive immune cells. RNA-seq analysis of in vivo IFN-γ primed macrophages revealed a rapid up-regulation of IFN-γ and STAT1 signaling pathways following secondary challenge. The enhanced cytokine recall responses appeared to be pathogen-specific, dependent on changes in histone methylation and acetylation, and correlated with increased STAT1 binding to promoter regions of genes associated with protective anti-fungal immunity. Thus, we demonstrate an alternative mechanism to induce macrophage innate memory in vivo that facilitates pathogen-specific vaccine-mediated immune responses. Fungal infections are a significant global health problem that can affect anyone, however, individuals with a weakened immune system are most at risk. Cryptococcus neoformans infections can progress to meningitis in immune compromised individuals accounting for nearly 220,000 new cases annually, resulting in 181,000 deaths. Vaccine strategies tend to target CD4+ T cells for the generation of protective memory responses. However, immune compromised individuals have decreased numbers of these adaptive cells, providing a challenge for anti-fungal vaccine design. Here, we define a cellular mechanism by which macrophages, an innate cell population, generate protective immune responses against C. neoformans following initial exposure to a C. neoformans strain that secretes IFN-γ. We determined that the macrophages primed in vivo have heightened proinflammatory cytokine responses upon secondary exposure to C. neoformans in a manner that is mTOR-independent, yet dependent on histone modification dynamics. We show that IFN-γ primed macrophages can maintain STAT1 binding to the promoter regions of key proinflammatory genes long after the initial exposure. Remarkably, our studies show long-lived, cryptococcal-specific protective immunity in vivo. The results presented herein demonstrate that innate cell populations, namely macrophages, can be utilized as vaccine targets to protect against cryptococcal infections in immune compromised populations.
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Affiliation(s)
- Chrissy M. Leopold Wager
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States of America
- The South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Camaron R. Hole
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States of America
- The South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Althea Campuzano
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States of America
- The South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Natalia Castro-Lopez
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States of America
- The South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Hong Cai
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States of America
- The South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Marley C. Caballero Van Dyke
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States of America
- The South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Karen L. Wozniak
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States of America
- The South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Yufeng Wang
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States of America
- The South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Floyd L. Wormley
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States of America
- The South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States of America
- * E-mail:
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Onodera A, Kiuchi M, Kokubo K, Kato M, Ogino T, Horiuchi S, Kanai U, Hirahara K, Nakayama T. Menin Controls the Memory Th2 Cell Function by Maintaining the Epigenetic Integrity of Th2 Cells. THE JOURNAL OF IMMUNOLOGY 2017; 199:1153-1162. [DOI: 10.4049/jimmunol.1602129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/02/2017] [Indexed: 12/24/2022]
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10
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Bevington SL, Cauchy P, Withers DR, Lane PJL, Cockerill PN. T Cell Receptor and Cytokine Signaling Can Function at Different Stages to Establish and Maintain Transcriptional Memory and Enable T Helper Cell Differentiation. Front Immunol 2017; 8:204. [PMID: 28316598 PMCID: PMC5334638 DOI: 10.3389/fimmu.2017.00204] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/14/2017] [Indexed: 12/24/2022] Open
Abstract
Experienced T cells exhibit immunological memory via a rapid recall response, responding to restimulation much faster than naïve T cells. The formation of immunological memory starts during an initial slow response, when naïve T cells become transformed to proliferating T blast cells, and inducible immune response genes are reprogrammed as active chromatin domains. We demonstrated that these active domains are supported by thousands of priming elements which cooperate with inducible transcriptional enhancers to enable efficient responses to stimuli. At the conclusion of this response, a small proportion of these cells return to the quiescent state as long-term memory T cells. We proposed that priming elements can be established in a hit-and-run process dependent on the inducible factor AP-1, but then maintained by the constitutive factors RUNX1 and ETS-1. This priming mechanism may also function to render genes receptive to additional differentiation-inducing factors such as GATA3 and TBX21 that are encountered under polarizing conditions. The proliferation of recently activated T cells and the maintenance of immunological memory in quiescent memory T cells are also dependent on various cytokine signaling pathways upstream of AP-1. We suggest that immunological memory is established by T cell receptor signaling, but maintained by cytokine signaling.
