1
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Akanyibah FA, Zhu Y, Wan A, Ocansey DKW, Xia Y, Fang AN, Mao F. Effects of DNA methylation and its application in inflammatory bowel disease (Review). Int J Mol Med 2024; 53:55. [PMID: 38695222 DOI: 10.3892/ijmm.2024.5379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) is marked by persistent inflammation, and its development and progression are linked to environmental, genetic, immune system and gut microbial factors. DNA methylation (DNAm), as one of the protein modifications, is a crucial epigenetic process used by cells to control gene transcription. DNAm is one of the most common areas that has drawn increasing attention recently, with studies revealing that the interleukin (IL)‑23/IL‑12, wingless‑related integration site, IL‑6‑associated signal transducer and activator of transcription 3, suppressor of cytokine signaling 3 and apoptosis signaling pathways are involved in DNAm and in the pathogenesis of IBD. It has emerged that DNAm‑associated genes are involved in perpetuating the persistent inflammation that characterizes a number of diseases, including IBD, providing a novel therapeutic strategy for exploring their treatment. The present review discusses DNAm‑associated genes in the pathogenesis of IBD and summarizes their application as possible diagnostic, prognostic and therapeutic biomarkers in IBD. This may provide a reference for the particular form of IBD and its related methylation genes, aiding in clinical decision‑making and encouraging therapeutic alternatives.
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Affiliation(s)
- Francis Atim Akanyibah
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
| | - Yi Zhu
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, Jiangsu 212300, P.R. China
| | - Aijun Wan
- Zhenjiang College, Zhenjiang, Jiangsu 212028, P.R. China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Yuxuan Xia
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - An-Ning Fang
- Basic Medical School, Anhui Medical College, Hefei, Anhui 230061, P.R. China
| | - Fei Mao
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
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2
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Hussain S, Sadouni N, van Essen D, Dao LTM, Ferré Q, Charbonnier G, Torres M, Gallardo F, Lecellier CH, Sexton T, Saccani S, Spicuglia S. Short tandem repeats are important contributors to silencer elements in T cells. Nucleic Acids Res 2023; 51:4845-4866. [PMID: 36929452 PMCID: PMC10250210 DOI: 10.1093/nar/gkad187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 02/26/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
The action of cis-regulatory elements with either activation or repression functions underpins the precise regulation of gene expression during normal development and cell differentiation. Gene activation by the combined activities of promoters and distal enhancers has been extensively studied in normal and pathological contexts. In sharp contrast, gene repression by cis-acting silencers, defined as genetic elements that negatively regulate gene transcription in a position-independent fashion, is less well understood. Here, we repurpose the STARR-seq approach as a novel high-throughput reporter strategy to quantitatively assess silencer activity in mammals. We assessed silencer activity from DNase hypersensitive I sites in a mouse T cell line. Identified silencers were associated with either repressive or active chromatin marks and enriched for binding motifs of known transcriptional repressors. CRISPR-mediated genomic deletions validated the repressive function of distinct silencers involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Finally, we unravel an association of silencer activity with short tandem repeats, highlighting the role of repetitive elements in silencer activity. Our results provide a general strategy for genome-wide identification and characterization of silencer elements.
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Affiliation(s)
- Saadat Hussain
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Nori Sadouni
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Dominic van Essen
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Lan T M Dao
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Quentin Ferré
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Magali Torres
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Frederic Gallardo
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Charles-Henri Lecellier
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- LIRMM, University of Montpellier, CNRS, Montpellier, France
| | - Tom Sexton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire – IGBMC (CNRS UMR 7104, INSERM U1258, Université de Strasbourg), 67404 Illkirch, France
| | - Simona Saccani
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
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3
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Jayanthi BE, Jayanthi S, Segatori L. Design of Oscillatory Networks through Post-Translational Control of Network Components. SYNTHETIC BIOLOGY AND ENGINEERING 2023; 1:10004. [PMID: 38590452 PMCID: PMC11000592 DOI: 10.35534/sbe.2023.10004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Many essential functions in biological systems, including cell cycle progression and circadian rhythm regulation, are governed by the periodic behaviors of specific molecules. These periodic behaviors arise from the precise arrangement of components in biomolecular networks that generate oscillatory output signals. The dynamic properties of individual components of these networks, such as maturation delays and degradation rates, often play a key role in determining the network's oscillatory behavior. In this study, we explored the post-translational modulation of network components as a means to generate genetic circuits with oscillatory behaviors and perturb the oscillation features. Specifically, we used the NanoDeg platform-A bifunctional molecule consisting of a target-specific nanobody and a degron tag-to control the degradation rates of the circuit's components and predicted the effect of NanoDeg-mediated post-translational depletion of a key circuit component on the behavior of a series of proto-oscillating network topologies. We modeled the behavior of two main classes of oscillators, namely relaxation oscillator topologies (the activator-repressor and the Goodwin oscillator) and ring oscillator topologies (repressilators). We identified two main mechanisms by which non-oscillating networks could be induced to oscillate through post-translational modulation of network components: an increase in the separation of timescales of network components and mitigation of the leaky expression of network components. These results are in agreement with previous findings describing the effect of timescale separation and mitigation of leaky expression on oscillatory behaviors. This work thus validates the use of tools to control protein degradation rates as a strategy to modulate existing oscillatory signals and construct oscillatory networks. In addition, this study provides the design rules to implement such an approach based on the control of protein degradation rates using the NanoDeg platform, which does not require genetic manipulation of the network components and can be adapted to virtually any cellular protein. This work also establishes a framework to explore the use of tools for post-translational perturbations of biomolecular networks and generates desired behaviors of the network output.
