1
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Crater JM, Dunn DC, Nixon DF, Furler O’Brien RL. A History and Atlas of the Human CD4 + T Helper Cell. Biomedicines 2023; 11:2608. [PMID: 37892982 PMCID: PMC10604283 DOI: 10.3390/biomedicines11102608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
CD4+ T cells have orchestrated and regulated immunity since the introduction of jawed vertebrates, yet our understanding of CD4+ T cell evolution, development, and cellular physiology has only begun to be unearthed in the past few decades. Discoveries of genetic diseases that ablate this cellular population have provided insight into their critical functions while transcriptomics, proteomics, and high-resolution microscopy have recently revealed new insights into CD4+ T cell anatomy and physiology. This article compiles historical, microscopic, and multi-omics data that can be used as a reference atlas and index to dissect cellular physiology within these influential cells and further understand pathologies like HIV infection that inflict human CD4+ T cells.
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Affiliation(s)
| | | | | | - Robert L. Furler O’Brien
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 413 E 69th St., Belfer Research Building, New York, NY 10021, USA
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2
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Micevic G, Daniels A, Flem-Karlsen K, Park K, Talty R, McGeary M, Mirza H, Blackburn HN, Sefik E, Cheung JF, Hornick NI, Aizenbud L, Joshi NS, Kluger H, Iwasaki A, Bosenberg MW, Flavell RA. IL-7R licenses a population of epigenetically poised memory CD8 + T cells with superior antitumor efficacy that are critical for melanoma memory. Proc Natl Acad Sci U S A 2023; 120:e2304319120. [PMID: 37459511 PMCID: PMC10372654 DOI: 10.1073/pnas.2304319120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/08/2023] [Indexed: 07/20/2023] Open
Abstract
Recurrence of advanced melanoma after therapy is a major risk factor for reduced survival, and treatment options are limited. Antitumor immune memory plays a critical role in preventing melanoma recurrence and memory T cells could be a potent cell-based therapy, but the identity, and functional properties of the required immune cells are incompletely understood. Here, we show that an IL-7Rhi tumor-specific CD8+ population is critical for antitumor memory and can be epigenetically augmented to drive powerful antitumor immune responses. Using a model of functional antimelanoma memory, we found that high IL-7R expression selectively marks a CD8+ population in lymphoid organs that plays critical roles in maintaining tumor remission after immunotherapy or surgical resection. This population has intrinsic cytotoxic activity, lacks markers of exhaustion and has superior antitumor efficacy. IL-7Rhi cells have a functionally poised epigenetic landscape regulated by DNA methylation, which can be augmented by hypomethylating agents to confer improved survival and complete melanoma clearance in naive mice. Importantly, greater than 95% of tumor-specific T cells in draining lymph nodes after therapy express high levels of IL-7R. This overlap between IL-7Rhi and antigen-specific T cells allows for enrichment of a potent functional CD8+ population without determining antigen-specificity, which we demonstrate in a melanoma model without a known antigen. We identify that IL-7R expression in human melanoma is an independent prognostic factor of improved survival. These findings advance our basic understanding of antitumor memory and suggest a cell-based therapy using high IL-7R expression to enrich for a lymph node population with superior antitumor activity that can be augmented by hypomethylating agents.
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Affiliation(s)
- Goran Micevic
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Department of Dermatology, Yale School of Medicine, New Haven, CT06520
| | - Andrew Daniels
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Department of Pathology, Yale School of Medicine, New Haven, CT06520
| | | | - Koonam Park
- Department of Dermatology, Yale School of Medicine, New Haven, CT06520
| | - Ronan Talty
- Department of Pathology, Yale School of Medicine, New Haven, CT06520
| | - Meaghan McGeary
- Department of Pathology, Yale School of Medicine, New Haven, CT06520
| | - Haris Mirza
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Department of Pathology, Yale School of Medicine, New Haven, CT06520
| | - Holly N. Blackburn
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Department of Surgery, Yale School of Medicine, New Haven, CT06520
| | - Esen Sefik
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
| | - Julie F. Cheung
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
| | - Noah I. Hornick
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
| | - Lilach Aizenbud
- Yale Cancer Center, Yale School of Medicine, New Haven, CT06520
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, CT06520
| | - Nikhil S. Joshi
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
| | - Harriet Kluger
- Yale Cancer Center, Yale School of Medicine, New Haven, CT06520
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, CT06520
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT06520
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT06520
- HHMI, Chevy Chase, MD20815
| | - Marcus W. Bosenberg
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Department of Dermatology, Yale School of Medicine, New Haven, CT06520
- Department of Pathology, Yale School of Medicine, New Haven, CT06520
- Yale Cancer Center, Yale School of Medicine, New Haven, CT06520
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT06520
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT06520
| | - Richard A. Flavell
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Yale Cancer Center, Yale School of Medicine, New Haven, CT06520
- HHMI, Chevy Chase, MD20815
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3
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Onrust-van Schoonhoven A, de Bruijn MJW, Stikker B, Brouwer RWW, Braunstahl GJ, van IJcken WFJ, Graf T, Huylebroeck D, Hendriks RW, Stik G, Stadhouders R. 3D chromatin reprogramming primes human memory T H2 cells for rapid recall and pathogenic dysfunction. Sci Immunol 2023; 8:eadg3917. [PMID: 37418545 DOI: 10.1126/sciimmunol.adg3917] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/13/2023] [Indexed: 07/09/2023]
Abstract
Memory T cells provide long-lasting defense responses through their ability to rapidly reactivate, but how they efficiently "recall" an inflammatory transcriptional program remains unclear. Here, we show that human CD4+ memory T helper 2 (TH2) cells carry a chromatin landscape synergistically reprogrammed at both one-dimensional (1D) and 3D levels to accommodate recall responses, which is absent in naive T cells. In memory TH2 cells, recall genes were epigenetically primed through the maintenance of transcription-permissive chromatin at distal (super)enhancers organized in long-range 3D chromatin hubs. Precise transcriptional control of key recall genes occurred inside dedicated topologically associating domains ("memory TADs"), in which activation-associated promoter-enhancer interactions were preformed and exploited by AP-1 transcription factors to promote rapid transcriptional induction. Resting memory TH2 cells from patients with asthma showed premature activation of primed recall circuits, linking aberrant transcriptional control of recall responses to chronic inflammation. Together, our results implicate stable multiscale reprogramming of chromatin organization as a key mechanism underlying immunological memory and dysfunction in T cells.