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Affiliation(s)
- Sarah L Bevington
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham , Birmingham , UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham , Birmingham , UK
| | - David R Withers
- Institute of Immunology and Immunotherapy, Institute of Biomedical Research, University of Birmingham , Birmingham , UK
| | - Peter J L Lane
- Institute of Immunology and Immunotherapy, Institute of Biomedical Research, University of Birmingham , Birmingham , UK
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham , Birmingham , UK
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Bonifer C, Cockerill PN. Chromatin priming of genes in development: Concepts, mechanisms and consequences. Exp Hematol 2017; 49:1-8. [PMID: 28185904 DOI: 10.1016/j.exphem.2017.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/19/2017] [Accepted: 01/21/2017] [Indexed: 01/06/2023]
Abstract
During ontogeny, cells progress through multiple alternate differentiation states by activating distinct gene regulatory networks. In this review, we highlight the important role of chromatin priming in facilitating gene activation during lineage specification and in maintaining an epigenetic memory of previous gene activation. We show that chromatin priming is part of a hugely diverse repertoire of regulatory mechanisms that genes use to ensure that they are expressed at the correct time, in the correct cell type, and at the correct level, but also that they react to signals. We also emphasize how increasing our knowledge of these principles could inform our understanding of developmental failure and disease.
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Affiliation(s)
- Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK.
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK.
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12
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Tu W, Rao S. Mechanisms Underlying T Cell Immunosenescence: Aging and Cytomegalovirus Infection. Front Microbiol 2016; 7:2111. [PMID: 28082969 PMCID: PMC5186782 DOI: 10.3389/fmicb.2016.02111] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 12/13/2016] [Indexed: 01/03/2023] Open
Abstract
The ability of the human immune system to protect against infectious disease declines with age and efficacy of vaccination reduces significantly in the elderly. Aging of the immune system, also termed as immunosenescence, involves many changes in human T cell immunity that is characterized by a loss in naïve T cell population and an increase in highly differentiated CD28- memory T cell subset. There is extensive data showing that latent persistent human cytomegalovirus (HCMV) infection is also associated with age-related immune dysfunction in the T cells, which might enhance immunosenescence. Understanding the molecular mechanisms underlying age-related and HCMV-related immunosenescence is critical for the development of effective age-targeted vaccines and immunotherapies. In this review, we will address the role of both aging and HCMV infection that contribute to the T cell senescence and discuss the potential molecular mechanisms in aged T cells.
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Affiliation(s)
- Wenjuan Tu
- Faculty of ESTeM, Health Research Institute, University of Canberra Canberra, ACT, Australia
| | - Sudha Rao
- Faculty of ESTeM, Health Research Institute, University of Canberra Canberra, ACT, Australia
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13
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Bevington SL, Cauchy P, Cockerill PN. Chromatin priming elements establish immunological memory in T cells without activating transcription: T cell memory is maintained by DNA elements which stably prime inducible genes without activating steady state transcription. Bioessays 2016; 39. [PMID: 28026028 DOI: 10.1002/bies.201600184] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We have identified a simple epigenetic mechanism underlying the establishment and maintenance of immunological memory in T cells. By studying the transcriptional regulation of inducible genes we found that a single cycle of activation of inducible factors is sufficient to initiate stable binding of pre-existing transcription factors to thousands of newly activated distal regulatory elements within inducible genes. These events lead to the creation of islands of active chromatin encompassing nearby enhancers, thereby supporting the accelerated activation of inducible genes, without changing steady state levels of transcription in memory T cells. These studies also highlighted the need for more sophisticated definitions of gene regulatory elements. The chromatin priming elements defined here are distinct from classical enhancers because they function by maintaining chromatin accessibility rather than directly activating transcription. We propose that these priming elements are members of a wider class of genomic elements that support correct developmentally regulated gene expression.
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Affiliation(s)
- Sarah L Bevington
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, West Midlands, UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, West Midlands, UK
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, West Midlands, UK
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14
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Nakayama T, Hirahara K, Onodera A, Endo Y, Hosokawa H, Shinoda K, Tumes DJ, Okamoto Y. Th2 Cells in Health and Disease. Annu Rev Immunol 2016; 35:53-84. [PMID: 27912316 DOI: 10.1146/annurev-immunol-051116-052350] [Citation(s) in RCA: 240] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Helper T (Th) cell subsets direct immune responses by producing signature cytokines. Th2 cells produce IL-4, IL-5, and IL-13, which are important in humoral immunity and protection from helminth infection and are central to the pathogenesis of many allergic inflammatory diseases. Molecular analysis of Th2 cell differentiation and maintenance of function has led to recent discoveries that have refined our understanding of Th2 cell biology. Epigenetic regulation of Gata3 expression by chromatin remodeling complexes such as Polycomb and Trithorax is crucial for maintaining Th2 cell identity. In the context of allergic diseases, memory-type pathogenic Th2 cells have been identified in both mice and humans. To better understand these disease-driving cell populations, we have developed a model called the pathogenic Th population disease induction model. The concept of defined subsets of pathogenic Th cells may spur new, effective strategies for treating intractable chronic inflammatory disorders.