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Affiliation(s)
- Brianna E.K. Jayanthi
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX 77005, USA
| | - Shridhar Jayanthi
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Laura Segatori
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX 77005, USA
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
- Department of Chemical & Biomolecular Engineering, Rice University, Houston, TX 77005, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
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4
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Liman N, Park JH. Markers and makers of NKT17 cells. Exp Mol Med 2023; 55:1090-1098. [PMID: 37258582 PMCID: PMC10317953 DOI: 10.1038/s12276-023-01015-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 06/02/2023] Open
Abstract
Invariant natural killer T (iNKT) cells are thymus-generated innate-like αβ T cells that undergo terminal differentiation in the thymus. Such a developmental pathway differs from that of conventional αβ T cells, which are generated in the thymus but complete their functional maturation in peripheral tissues. Multiple subsets of iNKT cells have been described, among which IL-17-producing iNKT cells are commonly referred to as NKT17 cells. IL-17 is considered a proinflammatory cytokine that can play both protective and pathogenic roles and has been implicated as a key regulatory factor in many disease settings. Akin to other iNKT subsets, NKT17 cells acquire their effector function during thymic development. However, the cellular mechanisms that drive NKT17 subset specification, and how iNKT cells in general acquire their effector function prior to antigen encounter, remain largely unknown. Considering that all iNKT cells express the canonical Vα14-Jα18 TCRα chain and all iNKT subsets display the same ligand specificity, i.e., glycolipid antigens in the context of the nonclassical MHC-I molecule CD1d, the conundrum is explaining how thymic NKT17 cell specification is determined. Mapping of the molecular circuitry of NKT17 cell differentiation, combined with the discovery of markers that identify NKT17 cells, has provided new insights into the developmental pathway of NKT17 cells. The current review aims to highlight recent advances in our understanding of thymic NKT17 cell development and to place these findings in the larger context of iNKT subset specification and differentiation.
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Affiliation(s)
- Nurcin Liman
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Jung-Hyun Park
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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5
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Rahmberg AR, Markowitz TE, Mudd JC, Hirsch V, Brenchley JM. Epigenetic Reprogramming Leads to Downregulation of CD4 and Functional Changes in African Green Monkey Memory CD4 + T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:337-345. [PMID: 35750337 PMCID: PMC9283288 DOI: 10.4049/jimmunol.2200109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/05/2022] [Indexed: 05/12/2023]
Abstract
African green monkeys (AGMs), Chlorocebus pygerythrus, are a natural host for a lentivirus related to HIV, SIV. SIV-infected AGMs rarely progress to AIDS despite robust viral replication. Though multiple mechanisms are involved, a primary component is the animals' ability to downregulate CD4 expression on mature CD4+ Th cells, rendering these cells resistant to infection by SIV. These CD8αα+ T cells retain functional characteristics of CD4+ Th cells while simultaneously acquiring abilities of cytotoxic CD8αβ+ T cells. To determine mechanisms underlying functional differences between T cell subsets in AGMs, chromatin accessibility in purified populations was determined by assay for transposase-accessible chromatin sequencing. Differences in chromatin accessibility alone were sufficient to cluster cells by subtype, and accessibility at the CD4 locus reflected changes in CD4 expression. DNA methylation at the CD4 locus also correlated with inaccessible chromatin. By associating accessible regions with nearby genes, gene expression was found to correlate with accessibility changes. T cell and immune system activation pathways were identified when comparing regions that changed accessibility from CD4+ T cells to CD8αα+ T cells. Different transcription factor binding sites are revealed as chromatin accessibility changes, and these differences may elicit downstream changes in differentiation. This comprehensive description of the epigenetic landscape of AGM T cells identified genes and pathways that could have translational value in therapeutic approaches recapitulating the protective effects CD4 downregulation.
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Affiliation(s)
- Andrew R Rahmberg
- Barrier Immunity Section, Lab of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Tovah E Markowitz
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Axle Informatics, Bethesda, MD
| | - Joseph C Mudd
- Tulane National Primate Research Center, Division of Immunology, Tulane University, New Orleans, LA; and
| | - Vanessa Hirsch
- Nonhuman Primate Virology Section, Lab of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Jason M Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD;
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6
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Han J, Wan M, Ma Z, He P. The TOX subfamily: all-round players in the immune system. Clin Exp Immunol 2022; 208:268-280. [PMID: 35485425 PMCID: PMC9226143 DOI: 10.1093/cei/uxac037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/29/2022] [Accepted: 04/26/2022] [Indexed: 12/14/2022] Open
Abstract
The thymocyte selection-related HMG box protein (TOX) subfamily comprises evolutionarily conserved DNA-binding proteins, and is expressed in certain immune cell subsets and plays key roles in the development of CD4+ T cells, innate lymphoid cells (ILCs), T follicular helper (Tfh) cells, and in CD8+ T-cell exhaustion. Although its roles in CD4+ T and natural killer (NK) cells have been extensively studied, recent findings have demonstrated previously unknown roles for TOX in the development of ILCs, Tfh cells, as well as CD8+ T-cell exhaustion; however, the molecular mechanism underlying TOX regulation of these immune cells remains to be elucidated. In this review, we discuss recent studies on the influence of TOX on the development of various immune cells and CD8+ T-cell exhaustion and the roles of specific TOX family members in the immune system. Moreover, this review suggests candidate regulatory targets for cell therapy and immunotherapies.