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Affiliation(s)
- Anne Onrust-van Schoonhoven
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marjolein J W de Bruijn
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Bernard Stikker
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Gert-Jan Braunstahl
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Respiratory Medicine, Franciscus Gasthuis and Vlietland, Rotterdam, Netherlands
| | - Wilfred F J van IJcken
- Center for Biomics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Thomas Graf
- Centre for Genomic Regulation (CRG) and Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Grégoire Stik
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
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4
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Luoma S, Sergeev P, Javarappa KK, Öhman TJ, Varjosalo M, Säily M, Anttila P, Sankelo M, Partanen A, Nihtinen A, Heckman CA, Silvennoinen R. Deep Immune Profiling of Multiple Myeloma at Diagnosis and under Lenalidomide Maintenance Therapy. Cancers (Basel) 2023; 15:cancers15092604. [PMID: 37174069 PMCID: PMC10177338 DOI: 10.3390/cancers15092604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
The bone marrow microenvironment interacts with malignant cells and regulates cancer survival and immune evasion in multiple myeloma (MM). We investigated the immune profiles of longitudinal bone marrow samples from patients with newly diagnosed MM (n = 18) using cytometry by time-of-flight. The results before and during treatment were compared between patients with good (GR, n = 11) and bad (BR, n = 7) responses to lenalidomide/bortezomib/dexamethasone-based treatment. Before treatment, the GR group had a lower tumor cell burden and a higher number of T cells with a phenotype shifted toward CD8+ T cells expressing markers attributed to cytotoxicity (CD45RA and CD57), a higher abundance of CD8+ terminal effector cells, and a lower abundance of CD8+ naïve T cells. On natural killer (NK) cells, increased expression of CD56 (NCAM), CD57, and CD16 was seen at baseline in the GR group, indicating their maturation and cytotoxic potential. During lenalidomide-based treatment, the GR patients showed an increase in effector memory CD4+ and CD8+ T-cell subsets. These findings support distinct immune patterns in different clinical contexts, suggesting that deep immune profiling could be used for treatment guidance and warrants further exploration.
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Affiliation(s)
- Sini Luoma
- Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland
| | - Philipp Sergeev
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00290 Helsinki, Finland
| | - Komal Kumar Javarappa
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00290 Helsinki, Finland
| | - Tiina J Öhman
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Marjaana Säily
- Hematology-Oncology Unit, Oulu University Hospital, 90220 Oulu, Finland
| | - Pekka Anttila
- Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland
| | - Marja Sankelo
- Hematology Unit, Department of Internal Medicine, Tampere University Hospital, 33520 Tampere, Finland
| | - Anu Partanen
- Department of Medicine, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Anne Nihtinen
- Department of Internal Medicine, North Carelia Central Hospital, 80210 Joensuu, Finland
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00290 Helsinki, Finland
| | - Raija Silvennoinen
- Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland
- Department of Medicine, Kuopio University Hospital, 70210 Kuopio, Finland
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5
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Rose JR, Akdogan-Ozdilek B, Rahmberg AR, Powell MD, Hicks SL, Scharer CD, Boss JM. Distinct transcriptomic and epigenomic modalities underpin human memory T cell subsets and their activation potential. Commun Biol 2023; 6:363. [PMID: 37012418 PMCID: PMC10070634 DOI: 10.1038/s42003-023-04747-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Human memory T cells (MTC) are poised to rapidly respond to antigen re-exposure. Here, we derived the transcriptional and epigenetic programs of resting and ex vivo activated, circulating CD4+ and CD8+ MTC subsets. A progressive gradient of gene expression from naïve to TCM to TEM is observed, which is accompanied by corresponding changes in chromatin accessibility. Transcriptional changes suggest adaptations of metabolism that are reflected in altered metabolic capacity. Other differences involve regulatory modalities comprised of discrete accessible chromatin patterns, transcription factor binding motif enrichment, and evidence of epigenetic priming. Basic-helix-loop-helix factor motifs for AHR and HIF1A distinguish subsets and predict transcription networks to sense environmental changes. Following stimulation, primed accessible chromatin correlate with an augmentation of MTC gene expression as well as effector transcription factor gene expression. These results identify coordinated epigenetic remodeling, metabolic, and transcriptional changes that enable MTC subsets to ultimately respond to antigen re-encounters more efficiently.
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Affiliation(s)
- James R Rose
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Bagdeser Akdogan-Ozdilek
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Andrew R Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Michael D Powell
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sakeenah L Hicks
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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6
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Petinati N, Davydova Y, Nikiforova K, Bigildeev A, Belyavsky A, Arapidi G, Drize N, Kuzmina L, Parovichnikova E, Savchenko V. T Cell and Cytokine Dynamics in the Blood of Patients after Hematopoietic Stem Cell Transplantation and Multipotent Mesenchymal Stromal Cell Administration. Transplant Cell Ther 2023; 29:109.e1-109.e10. [PMID: 36372356 DOI: 10.1016/j.jtct.2022.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 09/28/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022]
Abstract
Multipotent mesenchymal stromal cells (MSCs) are currently under intensive investigation for the treatment and prevention of graft-versus-host disease (GVHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT), owing to their substantial immunomodulatory properties. The responses of recipients to MSC infusion following allo-HSCT are not yet well understood. T cells are central to the adaptive immune system, protecting the organism from infection and malignant cells. Memory T cells with different phenotypes, gene expression profiles, and functional properties are critical for immune processes regulation. The aim of this study was to study the dynamics of memory T cell subpopulations and cytokines in the blood of allo-HSCT recipients after MSC administration. In clinical trial NCT01941394, patients after allo-HSCT were randomized into 2 groups, one receiving standard GVHD prophylaxis and the other also receiving MSC infusion on the day of leukocyte recovery to 1000 cells/μL (engraftment, day E0). Blood samples of patients from both groups were analyzed on days E0, E+3, and E+30. T cell subpopulations were studied by flow cytometry, and cytokine concentrations were evaluated by the Bio-Plex Pro Human Cytokine Panel. Administration of MSCs to patients on day E0 did not affect the overall dynamics of restoration of absolute numbers and proportions of T and B lymphocytes after 3 and 30 days. At 3 days after MSC injection, only the numbers of CD8+ effector cells (CD8+TE, CD8+TM, and CD8+EM) were found to increase significantly. A significant increase in the number of CD4+ cells after 30 days compared to day E0 was observed only in patients who received MSCs, indicating faster recovery of the CD4+ cell population following MSC injection. An increase in CD8+ cell number by day E+30 was significant regardless of MSC administration. To characterize the immune status of patients following allo-HSCT in more detail, changes in the cytokine concentration in the peripheral blood of patients on days E0, E+3, and E+30 after MSC administration were investigated. On day E+30, significant increases in the numbers of CD4+CM and activated CD4+CD25+ cells were observed. The concentrations of proinflammatory and anti-inflammatory cytokines IL-6, IL-8, IL-17, TNF-α, and IFN-γ were increased significantly in patients injected with MSCs. Analysis of growth factor levels showed that in the group of patients who received MSCs, the concentrations of G-CSF, GM-CSF, PDGFbb, FGFb, and IL-5 increased by day E+30. Among the cytokines involved in regulation of the immune response, concentrations of IL-9, eotaxin, IP-10, MCP-1, and MIP-1a were increased after 30 days irrespective of MSC administration. The administration of MSCs exerts a positive effect on the restoration of T cell subpopulations and immune system recovery in patients after allo-HSCT.