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Affiliation(s)
- Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; , , , , , , , .,AMED-CREST, AMED, Chiba 260-8670, Japan
| | - Kiyoshi Hirahara
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; , , , , , , ,
| | - Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; , , , , , , , .,Institute for Global Prominent Research, Chiba University, Chiba 260-8670, Japan
| | - Yusuke Endo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; , , , , , , ,
| | - Hiroyuki Hosokawa
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; , , , , , , ,
| | - Kenta Shinoda
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; , , , , , , ,
| | - Damon J Tumes
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; , , , , , , , .,South Australian Health and Medical Research Institute, North Terrace, Adelaide SA 5000, Australia
| | - Yoshitaka Okamoto
- Department of Otorhinolaryngology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
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15
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Villegas-Mendez A, Inkson CA, Shaw TN, Strangward P, Couper KN. Long-Lived CD4+IFN-γ+ T Cells rather than Short-Lived CD4+IFN-γ+IL-10+ T Cells Initiate Rapid IL-10 Production To Suppress Anamnestic T Cell Responses during Secondary Malaria Infection. THE JOURNAL OF IMMUNOLOGY 2016; 197:3152-3164. [PMID: 27630165 PMCID: PMC5055201 DOI: 10.4049/jimmunol.1600968] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/21/2016] [Indexed: 01/01/2023]
Abstract
CD4+ T cells that produce IFN-γ are the source of host-protective IL-10 during primary infection with a number of different pathogens, including Plasmodium spp. The fate of these CD4+IFN-γ+IL-10+ T cells following clearance of primary infection and their subsequent influence on the course of repeated infections is, however, presently unknown. In this study, utilizing IFN-γ-yellow fluorescent protein (YFP) and IL-10-GFP dual reporter mice, we show that primary malaria infection-induced CD4+YFP+GFP+ T cells have limited memory potential, do not stably express IL-10, and are disproportionately lost from the Ag-experienced CD4+ T cell memory population during the maintenance phase postinfection. CD4+YFP+GFP+ T cells generally exhibited a short-lived effector rather than effector memory T cell phenotype postinfection and expressed high levels of PD-1, Lag-3, and TIGIT, indicative of cellular exhaustion. Consistently, the surviving CD4+YFP+GFP+ T cell-derived cells were unresponsive and failed to proliferate during the early phase of secondary infection. In contrast, CD4+YFP+GFP- T cell-derived cells expanded rapidly and upregulated IL-10 expression during secondary infection. Correspondingly, CD4+ T cells were the major producers within an accelerated and amplified IL-10 response during the early stage of secondary malaria infection. Notably, IL-10 exerted quantitatively stronger regulatory effects on innate and CD4+ T cell responses during primary and secondary infections, respectively. The results in this study significantly improve our understanding of the durability of IL-10-producing CD4+ T cells postinfection and provide information on how IL-10 may contribute to optimized parasite control and prevention of immune-mediated pathology during repeated malaria infections.
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Affiliation(s)
- Ana Villegas-Mendez
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Colette A Inkson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Tovah N Shaw
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Patrick Strangward
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Kevin N Couper
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
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16
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Dunn J, McCuaig R, Tu WJ, Hardy K, Rao S. Multi-layered epigenetic mechanisms contribute to transcriptional memory in T lymphocytes. BMC Immunol 2015; 16:27. [PMID: 25943594 PMCID: PMC4422045 DOI: 10.1186/s12865-015-0089-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/31/2015] [Indexed: 12/24/2022] Open
Abstract
Background Immunological memory is the ability of the immune system to respond more rapidly and effectively to previously encountered pathogens, a key feature of adaptive immunity. The capacity of memory T cells to “remember” previous cellular responses to specific antigens ultimately resides in their unique patterns of gene expression. Following re-exposure to an antigen, previously activated genes are transcribed more rapidly and robustly in memory T cells compared to their naïve counterparts. The ability for cells to remember past transcriptional responses is termed “adaptive transcriptional memory”. Results Recent global epigenome studies suggest that epigenetic mechanisms are central to establishing and maintaining transcriptional memory, with elegant studies in model organisms providing tantalizing insights into the epigenetic programs that contribute to adaptive immunity. These epigenetic mechanisms are diverse, and include not only classical acetylation and methylation events, but also exciting and less well-known mechanisms involving histone structure, upstream signalling pathways, and nuclear localisation of genomic regions. Conclusions Current global health challenges in areas such as tuberculosis and influenza demand not only more effective and safer vaccines, but also vaccines for a wider range of health priorities, including HIV, cancer, and emerging pathogens such as Ebola. Understanding the multi-layered epigenetic mechanisms that underpin the rapid recall responses of memory T cells following reactivation is a critical component of this development pathway.