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Affiliation(s)
- Jiawen Han
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Minjie Wan
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China.,Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhanchuan Ma
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Ping He
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, Jilin, China
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7
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Gao Y, Zamisch M, Vacchio M, Chopp L, Ciucci T, Paine EL, Lyons GC, Nie J, Xiao Q, Zvezdova E, Love PE, Vinson CR, Jenkins LM, Bosselut R. NuRD complex recruitment to Thpok mediates CD4 + T cell lineage differentiation. Sci Immunol 2022; 7:eabn5917. [PMID: 35687698 DOI: 10.1126/sciimmunol.abn5917] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although BTB-zinc finger (BTB-ZF) transcription factors control the differentiation of multiple hematopoietic and immune lineages, how they function is poorly understood. The BTB-ZF factor Thpok controls intrathymic CD4+ T cell development and the expression of most CD4+ and CD8+ lineage genes. Here, we identify the nucleosome remodeling and deacetylase (NuRD) complex as a critical Thpok cofactor. Using mass spectrometry and coimmunoprecipitation in primary T cells, we show that Thpok binds NuRD components independently of DNA association. We locate three amino acid residues within the Thpok BTB domain that are required for both NuRD binding and Thpok functions. Conversely, a chimeric protein merging the NuRD component Mta2 to a BTB-less version of Thpok supports CD4+ T cell development, indicating that NuRD recruitment recapitulates the functions of the Thpok BTB domain. We found that NuRD mediates Thpok repression of CD8+ lineage genes, including the transcription factor Runx3, but is dispensable for Cd4 expression. We show that these functions cannot be performed by the BTB domain of the Thpok-related factor Bcl6, which fails to bind NuRD. Thus, cofactor binding critically contributes to the functional specificity of BTB-ZF factors, which control the differentiation of most hematopoietic subsets.
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Affiliation(s)
- Yayi Gao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Monica Zamisch
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Melanie Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Laura Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.,Immunology Graduate Group, University of Pennsylvania Medical School, Philadelphia, PA, USA
| | - Thomas Ciucci
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Elliott L Paine
- Collaborative Protein Technology Resource, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gaelyn C Lyons
- Collaborative Protein Technology Resource, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jia Nie
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Qi Xiao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ekaterina Zvezdova
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Paul E Love
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Charles R Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa M Jenkins
- Immunology Graduate Group, University of Pennsylvania Medical School, Philadelphia, PA, USA
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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8
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Schad SE, Chow A, Mangarin L, Pan H, Zhang J, Ceglia N, Caushi JX, Malandro N, Zappasodi R, Gigoux M, Hirschhorn D, Budhu S, Amisaki M, Arniella M, Redmond D, Chaft J, Forde PM, Gainor JF, Hellmann MD, Balachandran V, Shah S, Smith KN, Pardoll D, Elemento O, Wolchok JD, Merghoub T. Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions. J Exp Med 2022; 219:e20212169. [PMID: 35604411 PMCID: PMC9130031 DOI: 10.1084/jem.20212169] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/04/2022] [Accepted: 03/08/2022] [Indexed: 11/04/2022] Open
Abstract
Transcription factors ThPOK and Runx3 regulate the differentiation of "helper" CD4+ and "cytotoxic" CD8+ T cell lineages respectively, inducing single positive (SP) T cells that enter the periphery with the expression of either the CD4 or CD8 co-receptor. Despite the expectation that these cell fates are mutually exclusive and that mature CD4+CD8+ double positive (DP) T cells are present in healthy individuals and augmented in the context of disease, yet their molecular features and pathophysiologic role are disputed. Here, we show DP T cells in murine and human tumors as a heterogenous population originating from SP T cells which re-express the opposite co-receptor and acquire features of the opposite cell type's phenotype and function following TCR stimulation. We identified distinct clonally expanded DP T cells in human melanoma and lung cancer by scRNA sequencing and demonstrated their tumor reactivity in cytotoxicity assays. Our findings indicate that antigen stimulation induces SP T cells to differentiate into DP T cell subsets gaining in polyfunctional characteristics.
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Affiliation(s)
- Sara E. Schad
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Andrew Chow
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Levi Mangarin
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Heng Pan
- Weill Cornell Medical College, New York, NY
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY
| | - Jiajia Zhang
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justina X. Caushi
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Nicole Malandro
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Roberta Zappasodi
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Mathieu Gigoux
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel Hirschhorn
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sadna Budhu
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
| | - Masataka Amisaki
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Jamie Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Patrick M. Forde
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Justin F. Gainor
- Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Matthew D. Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vinod Balachandran
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sohrab Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kellie N. Smith
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Drew Pardoll
- John Hopkins University School of Medicine, Baltimore, MD
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at John Hopkins, Baltimore, MD
| | - Olivier Elemento
- Weill Cornell Medical College, New York, NY
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY
| | - Jedd D. Wolchok
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Taha Merghoub
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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9
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Castro-Piedras I, Sharma M, Brelsfoard J, Vartak D, Martinez EG, Rivera C, Molehin D, Bright RK, Fokar M, Guindon J, Pruitt K. Nuclear Dishevelled targets gene regulatory regions and promotes tumor growth. EMBO Rep 2021; 22:e50600. [PMID: 33860601 DOI: 10.15252/embr.202050600] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 12/18/2022] Open
Abstract
Dishevelled (DVL) critically regulates Wnt signaling and contributes to a wide spectrum of diseases and is important in normal and pathophysiological settings. However, how it mediates diverse cellular functions remains poorly understood. Recent discoveries have revealed that constitutive Wnt pathway activation contributes to breast cancer malignancy, but the mechanisms by which this occurs are unknown and very few studies have examined the nuclear role of DVL. Here, we have performed DVL3 ChIP-seq analyses and identify novel target genes bound by DVL3. We show that DVL3 depletion alters KMT2D binding to novel targets and changes their epigenetic marks and mRNA levels. We further demonstrate that DVL3 inhibition leads to decreased tumor growth in two different breast cancer models in vivo. Our data uncover new DVL3 functions through its regulation of multiple genes involved in developmental biology, antigen presentation, metabolism, chromatin remodeling, and tumorigenesis. Overall, our study provides unique insight into the function of nuclear DVL, which helps to define its role in mediating aberrant Wnt signaling.