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Abstract
PURPOSE OF REVIEW Aging leads to decline in bone mass and quality starting at age 30 in humans. All mammals undergo a basal age-dependent decline in bone mass. Osteoporosis is characterized by low bone mass and changes in bone microarchitecture that increases the risk of fracture. About a third of men over the age of 50 years are osteoporotic because they have higher than basal bone loss. In women, there is an additional acute decrement in bone mass, atop the basal rate, associated with loss of ovarian function (menopause) causing osteoporosis in about half of the women. Both genetics and environmental factors such as smoking, chronic infections, diet, microbiome, and metabolic disease can modulate basal age-dependent bone loss and eventual osteoporosis. Here, we review recent studies on the etiology of age-dependent decline in bone mass and propose a mechanism that integrates both genetic and environmental factors. RECENT FINDINGS Recent findings support that aging and menopause dysregulate the immune system leading to sterile low-grade inflammation. Both animal models and human studies demonstrate that certain kinds of inflammation, in both men and women, mediate bone loss. Senolytics, meant to block a wide array of age-induced effects by preventing cellular senescence, have been shown to improve bone mass in aged mice. Based on a synthesis of the recent data, we propose that aging activates long-lived tissue resident memory T-cells to become senescent and proinflammatory, leading to bone loss. Targeting this population may represent a promising osteoporosis therapy. Emerging data indicates that there are several mechanisms that lead to sterile low-grade chronic inflammation, inflammaging, that cause age- and estrogen-loss dependent osteoporosis in men and women.
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Affiliation(s)
- Rajeev Aurora
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 S. Grand Blvd., DRC605, St. Louis, MO, 63104, USA.
| | - Deborah Veis
- Division of Bone and Mineral Diseases and Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
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8
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Chen AF, Parks B, Kathiria AS, Ober-Reynolds B, Goronzy JJ, Greenleaf WJ. NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. Nat Methods 2022; 19:547-553. [PMID: 35501385 DOI: 10.1038/s41592-022-01461-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 03/20/2022] [Indexed: 02/08/2023]
Abstract
In this work, we describe NEAT-seq (sequencing of nuclear protein epitope abundance, chromatin accessibility and the transcriptome in single cells), enabling interrogation of regulatory mechanisms spanning the central dogma. We apply this technique to profile CD4 memory T cells using a panel of master transcription factors (TFs) that drive T cell subsets and identify examples of TFs with regulatory activity gated by transcription, translation and regulation of chromatin binding. We also link a noncoding genome-wide association study single-nucleotide polymorphism (SNP) within a GATA motif to a putative target gene, using NEAT-seq data to internally validate SNP impact on GATA3 regulation.
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Affiliation(s)
- Amy F Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin Parks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA
| | - Arwa S Kathiria
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Jorg J Goronzy
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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9
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Mittelstaedt NN, Becker AL, de Freitas DN, Zanin RF, Stein RT, Duarte de Souza AP. DNA Methylation and Immune Memory Response. Cells 2021; 10:2943. [PMID: 34831166 DOI: 10.3390/cells10112943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/16/2022] Open
Abstract
The generation of memory is a cardinal feature of the adaptive immune response, involving different factors in a complex process of cellular differentiation. This process is essential for protecting the second encounter with pathogens and is the mechanism by which vaccines work. Epigenetic changes play important roles in the regulation of cell differentiation events. There are three types of epigenetic regulation: DNA methylation, histone modification, and microRNA expression. One of these epigenetic changes, DNA methylation, occurs in cytosine residues, mainly in CpG dinucleotides. This brief review aimed to analyse the literature to verify the involvement of DNA methylation during memory T and B cell development. Several studies have highlighted the importance of the DNA methyltransferases, enzymes that catalyse the methylation of DNA, during memory differentiation, maintenance, and function. The methylation profile within different subsets of naïve activated and memory cells could be an interesting tool to help monitor immune memory response.
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10
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Korinfskaya S, Parameswaran S, Weirauch MT, Barski A. Runx Transcription Factors in T Cells-What Is Beyond Thymic Development? Front Immunol 2021; 12:701924. [PMID: 34421907 PMCID: PMC8377396 DOI: 10.3389/fimmu.2021.701924] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Runx proteins (also known as Runt-domain transcription factors) have been studied for a long time as key regulators of cellular differentiation. RUNX2 has been described as essential for osteogenesis, whereas RUNX1 and RUNX3 are known to control blood cell development during different stages of cell lineage specification. However, recent studies show evidence of complex relationships between RUNX proteins, chromatin-modifying machinery, the cytoskeleton and different transcription factors in various non-embryonic contexts, including mature T cell homeostasis, inflammation and cancer. In this review, we discuss the diversity of Runx functions in mature T helper cells, such as production of cytokines and chemokines by different CD4 T cell populations; apoptosis; and immunologic memory acquisition. We then briefly cover recent findings about the contribution of RUNX1, RUNX2 and RUNX3 to various immunologic diseases. Finally, we discuss areas that require further study to better understand the role that Runx proteins play in inflammation and immunity.