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Affiliation(s)
- Jennifer Dunn
- Faculty of Education, Science, Technology & Maths, University of Canberra, Canberra, ACT, Australia.
| | - Robert McCuaig
- Faculty of Education, Science, Technology & Maths, University of Canberra, Canberra, ACT, Australia.
| | - Wen Juan Tu
- Faculty of Education, Science, Technology & Maths, University of Canberra, Canberra, ACT, Australia.
| | - Kristine Hardy
- Faculty of Education, Science, Technology & Maths, University of Canberra, Canberra, ACT, Australia.
| | - Sudha Rao
- Faculty of Education, Science, Technology & Maths, University of Canberra, Canberra, ACT, Australia.
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17
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Epigenetics of T cells regulated by Polycomb/Trithorax molecules. Trends Mol Med 2015; 21:330-40. [DOI: 10.1016/j.molmed.2015.03.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/09/2015] [Accepted: 03/11/2015] [Indexed: 02/07/2023]
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18
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Obata Y, Furusawa Y, Hase K. Epigenetic modifications of the immune system in health and disease. Immunol Cell Biol 2015; 93:226-32. [PMID: 25666097 DOI: 10.1038/icb.2014.114] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/06/2014] [Indexed: 02/08/2023]
Abstract
Vertebrate animals have developed sophisticated host defense mechanisms against potentially hostile antigens. These mechanisms mainly involve the immune system and the epithelial cells that cover the body surface. Accumulating studies have revealed that epigenetic mechanisms in collaboration with signal transduction networks regulate gene expression over the course of differentiation, proliferation and function of immune and epithelial cells. The epigenetic status of these cells is fine-tuned under physiological conditions; however, its disturbance often results in the development of immunological disorders, namely inflammation. Certain environmental factors influence the differentiation and function of immune cells through epigenetic alterations. For example, commensal microbiota-derived metabolites inhibit histone deacetylases to induce regulatory T cells, whereas some infectious agents induce DNA methylation, resulting in the development of cancer. These data imply that epigenetic regulation of host defense cells, which are usually the first to encounter external antigens, is implicated in disease development. Here, we highlight recent advances in our understanding of the molecular mechanisms by which the epigenetic status of immune and epithelial cells is controlled.
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Affiliation(s)
- Yuuki Obata
- 1] Division of Mucosal Barriology, International Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan [2] Department of Immune Regulation, Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yukihiro Furusawa
- 1] Division of Mucosal Barriology, International Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan [2] Department of Biochemistry, Faculty of Pharmacy, Keio University, Tokyo, Japan
| | - Koji Hase
- 1] Division of Mucosal Barriology, International Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan [2] Department of Biochemistry, Faculty of Pharmacy, Keio University, Tokyo, Japan
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19
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Komori HK, Hart T, LaMere SA, Chew PV, Salomon DR. Defining CD4 T cell memory by the epigenetic landscape of CpG DNA methylation. THE JOURNAL OF IMMUNOLOGY 2015; 194:1565-79. [PMID: 25576597 DOI: 10.4049/jimmunol.1401162] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Memory T cells are primed for rapid responses to Ag; however, the molecular mechanisms responsible for priming remain incompletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpGs) mapped by deep sequencing of T cell activation in human naive and memory CD4 T cells. Four hundred sixty-six CpGs (132 genes) displayed differential methylation between naive and memory cells. Twenty-one genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 of 21 genes encode proteins closely studied in T cells, whereas 15 genes represent novel targets for further study. Eighty-four genes demonstrated differential methylation between memory and naive cells that correlated to differential gene expression following activation, of which 39 exhibited reduced methylation in memory cells coupled with increased gene expression upon activation compared with naive cells. These reveal a class of primed genes more rapidly expressed in memory compared with naive cells and putatively regulated by DNA methylation. These findings define a DNA methylation signature unique to memory CD4 T cells that correlates with activation-induced gene expression.