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Affiliation(s)
- Isabel Castro-Piedras
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Monica Sharma
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Jennifer Brelsfoard
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - David Vartak
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Edgar G Martinez
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Cristian Rivera
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Deborah Molehin
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Robert K Bright
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Mohamed Fokar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
| | - Josee Guindon
- Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Center of Excellence for Translational Neuroscience and Therapeutics, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Kevin Pruitt
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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10
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Ye J, Chen Q, Wang R. Logical modeling of thymus and natural killer lymphocyte differentiation. J Biol Phys 2021; 47:31-47. [PMID: 33735399 DOI: 10.1007/s10867-021-09563-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/05/2021] [Indexed: 10/21/2022] Open
Abstract
Thymus (T) and natural killer (NK) lymphocytes are important barriers against diseases. Therefore, it is necessary to understand regulatory mechanisms related to the cell fate decisions involved in the production of these cells. Although some individual information related to T and NK lymphocyte cell fate decisions have been revealed, the related network and its dynamical characteristics still have not been well understood. By integrating individual information and comparing with experimental data, we construct a comprehensive regulatory network and a logical model related to T and NK lymphocyte differentiation. We aim to explore possible mechanisms of how each lineage differentiation is realized by systematically screening individual perturbations. When determining the perturbation strategies, the state transition can be used to identify the roles of specific genes in cell type selection and reprogramming. In agreement with experimental observations, the dynamics of the model correctly restates the cell differentiation processes from common lymphoid progenitors to CD4+ T cells, CD8+ T cells, and NK cells. Our analysis reveals that some specific perturbations can give rise to directional cell differentiation or reprogramming. We test our in silico results by using known experimental observations. The integrated network and the logical model presented here might be a good candidate for providing qualitative mechanisms of cell fate specification involved in T and NK lymphocyte cell fate decisions.
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Affiliation(s)
- Jianting Ye
- Department of Mathematics, Shanghai University, Shanghai, China
| | - Qingxi Chen
- Department of Mathematics, Shanghai University, Shanghai, China
| | - Ruiqi Wang
- Department of Mathematics, Shanghai University, Shanghai, China.
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11
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ZBTB gene expression in HIV patients: a possible new molecular mechanism of viral control. Arch Virol 2020; 166:167-178. [PMID: 33130911 DOI: 10.1007/s00705-020-04854-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/09/2020] [Indexed: 10/23/2022]
Abstract
HIV infects its target cell and integrates into its genome as an essential step in its replication cycle. Proviral DNA is also subjected to the same transcriptional regulation as the host cell genome by its own transcriptional factors, with activating or repressive activity. There is a clear interaction between the presence of transcriptional repressors and a decrease in the rate of HIV replication, promoting gene silencing in infected cells, which serve as viral reservoirs. This represents a major obstacle for HIV eradication. The ZBTB gene family comprises 49 genes that encode transcription factors that have a repressor function in differentiation and development of cells of the lymphopoietic lineage, including the main target cells of HIV, CD4+ T cells. In this cross-sectional study, we evaluated the expression profile of ZBTB genes in CD4+ T cells of HIV-positive individuals with different levels of infection control. We found upregulation of gene expression of ZBTB4 (p < 0.01), ZBTB7B (p < 0.001), and ZBTB38 (p < 0.05) and downregulation of ZBTB16 (p < 0.01) in HIV-positive patients compared to HIV-negative individuals. Interestingly, in a deeper analysis, we observed that elite controllers had the highest levels of expression of the ZBTB38, ZBTB2, HIC1, ZBTB7A, ZBTB7B (ThPOK) and ZBTB4 genes, showing 2.56- to 7.60-fold upregulation compare to the ART-naïve group. These results suggest a possible contribution of these ZBTB transcriptional repressors in HIV-positive patients and a possible new molecular mechanism of viral control.
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12
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Zhao J, Han DX, Wang CB, Wang XL. Zbtb7b suppresses aseptic inflammation by regulating m6A modification of IL6 mRNA. Biochem Biophys Res Commun 2020; 530:336-341. [DOI: 10.1016/j.bbrc.2020.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 07/05/2020] [Indexed: 12/22/2022]
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13
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Transcriptomic features of tumour-infiltrating CD4 lowCD8 high double positive αβ T cells in melanoma. Sci Rep 2020; 10:5900. [PMID: 32246006 PMCID: PMC7125144 DOI: 10.1038/s41598-020-62664-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/17/2020] [Indexed: 12/17/2022] Open
Abstract
Peripheral CD4+CD8+ double positive (DP) T cells are a phenotypically and functionally heterogeneous population depending on their origin and pathologic context. We previously identified among tumour infiltrating lymphocytes in melanoma, a tumour-reactive MHC class-I restricted CD4lowCD8high DP αβ T-cell subpopulation with CD4-like function. In this study, we used an in-depth comparative transriptomic analysis of intra-melanoma DP T cells and CD4 and CD8 single positive (SP) T cells, to better comprehend the origin of this DP phenotype, and define the transcriptomic signature of activated DP T cells. We observed that intra-melanoma DP T cells were transcriptome-wise closer to their CD8 SP T-cell counterparts in terms of number of genes differentially expressed (97 in common with CD8 SP T cells and 15 with CD4 SP T cells) but presented hallmarks of a transition to a CD4-like functional profile (CD40LG) with a decreased cytotoxic signature (KLRC1) in favour of an increased cytokine-receptor interaction signature (IL4, IL24, IL17A…). This unleashed CD4-like program could be the results of the observed unbalanced expression of the THPOK/Runx3 transcription factors in DP T cells. Overall, this study allow us to speculate that intra-melanoma DP T cells arise from CD8 SP T cells being reprogrammed to a helper function.