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Affiliation(s)
- Svetlana Korinfskaya
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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11
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Devenish LP, Mhlanga MM, Negishi Y. Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses. Front Immunol 2021; 12:662565. [PMID: 34046034 PMCID: PMC8144502 DOI: 10.3389/fimmu.2021.662565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/27/2022] Open
Abstract
Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Therefore, the fine control of immune effector functions to provide for a rapid, robust response to challenge is essential. Importantly, immune cells are heterogeneous due to various factors relating to cytokine exposure and cell-cell interaction. For instance, tissue-resident macrophages and T cells are phenotypically, transcriptionally, and functionally distinct from their circulating counterparts. Indeed, even the same cell types in the same environment show distinct transcription patterns at the single cell level due to cellular noise, despite being robust in concert. Additionally, immune cells must remain quiescent in a naive state to avoid autoimmunity or chronic inflammatory states but must respond robustly upon activation regardless of their microenvironment or cellular noise. In recent years, accruing evidence from next-generation sequencing, chromatin capture techniques, and high-resolution imaging has shown that local- and long-range genome architecture plays an important role in coordinating rapid and robust transcriptional responses. Here, we discuss the local- and long-range genome architecture of immune cells and the resultant changes upon pathogen or antigen exposure. Furthermore, we argue that genome structures contribute functionally to rapid and robust responses under noisy and distinct cellular environments and propose a model to explain this phenomenon.
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Affiliation(s)
- Liam P Devenish
- Division of Chemical, Systems, and Synthetic Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Musa M Mhlanga
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yutaka Negishi
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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12
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Abstract
The code of life is not only encrypted in the sequence of DNA but also in the way it is organized into chromosomes. Chromosome architecture is gradually being recognized as an important player in regulating cell activities (e.g., controlling spatiotemporal gene expression). In the past decade, the toolbox for elucidating genome structure has been expanding, providing an opportunity to explore this under charted territory. In this review, we will introduce the recent advancements in approaches for mapping spatial organization of the genome, emphasizing applications of these techniques to immune cells, and trying to bridge chromosome structure with immune cell activities.
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Affiliation(s)
- Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States
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13
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Maes K, Mondino A, Lasarte JJ, Agirre X, Vanderkerken K, Prosper F, Breckpot K. Epigenetic Modifiers: Anti-Neoplastic Drugs With Immunomodulating Potential. Front Immunol 2021; 12:652160. [PMID: 33859645 PMCID: PMC8042276 DOI: 10.3389/fimmu.2021.652160] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/09/2021] [Indexed: 12/16/2022] Open
Abstract
Cancer cells are under the surveillance of the host immune system. Nevertheless, a number of immunosuppressive mechanisms allow tumors to escape protective responses and impose immune tolerance. Epigenetic alterations are central to cancer cell biology and cancer immune evasion. Accordingly, epigenetic modulating agents (EMAs) are being exploited as anti-neoplastic and immunomodulatory agents to restore immunological fitness. By simultaneously acting on cancer cells, e.g. by changing expression of tumor antigens, immune checkpoints, chemokines or innate defense pathways, and on immune cells, e.g. by remodeling the tumor stroma or enhancing effector cell functionality, EMAs can indeed overcome peripheral tolerance to transformed cells. Therefore, combinations of EMAs with chemo- or immunotherapy have become interesting strategies to fight cancer. Here we review several examples of epigenetic changes critical for immune cell functions and tumor-immune evasion and of the use of EMAs in promoting anti-tumor immunity. Finally, we provide our perspective on how EMAs could represent a game changer for combinatorial therapies and the clinical management of cancer.
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Affiliation(s)
- Ken Maes
- Laboratory for Hematology and Immunology, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium.,Center for Medical Genetics, Vrije Universiteit Brussel (VUB), Universiteit Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Anna Mondino
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Juan José Lasarte
- Immunology and Immunotherapy Program, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona, Spain
| | - Xabier Agirre
- Laboratory of Cancer Epigenetics, Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Pamplona, Spain.,Hemato-oncology Program, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona, Spain
| | - Karin Vanderkerken
- Laboratory for Hematology and Immunology, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Felipe Prosper
- Laboratory of Cancer Epigenetics, Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Pamplona, Spain.,Hemato-oncology Program, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona, Spain.,Hematology and Cell Therapy Department, Clínica Universidad de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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14
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Bugya Z, Prechl J, Szénási T, Nemes É, Bácsi A, Koncz G. Multiple Levels of Immunological Memory and Their Association with Vaccination. Vaccines (Basel) 2021; 9:174. [PMID: 33669597 DOI: 10.3390/vaccines9020174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/25/2022] Open
Abstract
Immunological memory is divided into many levels to counteract the provocations of diverse and ever-changing infections. Fast functions of effector memory and the superposition of both quantitatively and qualitatively plastic anticipatory memory responses together form the walls of protection against pathogens. Here we provide an overview of the role of different B and T cell subsets and their interplay, the parallel and independent functions of the B1, marginal zone B cells, T-independent- and T-dependent B cell responses, as well as functions of central and effector memory T cells, tissue-resident and follicular helper T cells in the memory responses. Age-related limitations in the immunological memory of these cell types in neonates and the elderly are also discussed. We review how certain aspects of immunological memory and the interactions of components can affect the efficacy of vaccines, in order to link our knowledge of immunological memory with the practical application of vaccination.
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15
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Gao S, Liang X, Wang H, Bao B, Zhang K, Zhu Y, Shao Q. Stem cell-like memory T cells: A perspective from the dark side. Cell Immunol 2021; 361:104273. [PMID: 33422699 DOI: 10.1016/j.cellimm.2020.104273] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/10/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023]
Abstract
Much attention has been paid to a newly discovered subset of memory T (TM) cells-stem cell-like memory T (TSCM) cells for their high self-renewal ability, multi-differentiation potential and long-term effector function in adoptive therapy against tumors. Despite their application in cancer therapy, an excess of TSCM cells also contributes to the persistence of autoimmune diseases for their immune memory and HIV infection as a long-lived HIV reservoir. Signaling pathways Wnt, AMPK/mTOR and NF-κB are key determinants for TM cell generation, maintenance and proinflammatory effect. In this review, we focus on the phenotypic and functional characteristics of TSCM cells and discuss their role in autoimmune diseases and HIV-1 chronic infection. Also, we explore the potential mechanism and signaling pathways involved in immune memory and look into the future therapy strategies of targeting long-lived TM cells to suppress pathogenic immune memory.