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Affiliation(s)
- H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Traver Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Pamela V Chew
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
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20
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Furusawa Y, Obata Y, Hase K. Commensal microbiota regulates T cell fate decision in the gut. Semin Immunopathol 2014; 37:17-25. [PMID: 25315350 DOI: 10.1007/s00281-014-0455-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/02/2014] [Indexed: 12/15/2022]
Abstract
Commensal microbiota shapes the intestinal immune system by regulating T helper (TH) cell lineage differentiation. For example, Bacteroides fragilis colonization not only optimizes the systemic TH1/TH2 balance, but also can induce regulatory T (Treg) cell differentiation in the gut. In addition, segmented filamentous bacteria (SFB) facilitate the development of TH17 cells in the small intestine. The 17 strains within clusters IV, XIVa, and XVIII of Clostridiales found in human feces can also induce the differentiation and expansion of Treg cells in the colon. Thus, the regulation of TH cell differentiation by commensal bacteria is evident; however, the molecular mechanisms underlying these processes remain uncertain. Recent studies have demonstrated that bacterial components, as well as their metabolites, play a central role in regulating TH cell development. Furthermore, these metabolites can elicit changes in histone posttranslational modification to modify the expression of critical regulators of T cell fate. In this review, we discuss the mechanisms and biological significance of microbiota-dependent TH differentiation.
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Affiliation(s)
- Yukihiro Furusawa
- Department of Biochemistry, Graduate School of Pharmaceutical Science, Keio University, Tokyo, 105-8512, Japan
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21
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Watzl C, Urlaub D, Fasbender F, Claus M. Natural killer cell regulation - beyond the receptors. F1000PRIME REPORTS 2014; 6:87. [PMID: 25374665 PMCID: PMC4191275 DOI: 10.12703/p6-87] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Natural killer (NK) cells are lymphocytes that are important for early and effective immune responses against infections and cancer. In the last 40 years, many receptors, their corresponding ligands and signaling pathways that regulate NK cell functions have been identified. However, we now know that additional processes, such as NK cell education, differentiation and also the formation of NK cell memory, have a great impact on the reactivity of these cells. Here, we summarize the current knowledge about these modulatory processes.
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Affiliation(s)
- Carsten Watzl
- IfADo - Leibniz Research Centre for Working Environment and Human Factors Ardeystrasse 67, 44139 Dortmund Germany
| | - Doris Urlaub
- IfADo - Leibniz Research Centre for Working Environment and Human Factors Ardeystrasse 67, 44139 Dortmund Germany
| | - Frank Fasbender
- IfADo - Leibniz Research Centre for Working Environment and Human Factors Ardeystrasse 67, 44139 Dortmund Germany
| | - Maren Claus
- IfADo - Leibniz Research Centre for Working Environment and Human Factors Ardeystrasse 67, 44139 Dortmund Germany
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22
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Bruno A, Ferlazzo G, Albini A, Noonan DM. A think tank of TINK/TANKs: tumor-infiltrating/tumor-associated natural killer cells in tumor progression and angiogenesis. J Natl Cancer Inst 2014; 106:dju200. [PMID: 25178695 PMCID: PMC4344546 DOI: 10.1093/jnci/dju200] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Tumor-infiltrating leukocytes are often induced by the cancer microenvironment to display a protumor, proangiogenic phenotype. This “polarization” has been described for several myeloid cells, in particular macrophages. Natural killer (NK) cells represent another population of innate immune cells able to infiltrate tumors. The role of NK in tumor progression and angiogenesis has not yet been fully investigated. Several studies have shown that tumor-infiltrating NK (here referred to as “TINKs”) and tumor-associated NK (altered peripheral NK cells, which here we call “TANKs”) are compromised in their ability to lysew tumor cells. Recent data have suggested that they are potentially protumorigenic and can also acquire a proangiogenic phenotype. Here we review the properties of TINKs and TANKs and compare their activities to that of NK cells endowed with a physiological proangiogenic phenotype, in particular decidual NK cells. We speculate on the potential origins of TINKs and TANKs and on the immune signals involved in their differentiation and polarization. The TINK and TANK phenotype has broad implications in the immune response to tumors, ranging from a deficient control of cancer and cancer stem cells to an altered crosstalk with other relevant players of the immune response, such as dendritic cells, to induction of cancer angiogenesis. With this recently acquired knowledge that has not yet been put into perspective, we point out new potential avenues for therapeutic intervention involving NK cells as a target or an ally in oncology.