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14
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ZBTB7B (ThPOK) Is Required for Pathogenesis of Cerebral Malaria and Protection against Pulmonary Tuberculosis. Infect Immun 2020; 88:IAI.00845-19. [PMID: 31792077 DOI: 10.1128/iai.00845-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 11/20/2022] Open
Abstract
We used a genome-wide screen in N-ethyl-N-nitrosourea (ENU)-mutagenized mice to identify genes in which recessive loss-of-function mutations protect against pathological neuroinflammation. We identified an R367Q mutation in the ZBTB7B (ThPOK) protein in which homozygosity causes protection against experimental cerebral malaria (ECM) caused by infection with Plasmodium berghei ANKA. Zbtb7bR367Q homozygous mice show a defect in the lymphoid compartment expressed as severe reduction in the number of single-positive CD4 T cells in the thymus and in the periphery, reduced brain infiltration of proinflammatory leukocytes in P. berghei ANKA-infected mice, and reduced production of proinflammatory cytokines by primary T cells ex vivo and in vivo Dampening of proinflammatory immune responses in Zbtb7bR367Q mice is concomitant to increased susceptibility to infection with avirulent (Mycobacterium bovis BCG) and virulent (Mycobacterium tuberculosis H37Rv) mycobacteria. The R367Q mutation maps to the first DNA-binding zinc finger domain of ThPOK and causes loss of base contact by R367 in the major groove of the DNA, which is predicted to impair DNA binding. Global immunoprecipitation of ThPOK-containing chromatin complexes coupled to DNA sequencing (ChIP-seq) identified transcriptional networks and candidate genes likely to play key roles in CD4+ CD8+ T cell development and in the expression of lineage-specific functions of these cells. This study highlights ThPOK as a global regulator of immune function in which alterations may affect normal responses to infectious and inflammatory stimuli.
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15
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Vacchio MS, Ciucci T, Gao Y, Watanabe M, Balmaceno-Criss M, McGinty MT, Huang A, Xiao Q, McConkey C, Zhao Y, Shetty J, Tran B, Pepper M, Vahedi G, Jenkins MK, McGavern DB, Bosselut R. A Thpok-Directed Transcriptional Circuitry Promotes Bcl6 and Maf Expression to Orchestrate T Follicular Helper Differentiation. Immunity 2019; 51:465-478.e6. [PMID: 31422869 DOI: 10.1016/j.immuni.2019.06.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/08/2019] [Accepted: 06/21/2019] [Indexed: 01/19/2023]
Abstract
The generation of high-affinity neutralizing antibodies, the objective of most vaccine strategies, occurs in B cells within germinal centers (GCs) and requires rate-limiting "help" from follicular helper CD4+ T (Tfh) cells. Although Tfh differentiation is an attribute of MHC II-restricted CD4+ T cells, the transcription factors driving Tfh differentiation, notably Bcl6, are not restricted to CD4+ T cells. Here, we identified a requirement for the CD4+-specific transcription factor Thpok during Tfh cell differentiation, GC formation, and antibody maturation. Thpok promoted Bcl6 expression and bound to a Thpok-responsive region in the first intron of Bcl6. Thpok also promoted the expression of Bcl6-independent genes, including the transcription factor Maf, which cooperated with Bcl6 to mediate the effect of Thpok on Tfh cell differentiation. Our findings identify a transcriptional program that links the CD4+ lineage with Tfh differentiation, a limiting factor for efficient B cell responses, and suggest avenues to optimize vaccine generation.
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Affiliation(s)
- Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Thomas Ciucci
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yayi Gao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Masashi Watanabe
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Mariah Balmaceno-Criss
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Mitchell T McGinty
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Allan Huang
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Qi Xiao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Cameron McConkey
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yongmei Zhao
- Center for Cancer Research Sequencing Facility, Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jyoti Shetty
- Center for Cancer Research Sequencing Facility, Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Bao Tran
- Center for Cancer Research Sequencing Facility, Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Marion Pepper
- Department of Immunology, University of Washington, Seattle, WA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Marc K Jenkins
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Dorian B McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
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16
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Abstract
A fundamental question in developmental immunology is how bipotential thymocyte precursors generate both CD4+ helper and CD8+ cytotoxic T cell lineages. The MHC specificity of αβ T cell receptors (TCRs) on precursors is closely correlated with cell fate-determining processes, prompting studies to characterize how variations in TCR signaling are linked with genetic programs establishing lineage-specific gene expression signatures, such as exclusive CD4 or CD8 expression. The key transcription factors ThPOK and Runx3 have been identified as mediating development of helper and cytotoxic T cell lineages, respectively. Together with increasing knowledge of epigenetic regulators, these findings have advanced our understanding of the transcription factor network regulating the CD4/CD8 dichotomy. It has also become apparent that CD4+ T cells retain developmental plasticity, allowing them to acquire cytotoxic activity in the periphery. Despite such advances, further studies are necessary to identify the molecular links between TCR signaling and the nuclear machinery regulating expression of ThPOK and Runx3.
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Affiliation(s)
- Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan;
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17
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Zeidan N, Damen H, Roy DC, Dave VP. Critical Role for TCR Signal Strength and MHC Specificity in ThPOK-Induced CD4 Helper Lineage Choice. THE JOURNAL OF IMMUNOLOGY 2019; 202:3211-3225. [PMID: 31036767 DOI: 10.4049/jimmunol.1801464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/26/2019] [Indexed: 01/08/2023]
Abstract
Sustained TCR signaling is critical for ThPOK induction in MHC class II (MHCII)-signaled thymocytes leading to the CD4 helper lineage commitment. ThPOK suppresses the cytotoxic program in the signaled thymocytes and is shown to be necessary and sufficient for the CD4 helper lineage choice. Accordingly, loss and gain of ThPOK function redirects MHCII- and MHC class I (MHCI)-signaled thymocytes into the CD8 cytotoxic and CD4 helper lineage, respectively. However, the impact of a defined ThPOK level on the CD4 helper lineage choice of MHCII- and MHCI-specific thymocytes and the role of TCR signaling in this process is not evaluated. Equally, it is not clear if suppression of the cytotoxic program by ThPOK is sufficient in redirecting MHCI-restricted thymocytes into the CD4 helper lineage. In this study, we have investigated CD8 to CD4 helper lineage redirection in three independent ThPOK overexpressing transgenic mouse lines. Our analysis shows that one of the transgenic lines, despite overexpressing ThPOK compared with wild-type CD4 mature T cells and compromising cytotoxic program, failed to redirect all MHCI-signaled thymocytes into the CD4 helper lineage, resulting in the continued presence of CD8+ mature T cells and the generation of a large number of double negative mature T cells. Critically, the same ThPOK transgene completely restored the CD4 helper lineage commitment of MHCII-specific Thpok -/- thymocytes. Importantly, augmenting TCR signaling significantly enhanced the ThPOK-mediated CD4 helper lineage choice of MHCI-specific thymocytes but was still substantially less efficient than that of MHCII-specific thymocytes expressing the same amount of ThPOK. Together, these data suggest that the ThPOK-induced CD4 helper lineage commitment is strongly influenced by TCR signal strength and MHC specificity of developing thymocytes.