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16
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Bevington SL, Fiancette R, Gajdasik DW, Keane P, Soley JK, Willis CM, Coleman DJL, Withers DR, Cockerill PN. Stable Epigenetic Programming of Effector and Central Memory CD4 T Cells Occurs Within 7 Days of Antigen Exposure In Vivo. Front Immunol 2021; 12:642807. [PMID: 34108962 PMCID: PMC8181421 DOI: 10.3389/fimmu.2021.642807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/05/2021] [Indexed: 12/23/2022] Open
Abstract
T cell immunological memory is established within days of an infection, but little is known about the in vivo changes in gene regulatory networks accounting for their ability to respond more efficiently to secondary infections. To decipher the timing and nature of immunological memory we performed genome-wide analyses of epigenetic and transcriptional changes in a mouse model generating antigen-specific T cells. Epigenetic reprogramming for Th differentiation and memory T cell formation was already established by the peak of the T cell response after 7 days. The Th memory T cell program was associated with a gain of open chromatin regions, enriched for RUNX, ETS and T-bet motifs, which remained stable for 56 days. The epigenetic programs for both effector memory, associated with T-bet, and central memory, associated with TCF-1, were established in parallel. Memory T cell-specific regulatory elements were associated with greatly enhanced inducible Th1-biased responses during secondary exposures to antigen. Furthermore, memory T cells responded in vivo to re-exposure to antigen by rapidly reprograming the entire ETS factor gene regulatory network, by suppressing Ets1 and activating Etv6 expression. These data show that gene regulatory networks are epigenetically reprogrammed towards memory during infection, and undergo substantial changes upon re-stimulation.
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Affiliation(s)
- Sarah L Bevington
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Remi Fiancette
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Dominika W Gajdasik
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jake K Soley
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Claire M Willis
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Daniel J L Coleman
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - David R Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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17
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Pardons M, Fromentin R, Pagliuzza A, Routy JP, Chomont N. Latency-Reversing Agents Induce Differential Responses in Distinct Memory CD4 T Cell Subsets in Individuals on Antiretroviral Therapy. Cell Rep 2019; 29:2783-2795.e5. [PMID: 31775045 DOI: 10.1016/j.celrep.2019.10.101] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/11/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
Latent proviruses persist in central (TCM), transitional (TTM), and effector (TEM) memory cells. We measured the levels of cellular factors involved in HIV gene expression in these subsets. The highest levels of acetylated H4, active nuclear factor κB (NF-κB), and active positive transcription elongation factor b (P-TEFb) were measured in TEM, TCM, and TTM cells, respectively. Vorinostat and romidepsin display opposite abilities to induce H4 acetylation across subsets. Protein kinase C (PKC) agonists are more efficient at inducing NF-κB phosphorylation in TCM cells but more potent at activating PTEF-b in the TEM subset. We selected the most efficient latency-reversing agents (LRAs) and measured their ability to reverse latency in each subset. While ingenol alone has modest activities in the three subsets, its combination with a histone deacetylase inhibitor (HDACi) dramatically increases latency reversal in TCM cells. Altogether, these results indicate that cellular HIV reservoirs are differentially responsive to common LRAs and suggest that combination of compounds will be required to achieve latency reversal in all subsets.
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18
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Abstract
Amino acids are fundamental building blocks supporting life. Their role in protein synthesis is well defined, but they contribute to a host of other intracellular metabolic pathways, including ATP generation, nucleotide synthesis, and redox balance, to support cellular and organismal function. Immune cells critically depend on such pathways to acquire energy and biomass and to reprogram their metabolism upon activation to support growth, proliferation, and effector functions. Amino acid metabolism plays a key role in this metabolic rewiring, and it supports various immune cell functions beyond increased protein synthesis. Here, we review the mechanisms by which amino acid metabolism promotes immune cell function, and how these processes could be targeted to improve immunity in pathological conditions.
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Affiliation(s)
- Beth Kelly
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Erika L Pearce
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg 79108, Germany.
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19
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Abstract
Several studies have demonstrated that memory T cells including stem cell memory (Tscm) T cells and central memory (Tcm) T cells show superior persistence and antitumor immunity compared with effector memory T (Tem) cells and effector T (Teff) cells. Furthermore, the Tcm/Teff ratio has been reported to be a predictive biomarker of immune responses against some tumors. Thus, a system-level understanding of the mechanisms underlying the differentiation of effector and memory T cells is of increasing importance for developing immunological strategies against various tumors. This review focuses on recent advances in efficacy against tumors, the origin, formation mechanisms of memory T cells, and the role of the gut microbiota in memory T cell formation. Furthermore, we summarize strategies to generate memory T cells in (ex) vivo that, might be applicable in clinical practice.
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Affiliation(s)
- Qingjun Liu
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China.,Newish Technology (Beijing) Co., Ltd., Xihuan South Road 18, Economic & Technical Development Zone, Beijing, 100176, China.,Moon (Guangzhou) Biotech Co., Ltd., Room 301, Building B5, Enterprise Accelerator, No. 11 Kaiyuan Avenue, Huangpu District, Guangzhou, 510000, China
| | - Zhongjie Sun
- Newish Technology (Beijing) Co., Ltd., Xihuan South Road 18, Economic & Technical Development Zone, Beijing, 100176, China.
| | - Ligong Chen
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China. .,Advanced Innovation Center for Human Brain Protection, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100088, China.