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Affiliation(s)
- Antonino Bruno
- Scientific and Technology Park, IRCCS MultiMedica, Milano, Italy (AB, DMN); Department of Human Pathology, University of Messina, Messina, Italy (GF); Department of Research and Statistics, IRCCS Arcispedale Santa Maria Nuova, Reggio Emilia, Italy (AA); Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy (DMN)
| | - Guido Ferlazzo
- Scientific and Technology Park, IRCCS MultiMedica, Milano, Italy (AB, DMN); Department of Human Pathology, University of Messina, Messina, Italy (GF); Department of Research and Statistics, IRCCS Arcispedale Santa Maria Nuova, Reggio Emilia, Italy (AA); Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy (DMN)
| | - Adriana Albini
- Scientific and Technology Park, IRCCS MultiMedica, Milano, Italy (AB, DMN); Department of Human Pathology, University of Messina, Messina, Italy (GF); Department of Research and Statistics, IRCCS Arcispedale Santa Maria Nuova, Reggio Emilia, Italy (AA); Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy (DMN)
| | - Douglas M Noonan
- Scientific and Technology Park, IRCCS MultiMedica, Milano, Italy (AB, DMN); Department of Human Pathology, University of Messina, Messina, Italy (GF); Department of Research and Statistics, IRCCS Arcispedale Santa Maria Nuova, Reggio Emilia, Italy (AA); Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy (DMN)
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23
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Thiery J, Lieberman J. Perforin: a key pore-forming protein for immune control of viruses and cancer. Subcell Biochem 2014; 80:197-220. [PMID: 24798013 DOI: 10.1007/978-94-017-8881-6_10] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Perforin (PFN) is the key pore-forming molecule in the cytotoxic granules of immune killer cells. Expressed only in killer cells, PFN is the rate-limiting molecule for cytotoxic function, delivering the death-inducing granule serine proteases (granzymes) into target cells marked for immune elimination. In this chapter we describe our current understanding of how PFN accomplishes this task. We discuss where PFN is expressed and how its expression is regulated, the biogenesis and storage of PFN in killer cells and how they are protected from potential damage, how it is released, how it delivers Granzymes into target cells and the consequences of PFN deficiency.
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Affiliation(s)
- Jerome Thiery
- INSERM U753, University Paris Sud and Gustave Roussy Cancer Campus, Villejuif, France,
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24
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Tolerance and exhaustion: defining mechanisms of T cell dysfunction. Trends Immunol 2013; 35:51-60. [PMID: 24210163 DOI: 10.1016/j.it.2013.10.001] [Citation(s) in RCA: 483] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/29/2013] [Accepted: 10/05/2013] [Indexed: 02/08/2023]
Abstract
CD8 T cell activation and differentiation are tightly controlled, and dependent on the context in which naïve T cells encounter antigen, can either result in functional memory or T cell dysfunction, including exhaustion, tolerance, anergy, or senescence. With the identification of phenotypic and functional traits shared in different settings of T cell dysfunction, distinctions between such dysfunctional states have become blurred. Here, we discuss distinct states of CD8 T cell dysfunction, with an emphasis on: (i) T cell tolerance to self-antigens (self-tolerance); (ii) T cell exhaustion during chronic infections; and (iii) tumor-induced T cell dysfunction. We highlight recent findings on cellular and molecular characteristics defining these states, cell-intrinsic regulatory mechanisms that induce and maintain them, and strategies that can lead to their reversal.
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25
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Min-Oo G, Kamimura Y, Hendricks DW, Nabekura T, Lanier LL. Natural killer cells: walking three paths down memory lane. Trends Immunol 2013; 34:251-8. [PMID: 23499559 DOI: 10.1016/j.it.2013.02.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/11/2013] [Accepted: 02/14/2013] [Indexed: 11/17/2022]
Abstract
Immunological memory has traditionally been regarded as a unique feature of the adaptive immune response, mediated in an antigen-specific manner by T and B lymphocytes. All other hematopoietic cells, including natural killer (NK) cells, are classified as innate immune cells, which have been considered short-lived but can respond rapidly against pathogens in a manner not thought to be driven by antigen. Interestingly, NK cells have recently been shown to survive long term after antigen exposure and subsequently mediate antigen-specific recall responses. In this review, we address the similarities between, and the controversies surrounding, three major viewpoints of NK memory that have arisen from these recent studies: (i) mouse cytomegalovirus (MCMV)-induced memory; (ii) cytokine-induced memory; and (iii) liver-restricted memory cells.