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Affiliation(s)
- Nabil Zeidan
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada.,Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada; and
| | - Hassan Damen
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada
| | - Denis-Claude Roy
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Vibhuti P Dave
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada; .,Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada; and
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18
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Philips RL, Lee JH, Gaonkar K, Chanana P, Chung JY, Romero Arocha SR, Schwab A, Ordog T, Shapiro VS. HDAC3 restrains CD8-lineage genes to maintain a bi-potential state in CD4 +CD8 + thymocytes for CD4-lineage commitment. eLife 2019; 8:43821. [PMID: 30657451 PMCID: PMC6338460 DOI: 10.7554/elife.43821] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 12/30/2018] [Indexed: 12/20/2022] Open
Abstract
CD4 and CD8 T cells are vital components of the immune system. We found that histone deacetylase 3 (HDAC3) is critical for the development of CD4 T cells, as HDAC3-deficient DP thymocytes generate only CD8SP thymocytes in mice. In the absence of HDAC3, MHC Class II-restricted OT-II thymocytes are redirected to the CD8 cytotoxic lineage, which occurs with accelerated kinetics. Analysis of histone acetylation and RNA-seq reveals that HDAC3-deficient DP thymocytes are biased towards the CD8 lineage prior to positive selection. Commitment to the CD4 or CD8 lineage is determined by whether persistent TCR signaling or cytokine signaling predominates, respectively. Despite elevated IL-21R/γc/STAT5 signaling in HDAC3-deficient DP thymocytes, blocking IL-21R does not restore CD4 lineage commitment. Instead, HDAC3 binds directly to CD8-lineage promoting genes. Thus, HDAC3 is required to restrain CD8-lineage genes in DP thymocytes for the generation of CD4 T cells.
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Affiliation(s)
| | - Jeong-Heon Lee
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, United States
| | - Krutika Gaonkar
- Department of Health Science Research, Division of Biostatistics and Informatics, Mayo Clinic, Rochester, United States
| | - Pritha Chanana
- Department of Health Science Research, Division of Biostatistics and Informatics, Mayo Clinic, Rochester, United States
| | - Ji Young Chung
- Department of Immunology, Mayo Clinic, Rochester, United States
| | | | - Aaron Schwab
- Department of Immunology, Mayo Clinic, Rochester, United States
| | - Tamas Ordog
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, United States
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19
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Ciucci T, Vacchio MS, Gao Y, Tomassoni Ardori F, Candia J, Mehta M, Zhao Y, Tran B, Pepper M, Tessarollo L, McGavern DB, Bosselut R. The Emergence and Functional Fitness of Memory CD4 + T Cells Require the Transcription Factor Thpok. Immunity 2019; 50:91-105.e4. [PMID: 30638736 PMCID: PMC6503975 DOI: 10.1016/j.immuni.2018.12.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/19/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022]
Abstract
Memory CD4+ T cells mediate long-term immunity, and their generation is a key objective of vaccination strategies. However, the transcriptional circuitry controlling the emergence of memory cells from early CD4+ antigen-responders remains poorly understood. Here, using single-cell RNA-seq to study the transcriptome of virus-specific CD4+ T cells, we identified a gene signature that distinguishes potential memory precursors from effector cells. We found that both that signature and the emergence of memory CD4+ T cells required the transcription factor Thpok. We further demonstrated that Thpok cell-intrinsically protected memory cells from a dysfunctional, effector-like transcriptional program, similar to but distinct from the exhaustion pattern of cells responding to chronic infection. Mechanistically, Thpok- bound genes encoding the transcription factors Blimp1 and Runx3 and acted by antagonizing their expression. Thus, a Thpok-dependent circuitry promotes both memory CD4+ T cells' differentiation and functional fitness, two previously unconnected critical attributes of adaptive immunity.
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Affiliation(s)
- Thomas Ciucci
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yayi Gao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Francesco Tomassoni Ardori
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Julian Candia
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD, USA
| | - Monika Mehta
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yongmei Zhao
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bao Tran
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Dorian B McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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20
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Handel AE, Shikama-Dorn N, Zhanybekova S, Maio S, Graedel AN, Zuklys S, Ponting CP, Holländer GA. Comprehensively Profiling the Chromatin Architecture of Tissue Restricted Antigen Expression in Thymic Epithelial Cells Over Development. Front Immunol 2018; 9:2120. [PMID: 30283453 PMCID: PMC6156148 DOI: 10.3389/fimmu.2018.02120] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/28/2018] [Indexed: 01/11/2023] Open
Abstract
Thymic epithelial cells (TEC) effect crucial roles in thymopoiesis including the control of negative thymocyte selection. This process depends on their capacity to express promiscuously genes encoding tissue-restricted antigens. This competence is accomplished in medullary TEC (mTEC) in part by the presence of the transcriptional facilitator AutoImmune REgulator, AIRE. AIRE-regulated gene transcription is marked by repressive chromatin modifications, including H3K27me3. When during TEC development these chromatin marks are established, however, remains unclear. Here we use a comprehensive ChIP-seq dataset of multiple chromatin modifications in different TEC subtypes to demonstrate that the chromatin landscape is established early in TEC differentiation. Much of the chromatin architecture found in mature mTEC was found to be present already over earlier stages of mTEC lineage differentiation as well as in non-TEC tissues. This was reflected by the fact that a machine learning approach accurately classified genes as AIRE-induced or AIRE-independent both in immature and mature mTEC. Moreover, analysis of TEC specific enhancer elements identified candidate transcription factors likely to be important in mTEC development and function. Our findings indicate that the mature mTEC chromatin landscape is laid down early in mTEC differentiation, and that AIRE is not required for large-scale re-patterning of chromatin in mTEC.