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20
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Hall TJ, Vernimmen D, Browne JA, Mullen MP, Gordon SV, MacHugh DE, O’Doherty AM. Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection. Front Genet 2020; 10:1386. [PMID: 32117424 PMCID: PMC7020904 DOI: 10.3389/fgene.2019.01386] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/18/2019] [Indexed: 12/29/2022] Open
Abstract
Bovine tuberculosis is caused by infection with Mycobacterium bovis, which can also cause disease in a range of other mammals, including humans. Alveolar macrophages are the key immune effector cells that first encounter M. bovis and how the macrophage epigenome responds to mycobacterial pathogens is currently not well understood. Here, we have used chromatin immunoprecipitation sequencing (ChIP-seq), RNA-seq and miRNA-seq to examine the effect of M. bovis infection on the bovine alveolar macrophage (bAM) epigenome. We show that H3K4me3 is more prevalent, at a genome-wide level, in chromatin from M. bovis-infected bAM compared to control non-infected bAM; this was particularly evident at the transcriptional start sites of genes that determine programmed macrophage responses to mycobacterial infection (e.g. M1/M2 macrophage polarisation). This pattern was also supported by the distribution of RNA Polymerase II (Pol II) ChIP-seq results, which highlighted significantly increased transcriptional activity at genes demarcated by permissive chromatin. Identification of these genes enabled integration of high-density genome-wide association study (GWAS) data, which revealed genomic regions associated with resilience to infection with M. bovis in cattle. Through integration of these data, we show that bAM transcriptional reprogramming occurs through differential distribution of H3K4me3 and Pol II at key immune genes. Furthermore, this subset of genes can be used to prioritise genomic variants from a relevant GWAS data set.
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Affiliation(s)
- Thomas J. Hall
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
| | - Douglas Vernimmen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - John A. Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
| | - Michael P. Mullen
- Bioscience Research Institute, Athlone Institute of Technology, Athlone, Ireland
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - David E. MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Alan M. O’Doherty
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
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21
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Kwon KJ, Timmons AE, Sengupta S, Simonetti FR, Zhang H, Hoh R, Deeks SG, Siliciano JD, Siliciano RF. Different human resting memory CD4 + T cell subsets show similar low inducibility of latent HIV-1 proviruses. Sci Transl Med 2020; 12:eaax6795. [PMID: 31996465 PMCID: PMC7875249 DOI: 10.1126/scitranslmed.aax6795] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/10/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022]
Abstract
The latent reservoir of HIV-1 in resting CD4+ T cells is a major barrier to cure. It is unclear whether the latent reservoir resides principally in particular subsets of CD4+ T cells, a finding that would have implications for understanding its stability and developing curative therapies. Recent work has shown that proliferation of HIV-1-infected CD4+ T cells is a major factor in the generation and persistence of the latent reservoir and that latently infected T cells that have clonally expanded in vivo can proliferate in vitro without producing virions. In certain CD4+ memory T cell subsets, the provirus may be in a deeper state of latency, allowing the cell to proliferate without producing viral proteins, thus permitting escape from immune clearance. To evaluate this possibility, we used a multiple stimulation viral outgrowth assay to culture resting naïve, central memory (TCM), transitional memory (TTM), and effector memory (TEM) CD4+ T cells from 10 HIV-1-infected individuals on antiretroviral therapy. On average, only 1.7% of intact proviruses across all T cell subsets were induced to transcribe viral genes and release replication-competent virus after stimulation of the cells. We found no consistent enrichment of intact or inducible proviruses in any T cell subset. Furthermore, we observed notable plasticity among the canonical memory T cell subsets after activation in vitro and saw substantial person-to-person variability in the inducibility of infectious virus release. This finding complicates the vision for a targeted approach for HIV-1 cure based on T cell memory subsets.
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Affiliation(s)
- Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E Timmons
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Srona Sengupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hao Zhang
- Flow Cytometry and Immunology Core, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steven G Deeks
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Baltimore, MD, USA
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22
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Britt EC, John SV, Locasale JW, Fan J. Metabolic regulation of epigenetic remodeling in immune cells. Curr Opin Biotechnol 2020; 63:111-117. [PMID: 31954223 DOI: 10.1016/j.copbio.2019.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/01/2019] [Accepted: 12/08/2019] [Indexed: 02/06/2023]
Abstract
Immune cells are capable of sensing various signals in the microenvironment and turning on specific immune functions in response. The appropriate transition of immune cells into diverse functional states, which is crucial for immunity, involves complex and well-regulated changes in transcriptional program. Accumulating evidence shows that epigenetic remodeling plays a central role in mediating the transcriptional program for immune cell activation and immunological memory. Concurrently, immune cells undergo significant metabolic reprogramming during immune response. Here we review recent studies that demonstrate shifts in metabolic state can orchestrate immune cell functions through its impact on epigenetic remodeling, and the microenvironment can exert its influence on immune cells through the metabolic regulation of epigenetics. We also discuss the systems biology approaches that enabled these discoveries.
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Affiliation(s)
- Emily C Britt
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Steven V John
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Jing Fan
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
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23
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Tough DF, Rioja I, Modis LK, Prinjha RK. Epigenetic Regulation of T Cell Memory: Recalling Therapeutic Implications. Trends Immunol 2019; 41:29-45. [PMID: 31813765 DOI: 10.1016/j.it.2019.11.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023]
Abstract
Memory T cells possess functional differences from naïve T cells that powerfully contribute to the efficiency of secondary immune responses. These abilities are imprinted during the primary response, linked to the acquisition of novel patterns of gene expression. Underlying this are alterations at the chromatin level (epigenetic modifications) that regulate constitutive and inducible gene transcription. T cell epigenetic memory can persist long-term, contributing to long-lasting immunity after infection or vaccination. However, acquired epigenetic states can also hinder effective tumor immunity or contribute to autoimmunity. The growing understanding of epigenetic gene regulation as it relates to both the stability and malleability of T cell memory may offer the potential to selectively modify T cell memory in disease by targeting epigenetic mechanisms.
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Affiliation(s)
- David F Tough
- Epigenetics Research Unit, Oncology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, UK
| | - Inma Rioja
- Epigenetics Research Unit, Oncology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, UK
| | - Louise K Modis
- Adaptive Immunity Research Unit, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, UK
| | - Rab K Prinjha
- Epigenetics Research Unit, Oncology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, UK; Adaptive Immunity Research Unit, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, UK.