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Affiliation(s)
- Gundula Min-Oo
- Department of Microbiology and Immunology and the Cancer Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
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26
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Rodriguez RM, Suarez-Alvarez B, Salvanés R, Muro M, Martínez-Camblor P, Colado E, Sánchez MA, Díaz MG, Fernandez AF, Fraga MF, Lopez-Larrea C. DNA methylation dynamics in blood after hematopoietic cell transplant. PLoS One 2013; 8:e56931. [PMID: 23451113 PMCID: PMC3579934 DOI: 10.1371/journal.pone.0056931] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/16/2013] [Indexed: 12/20/2022] Open
Abstract
Epigenetic deregulation is considered a common hallmark of cancer. Nevertheless, recent publications have demonstrated its association with a large array of human diseases. Here, we explore the DNA methylation dynamics in blood samples during hematopoietic cell transplant and how they are affected by pathophysiological events during transplant evolution. We analyzed global DNA methylation in a cohort of 47 patients with allogenic transplant up to 12 months post-transplant. Recipients stably maintained the donor’s global methylation levels after transplant. Nonetheless, global methylation is affected by chimerism status. Methylation analysis of promoters revealed that methylation in more than 200 genes is altered 1 month post-transplant when compared with non-pathological methylation levels in the donor. This number decreased by 6 months post-transplant. Finally, we analyzed methylation in IFN-γ, FASL, IL-10, and PRF1 and found association with the severity of the acute graft-versus-host disease. Our results provide strong evidence that methylation changes in blood are linked to underlying physiological events and demonstrate that DNA methylation analysis is a viable strategy for the study of transplantation and for development of biomarkers.
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Affiliation(s)
- Ramon M. Rodriguez
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | | | - Rubén Salvanés
- Department of Immunology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Manuel Muro
- Department of Immunology, Hospital Virgen de la Arrixaca, Murcia, Spain
| | | | - Enrique Colado
- Department of Hematology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Miguel Alcoceba Sánchez
- Servicio de Hematología y Hemoterapia, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Marcos González Díaz
- Servicio de Hematología y Hemoterapia, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Agustin F. Fernandez
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Mario F. Fraga
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
- Department of Immunology and Oncology, Centro Nacional de Biotecnologıa/CNB-CSIC, Cantoblanco, Madrid, Spain
- * E-mail: (MFF); (CLL)
| | - Carlos Lopez-Larrea
- Department of Immunology, Hospital Universitario Central de Asturias, Oviedo, Spain
- Fundación Renal “Iñigo Álvarez de Toledo”, Madrid, Spain
- * E-mail: (MFF); (CLL)
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27
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Suarez-Alvarez B, Rodriguez RM, Fraga MF, López-Larrea C. DNA methylation: a promising landscape for immune system-related diseases. Trends Genet 2012; 28:506-14. [PMID: 22824525 DOI: 10.1016/j.tig.2012.06.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/13/2012] [Accepted: 06/20/2012] [Indexed: 01/31/2023]
Abstract
During hematopoiesis, a unique hematopoietic stem cell (HSC) from the bone marrow gives rise to a subset of mature blood cells that directs all the immune responses. Recent studies have shown that this well-defined, hierarchical process is regulated in part by epigenetic mechanisms. Changes in the DNA methylation profile have a critical role in the division of these stem cells into the myeloid and lymphoid lineages and in the establishment of a specific phenotype and functionality in each terminally differentiated cell type. In this review, we describe how the DNA methylation patterns are modified during hematopoietic differentiation and what their role is in cell plasticity and immune function. An in-depth knowledge of these epigenetic mechanisms will help clarify how cell type-specific gene programs are established, and how they can be leveraged in the development of novel strategies for treating immune system-related pathologies.
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28
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Tokoyoda K, Radbruch A. Signals controlling rest and reactivation of T helper memory lymphocytes in bone marrow. Cell Mol Life Sci 2012; 69:1609-13. [PMID: 22460581 PMCID: PMC11114998 DOI: 10.1007/s00018-012-0969-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 03/13/2012] [Accepted: 03/13/2012] [Indexed: 12/18/2022]
Abstract
Established views on the maintenance of immunological memory have been challenged recently by the description of memory plasma cells and memory T helper (Th) lymphocytes residing in the bone marrow (BM) in dedicated survival niches, resting in terms of proliferation and migration. While memory plasma cells are no longer reactive to antigen, memory Th lymphocytes are in a state of attentive rest, and can be reactivated fast and efficiently. Here, we discuss the signals controlling these resting states, which the memory lymphocytes receive from their microenvironment.
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Affiliation(s)
- Koji Tokoyoda
- German Rheumatism Research Center Berlin, Chariteplatz 1, Berlin, Germany.