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Affiliation(s)
- Adam E. Handel
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Department of Paediatrics, University of Oxford, OxfordUnited Kingdom
| | | | | | - Stefano Maio
- Department of Paediatrics, University of Oxford, OxfordUnited Kingdom
| | - Annina N. Graedel
- Department of Paediatrics, University of Oxford, OxfordUnited Kingdom
| | - Saulius Zuklys
- Department of Biomedicine, Universität Basel, BaselSwitzerland
| | - Chris P. Ponting
- MRC Human Genetics Unit, University of Edinburgh, EdinburghUnited Kingdom
| | - Georg A. Holländer
- Department of Paediatrics, University of Oxford, OxfordUnited Kingdom
- Department of Biomedicine, Universität Basel, BaselSwitzerland
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21
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Runx-dependent and silencer-independent repression of a maturation enhancer in the Cd4 gene. Nat Commun 2018; 9:3593. [PMID: 30185787 PMCID: PMC6125603 DOI: 10.1038/s41467-018-05803-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/30/2018] [Indexed: 02/06/2023] Open
Abstract
An intronic silencer, S4, in the Cd4 gene has been shown to be responsible for the helper-lineage-specific expression of CD4; S4 requires Runx complex binding to exert its silencer function against the enhancer-mediated Cd4 activation by modulating the epigenetic state of the Cd4 gene. Here we identify a late-acting maturation enhancer. Bcl11b plays essential roles for activation of both the early-acting proximal enhancer and maturation enhancer of Cd4. Notably, Runx complexes suppress these enhancers by distinct mechanisms. Whereas repression of the proximal enhancer depends on the S4 silencer, the maturation enhancer is repressed by Runx in the absence of S4. Moreover, ThPOK, known to antagonize S4-mediated Cd4 repression, assists Runx complexes to restrain maturation enhancer activation. Distinct modes of S4 silencer action upon distinct enhancers thus unravel a pathway that restricts CD4 expression to helper-lineage cells by silencer-independent and Runx-dependent repression of maturation enhancer activity in cytotoxic-lineage cells. The commitment of helper and cytotoxic lineages for CD4 and CD8 T cells, respectively, is associated with the regulation of Cd4 gene expression. Here the authors show that an intronic silencer, S4, has differential effects and synergy with the RUNX complex to act on two enhancer elements of the CD4 gene to control T cell lineage commitment in the thymus.
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22
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A STAT3-dependent transcriptional circuitry inhibits cytotoxic gene expression in T cells. Proc Natl Acad Sci U S A 2017; 114:13236-13241. [PMID: 29180433 DOI: 10.1073/pnas.1711160114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
CD8+ T cells are preprogrammed for cytotoxic differentiation in the thymus as they acquire expression of the transcription factor Runx3. However, a subset of effector CD8+ T cells (Tc17) produce IL-17 and fail to express cytotoxic genes. Here, we show that the transcription factors directing IL-17 production, STAT3 and RORγt, inhibit cytotoxicity despite persistent Runx3 expression. Cytotoxic gene repression did not require the transcription factor Thpok, which in CD4+ T cells restrains Runx3 functions and cytotoxicity; and STAT3 restrained cytotoxic gene expression in CD8+ T cells responding to viral infection in vivo. STAT3-induced RORγt represses cytotoxic genes by inhibiting the functions but not the expression of the "cytotoxic" transcription factors T-bet and Eomesodermin. Thus, the transcriptional circuitry directing IL-17 expression inhibits cytotoxic functions. However, by allowing expression of activators of the cytotoxic program, this inhibitory mechanism contributes to the instability of IL-17-producing T cells.
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23
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Vacchio MS, Bosselut R. What Happens in the Thymus Does Not Stay in the Thymus: How T Cells Recycle the CD4+-CD8+ Lineage Commitment Transcriptional Circuitry To Control Their Function. THE JOURNAL OF IMMUNOLOGY 2017; 196:4848-56. [PMID: 27260768 DOI: 10.4049/jimmunol.1600415] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/06/2016] [Indexed: 12/24/2022]
Abstract
MHC-restricted CD4(+) and CD8(+) T cells are at the core of most adaptive immune responses. Although these cells carry distinct functions, they arise from a common precursor during thymic differentiation, in a developmental sequence that matches CD4 and CD8 expression and functional potential with MHC restriction. Although the transcriptional control of CD4(+)-CD8(+) lineage choice in the thymus is now better understood, less was known about what maintains the CD4(+) and CD8(+) lineage integrity of mature T cells. In this review, we discuss the mechanisms that establish in the thymus, and maintain in postthymic cells, the separation of these lineages. We focus on recent studies that address the mechanisms of epigenetic control of Cd4 expression and emphasize how maintaining a transcriptional circuitry nucleated around Thpok and Runx proteins, the key architects of CD4(+)-CD8(+) lineage commitment in the thymus, is critical for CD4(+) T cell helper functions.