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24
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Schmidl C, Delacher M, Huehn J, Feuerer M. Epigenetic mechanisms regulating T-cell responses. J Allergy Clin Immunol 2018; 142:728-43. [PMID: 30195378 DOI: 10.1016/j.jaci.2018.07.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022]
Abstract
During the last decade, advances in sequencing technologies allowed production of a wealth of information on epigenetic modifications in T cells. Epigenome maps, in combination with mechanistic studies, have demonstrated that T cells undergo extensive epigenome remodeling in response to signals, which has a strong effect on phenotypic stability and function of lymphocytes. In this review we focus on DNA methylation, histone modifications, and chromatin structure as important epigenetic mechanisms involved in controlling T-cell responses. In particular, we discuss epigenetic processes in light of the development, activation, and differentiation of CD4+ T helper (TH), regulatory T, and CD8+ T cells. As central aspects of the adaptive immune system, we review mechanisms that ensure molecular memory, stability, plasticity, and exhaustion of T cells. We further discuss the effect of the tissue environment on imprinting T-cell epigenomes with potential implications for immunotherapy.
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25
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Abstract
Immune cells are pivotal in the reaction to injury, whereupon, under ideal conditions, repair and resolution phases restore homeostasis following initial acute inflammation. Immune cell activation and reprogramming require transcriptional changes that can only be initiated if epigenetic alterations occur. Recently, accelerated deciphering of epigenetic mechanisms has extended knowledge of epigenetic regulation, including long-distance chromatin remodeling, DNA methylation, posttranslational histone modifications, and involvement of small and long noncoding RNAs. Epigenetic changes have been linked to aspects of immune cell development, activation, and differentiation. Furthermore, genome-wide epigenetic landscapes have been established for some immune cells, including tissue-resident macrophages, and blood-derived cells including T cells. The epigenetic mechanisms underlying developmental steps from hematopoietic stem cells to fully differentiated immune cells led to development of epigenetic technologies and insights into general rules of epigenetic regulation. Compared with more advanced research areas, epigenetic reprogramming of immune cells in injury remains in its infancy. While the early epigenetic mechanisms supporting activation of the immune response to injury have been studied, less is known about resolution and repair phases and cell type-specific changes. We review prominent recent findings concerning injury-mediated epigenetic reprogramming, particularly in stroke and myocardial infarction. Lastly, we illustrate how single-cell technologies will be crucial to understanding epigenetic reprogramming in the complex sequential processes following injury.
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Affiliation(s)
- Katarzyna Placek
- Immunology and Metabolism, LIMES Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Anna C Aschenbrenner
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
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26
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Abstract
PURPOSE OF REVIEW In recent years, a vast body of evidence has accumulated indicating the role of the immune system in the regulation of blood pressure and modulation of hypertensive pathology. Numerous cells of the immune system, both innate and adaptive immunity, have been indicated to play an important role in the development and maintenance of hypertension. The purpose of this review was to summarize the role of adaptive immunity in experimental models of hypertension (genetic, salt-sensitive, and Angiotensin (Ang) II induced) and in human studies. In particular, the role of T and B cells is discussed. RECENT FINDINGS In response to hypertensive stimuli such as Ang II and high salt, T cells become pro-inflammatory and they infiltrate the brain, blood vessel adventitia and periadventitial fat, heart, and the kidney. Pro-inflammatory T cell-derived cytokines such as IFN-γ and TNF-α (from CD8+ and CD4+Th1) and IL-17A (from the γδ-T cell and CD4+Th17) exacerbate hypertensive responses mediating both endothelial dysfunction and cardiac, renal, and neurodegenerative injury. The modulation of adaptive immune activation in hypertension has been attributed to target organ oxidative stress that leads to the generation of neoantigens, including isolevuglandin-modified proteins. The role of adaptive immunity is sex-specific with much more pronounced mechanisms in males than that in females. Hypertension is also associated with B cell activation and production of autoantibodies (anti-Hsp70, anti-Hsp65, anti-Hsp60, anti-AT1R, anti-α1AR, and anti-β1AR). The hypertensive responses can be inhibited by T regulatory lymphocytes (Tregs) and their anti-inflammatory IL-10. Adaptive immunity and its interface with innate mechanisms may represent valuable targets in the modulation of blood pressure, as well as hypertension-related residual risk.
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Affiliation(s)
- Tomasz P Mikolajczyk
- Department of Internal and Agricultural Medicine, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Tomasz J Guzik
- Department of Internal and Agricultural Medicine, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland.
- BHF Centre for Excellence, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK.
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Netea MG, Schlitzer A, Placek K, Joosten LAB, Schultze JL. Innate and Adaptive Immune Memory: an Evolutionary Continuum in the Host's Response to Pathogens. Cell Host Microbe 2019; 25:13-26. [PMID: 30629914 DOI: 10.1016/j.chom.2018.12.006] [Citation(s) in RCA: 255] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Immunological memory is an important evolutionary trait that improves host survival upon reinfection. Memory is a characteristic recognized within both the innate and adaptive arms of the immune system. Although the mechanisms and properties through which innate and adaptive immune memory are induced are distinct, they collude to improve host defense to pathogens. Here, we propose that innate immune memory, or "trained immunity," is a primitive form of adaptation in host defense, resulting from chromatin structure rearrangement, which provides an increased but non-specific response to reinfection. In contrast, adaptive immune memory is more advanced, with increased magnitude of response mediated through epigenetic changes, as well as specificity mediated by gene recombination. An integrative model of immune memory is important for broad understanding of host defense, and for identifying the most effective approaches to modulate it for the benefit of patients with infections and immune-mediated diseases.
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Kelly D, Kotliar M, Woo V, Jagannathan S, Whitt J, Moncivaiz J, Aronow BJ, Dubinsky MC, Hyams JS, Markowitz JF, Baldassano RN, Stephens MC, Walters TD, Kugathasan S, Haberman Y, Sundaram N, Rosen MJ, Helmrath M, Karns R, Barski A, Denson LA, Alenghat T. Microbiota-sensitive epigenetic signature predicts inflammation in Crohn's disease. JCI Insight 2018; 3:122104. [PMID: 30232290 PMCID: PMC6237229 DOI: 10.1172/jci.insight.122104] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/07/2018] [Indexed: 12/19/2022] Open
Abstract
Altered response to the intestinal microbiota strongly associates with inflammatory bowel disease (IBD); however, how commensal microbial cues are integrated by the host during the pathogenesis of IBD is not understood. Epigenetics represents a potential mechanism that could enable intestinal microbes to modulate transcriptional output during the development of IBD. Here, we reveal a histone methylation signature of intestinal epithelial cells isolated from the terminal ilea of newly diagnosed pediatric IBD patients. Genes characterized by significant alterations in histone H3-lysine 4 trimethylation (H3K4me3) showed differential enrichment in pathways involving immunoregulation, cell survival and signaling, and metabolism. Interestingly, a large subset of these genes was epigenetically regulated by microbiota in mice and several microbiota-sensitive epigenetic targets demonstrated altered expression in IBD patients. Remarkably though, a substantial proportion of these genes exhibited H3K4me3 levels that correlated with the severity of intestinal inflammation in IBD, despite lacking significant differential expression. Collectively, these data uncover a previously unrecognized epigenetic profile of IBD that can be primed by commensal microbes and indicate sensitive targets in the epithelium that may underlie how microbiota predispose to subsequent intestinal inflammation and disease.