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Acquired transcriptional programming in functional and exhausted virus-specific CD8 T cells. Curr Opin HIV AIDS 2012; 7:50-7. [PMID: 22134341 DOI: 10.1097/coh.0b013e32834ddcf2] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Failure to control viral infections such as HIV results in T-cell receptor (TCR) and inhibitory receptor driven exhaustion of antigen-specific T cells. Persistent signaling by these receptors during chronic viral infection sculpts the transcriptional regulatory programs of virus-specific T cells. The resulting gene expression profile is tailored to temper the potentially damaging effector functions of cytotoxic T cells and adapt them to an antigen-rich and inflammation-rich environment. Here we review recent studies investigating mechanisms of transcriptional regulation of effector, functional memory, and exhausted T-cell functions during acute versus chronic infections. RECENT FINDINGS Patterns of gene expression in virus-specific CD8 T cells are a result of a combination of pro and inhibitory signals from antigen presentation (TCR-mediated) and co-inhibitory receptor ligation (PD-1, 2B4). Further, memory-specific transcriptional regulation of 2B4 expression and signaling impose a self-limiting secondary effector response to a prolonged viral infection. Additionally, differentiation of functional memory CD8 T cells is coupled with acquisition of a repressive epigenetic program for PD-1 expression. However, chronic infection provides a signal that blocks the acquisition of these epigenetic modifications reinforcing the suppression of cytotoxic lymphocyte (CTL) functions in exhausted cells. SUMMARY Current findings suggest that the mechanism(s) that delineate functional memory versus exhaustion are coupled with acquisition of transcriptional programs at the effector stage of differentiation, reinforced by cessation or persistence of TCR signaling.
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Maturation-related histone modifications in the PU.1 promoter regulate Th9-cell development. Blood 2012; 119:4665-74. [PMID: 22446486 DOI: 10.1182/blood-2011-11-392589] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Epigenetic histone modifications are thought to underlie the rapid memory immune response to recall antigen that develops after vaccination. However, histone-modification patterns in genes encoding transcription factors regulating cytokine production have not been investigated in either memory and naive T cells or as the immune system matures to understand the differences in cytokine response patterns. In the present study, we analyzed histone modifications in promoter regions of T-bet, GATA-3, PU.1, IRF4, and RORC in neonatal naive T cells and in adult naive and memory CD4 T cells, and found a unique and dynamic histone-modification pattern in the PU.1 promoter that was related to age and the naive/memory status of a T cell. Naive T cells required more intense stimulation to switch the chromatin pattern in the PU.1 promoter from a repressive to permissive state, and therefore to produce IL-9 than did memory T cells. Inhibition of repressive histone methylation by the specific inhibitor 3-deazaneplanocin induced Th9-specific PU.1 expression, even in conditions that would normally yield only Th0 cytokines. Conversely, prevention of histone acetylation by the histone acetyltransferase inhibitor curcumin diminished PU.1 expression after IL-9-inducing stimulation. Our findings identify age- and differentiation-status-related epigenetic modifications of PU.1 as a unique regulator of Th9 memory acquisition and Th9 immunity.
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Weng NP, Araki Y, Subedi K. The molecular basis of the memory T cell response: differential gene expression and its epigenetic regulation. Nat Rev Immunol 2012; 12:306-15. [PMID: 22421787 DOI: 10.1038/nri3173] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
How the immune system remembers a previous encounter with a pathogen and responds more efficiently to a subsequent encounter has been one of the central enigmas for immunologists for over a century. The identification of pathogen-specific memory lymphocytes that arise after an infection provided a cellular basis for immunological memory. But the molecular mechanisms of immunological memory remain only partially understood. The emerging evidence suggests that epigenetic changes have a key role in controlling the distinct transcriptional profiles of memory lymphocytes and thus in shaping their function. In this Review, we summarize the recent progress that has been made in assessing the differential gene expression and chromatin modifications in memory CD4(+) and CD8(+) T cells, and we present our current understanding of the molecular basis of memory T cell function.
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Affiliation(s)
- Nan-ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA.
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Regulation of primary response genes. Mol Cell 2011; 44:348-60. [PMID: 22055182 DOI: 10.1016/j.molcel.2011.09.014] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/29/2011] [Accepted: 09/22/2011] [Indexed: 12/24/2022]
Abstract
Primary response genes (PRGs) are a set of genes that are induced in response to both cell-extrinsic and cell-intrinsic signals and do not require de novo protein synthesis for their expression. These "first responders" in the waves of transcription of signal-responsive genes play pivotal roles in a wide range of biological responses, including neuronal survival and plasticity, cardiac stress response, innate and adaptive immune responses, glucose metabolism, and oncogeneic transformation. Here we bring together recent advances and our current understanding of the signal-induced transcriptional and epigenetic regulation of PRGs.
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