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Affiliation(s)
- Daniel Kelly
- Division of Immunobiology, Center for Inflammation and Tolerance
- Division of Gastroenterology, Hepatology, and Nutrition
| | | | - Vivienne Woo
- Division of Immunobiology, Center for Inflammation and Tolerance
| | | | - Jordan Whitt
- Division of Immunobiology, Center for Inflammation and Tolerance
| | | | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center (CCHMC) and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Marla C. Dubinsky
- Department of Pediatrics, Mount Sinai Hospital, New York, New York, USA
| | - Jeffrey S. Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children’s Medical Center, Hartford, Connecticut, USA
| | | | - Robert N. Baldassano
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael C. Stephens
- Department of Pediatric Gastroenterology, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas D. Walters
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yael Haberman
- Division of Gastroenterology, Hepatology, and Nutrition
- Sheba Medical Center, Tel Hashomer, affiliated with the Tel-Aviv University, Israel
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery, CCHMC and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Michael Helmrath
- Division of Pediatric General and Thoracic Surgery, CCHMC and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Rebekah Karns
- Division of Gastroenterology, Hepatology, and Nutrition
| | - Artem Barski
- Divisions of Allergy and Immunology and Human Genetics, and
| | - Lee A. Denson
- Division of Gastroenterology, Hepatology, and Nutrition
| | - Theresa Alenghat
- Division of Immunobiology, Center for Inflammation and Tolerance
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Bantug GR, Fischer M, Grählert J, Balmer ML, Unterstab G, Develioglu L, Steiner R, Zhang L, Costa ASH, Gubser PM, Burgener AV, Sauder U, Löliger J, Belle R, Dimeloe S, Lötscher J, Jauch A, Recher M, Hönger G, Hall MN, Romero P, Frezza C, Hess C. Mitochondria-Endoplasmic Reticulum Contact Sites Function as Immunometabolic Hubs that Orchestrate the Rapid Recall Response of Memory CD8 + T Cells. Immunity 2018; 48:542-555.e6. [PMID: 29523440 DOI: 10.1016/j.immuni.2018.02.012] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Glycolysis is linked to the rapid response of memory CD8+ T cells, but the molecular and subcellular structural elements enabling enhanced glucose metabolism in nascent activated memory CD8+ T cells are unknown. We found that rapid activation of protein kinase B (PKB or AKT) by mammalian target of rapamycin complex 2 (mTORC2) led to inhibition of glycogen synthase kinase 3β (GSK3β) at mitochondria-endoplasmic reticulum (ER) junctions. This enabled recruitment of hexokinase I (HK-I) to the voltage-dependent anion channel (VDAC) on mitochondria. Binding of HK-I to VDAC promoted respiration by facilitating metabolite flux into mitochondria. Glucose tracing pinpointed pyruvate oxidation in mitochondria, which was the metabolic requirement for rapid generation of interferon-γ (IFN-γ) in memory T cells. Subcellular organization of mTORC2-AKT-GSK3β at mitochondria-ER contact sites, promoting HK-I recruitment to VDAC, thus underpins the metabolic reprogramming needed for memory CD8+ T cells to rapidly acquire effector function.
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30
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Brignall R, Cauchy P, Bevington SL, Gorman B, Pisco AO, Bagnall J, Boddington C, Rowe W, England H, Rich K, Schmidt L, Dyer NP, Travis MA, Ott S, Jackson DA, Cockerill PN, Paszek P. Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells. J Immunol 2017; 199:2652-2667. [PMID: 28904128 PMCID: PMC5632840 DOI: 10.4049/jimmunol.1602033] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 08/21/2017] [Indexed: 01/20/2023]
Abstract
TCR signaling pathways cooperate to activate the inducible transcription factors NF-κB, NFAT, and AP-1. In this study, using the calcium ionophore ionomycin and/or PMA on Jurkat T cells, we show that the gene expression program associated with activation of TCR signaling is closely related to specific chromatin landscapes. We find that calcium and kinase signaling cooperate to induce chromatin remodeling at ∼2100 chromatin regions, which demonstrate enriched binding motifs for inducible factors and correlate with target gene expression. We found that these regions typically function as inducible enhancers. Many of these elements contain composite NFAT/AP-1 sites, which typically support cooperative binding, thus further reinforcing the need for cooperation between calcium and kinase signaling in the activation of genes in T cells. In contrast, treatment with PMA or ionomycin alone induces chromatin remodeling at far fewer regions (∼600 and ∼350, respectively), which mostly represent a subset of those induced by costimulation. This suggests that the integration of TCR signaling largely occurs at the level of chromatin, which we propose plays a crucial role in regulating T cell activation.
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Affiliation(s)
- Ruth Brignall
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Pierre Cauchy
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Sarah L Bevington
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Bethany Gorman
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Angela O Pisco
- Centre for Stem Cells and Regenerative Medicine, King's College London, London SE1 9RT, United Kingdom
| | - James Bagnall
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Christopher Boddington
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - William Rowe
- Department of Chemistry, Loughborough University, Loughborough LE11 3TU, United Kingdom
| | - Hazel England
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Kevin Rich
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester M13 9PT, United Kingdom
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, United Kingdom; and
| | - Lorraine Schmidt
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Nigel P Dyer
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mark A Travis
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester M13 9PT, United Kingdom
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, United Kingdom; and
| | - Sascha Ott
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Dean A Jackson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Peter N Cockerill
- Institute of Biomedical Research, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, United Kingdom;
| | - Pawel Paszek
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom;
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