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Affiliation(s)
- Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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24
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Carpenter AC, Wohlfert E, Chopp LB, Vacchio MS, Nie J, Zhao Y, Shetty J, Xiao Q, Deng C, Tran B, Cam M, Gaida MM, Belkaid Y, Bosselut R. Control of Regulatory T Cell Differentiation by the Transcription Factors Thpok and LRF. THE JOURNAL OF IMMUNOLOGY 2017; 199:1716-1728. [PMID: 28754678 DOI: 10.4049/jimmunol.1700181] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/06/2017] [Indexed: 01/10/2023]
Abstract
The CD4+ lineage-specific transcription factor Thpok is required for intrathymic CD4+ T cell differentiation and, together with its homolog LRF, supports CD4+ T cell helper effector responses. However, it is not known whether these factors are needed for the regulatory T cell (Treg) arm of MHC class II responses. In this study, by inactivating in mice the genes encoding both factors in differentiated Tregs, we show that Thpok and LRF are redundantly required to maintain the size and functions of the postthymic Treg pool. They support IL-2-mediated gene expression and the functions of the Treg-specific factor Foxp3. Accordingly, Treg-specific disruption of Thpok and Lrf causes a lethal inflammatory syndrome similar to that resulting from Treg deficiency. Unlike in conventional T cells, Thpok and LRF functions in Tregs are not mediated by their repression of the transcription factor Runx3. Additionally, we found that Thpok is needed for the differentiation of thymic Treg precursors, an observation in line with the fact that Foxp3+ Tregs are CD4+ cells. Thus, a common Thpok-LRF node supports both helper and regulatory arms of MHC class II responses.
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Affiliation(s)
- Andrea C Carpenter
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth Wohlfert
- Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.,Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Laura B Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.,Immunology Graduate Group, University of Pennsylvania Medical School, Philadelphia, PA 19104
| | - Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jia Nie
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Yongmei Zhao
- Center for Cancer Research Sequencing Facility, Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702
| | - Jyoti Shetty
- Center for Cancer Research Sequencing Facility, Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702
| | - Qi Xiao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Callie Deng
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Bao Tran
- Center for Cancer Research Sequencing Facility, Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702
| | - Margaret Cam
- Center for Cancer Research Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Matthias M Gaida
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.,Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Yasmine Belkaid
- Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.,Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892;
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25
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Soto-Feliciano YM, Bartlebaugh JME, Liu Y, Sánchez-Rivera FJ, Bhutkar A, Weintraub AS, Buenrostro JD, Cheng CS, Regev A, Jacks TE, Young RA, Hemann MT. PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. Genes Dev 2017; 31:973-989. [PMID: 28607179 PMCID: PMC5495126 DOI: 10.1101/gad.295857.117] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/15/2017] [Indexed: 12/17/2022]
Abstract
In this study, Soto-Feliciano et al. describe the function of the plant homeodomain finger 6 (PHF6) protein in leukemia and define its role in regulating chromatin accessibility to lineage-specific transcription factors. Their findings suggest that active maintenance of a precise chromatin landscape is essential for sustaining proper leukemia cell identity and that loss of a single factor (PHF6) can cause focal changes in chromatin accessibility and nucleosome positioning that render cells susceptible to lineage transition. Developmental and lineage plasticity have been observed in numerous malignancies and have been correlated with tumor progression and drug resistance. However, little is known about the molecular mechanisms that enable such plasticity to occur. Here, we describe the function of the plant homeodomain finger protein 6 (PHF6) in leukemia and define its role in regulating chromatin accessibility to lineage-specific transcription factors. We show that loss of Phf6 in B-cell leukemia results in systematic changes in gene expression via alteration of the chromatin landscape at the transcriptional start sites of B-cell- and T-cell-specific factors. Additionally, Phf6KO cells show significant down-regulation of genes involved in the development and function of normal B cells, show up-regulation of genes involved in T-cell signaling, and give rise to mixed-lineage lymphoma in vivo. Engagement of divergent transcriptional programs results in phenotypic plasticity that leads to altered disease presentation in vivo, tolerance of aberrant oncogenic signaling, and differential sensitivity to frontline and targeted therapies. These findings suggest that active maintenance of a precise chromatin landscape is essential for sustaining proper leukemia cell identity and that loss of a single factor (PHF6) can cause focal changes in chromatin accessibility and nucleosome positioning that render cells susceptible to lineage transition.
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Affiliation(s)
- Yadira M Soto-Feliciano
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Jordan M E Bartlebaugh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Yunpeng Liu
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Francisco J Sánchez-Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Arjun Bhutkar
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Abraham S Weintraub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Jason D Buenrostro
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Christine S Cheng
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Aviv Regev
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tyler E Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Richard A Young
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Michael T Hemann
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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26
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Issuree PDA, Ng CP, Littman DR. Heritable Gene Regulation in the CD4:CD8 T Cell Lineage Choice. Front Immunol 2017; 8:291. [PMID: 28382035 PMCID: PMC5360760 DOI: 10.3389/fimmu.2017.00291] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/28/2017] [Indexed: 12/04/2022] Open
Abstract
The adaptive immune system is dependent on functionally distinct lineages of T cell antigen receptor αβ-expressing T cells that differentiate from a common progenitor in the thymus. CD4+CD8+ progenitor thymocytes undergo selection following interaction with MHC class I and class II molecules bearing peptide self-antigens, giving rise to CD8+ cytotoxic and CD4+ helper or regulatory T cell lineages, respectively. The strict correspondence of CD4 and CD8 expression with distinct cellular phenotypes has made their genes useful surrogates for investigating molecular mechanisms of lineage commitment. Studies of Cd4 and Cd8 transcriptional regulation have uncovered cis-regulatory elements that are critical for mediating epigenetic modifications at distinct stages of development to establish heritable transcriptional programs. In this review, we examine the epigenetic mechanisms involved in Cd4 and Cd8 gene regulation during T cell lineage specification and highlight the features that make this an attractive system for uncovering molecular mechanisms of heritability.
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Affiliation(s)
- Priya D A Issuree
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine , New York, NY , USA
| | - Charles P Ng
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine , New York, NY , USA
| | - Dan R Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
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27
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Abstract
There has been speculation as to how bi-potent CD4(+) CD8(+) double-positive precursor thymocytes choose their distinct developmental fate, becoming either CD4(+) helper or CD8(+) cytotoxic T cells. Based on the clear correlation of αβT cell receptor (TCR) specificity to major histocompatibility complex (MHC) classes with this lineage choice, various studies have attempted to resolve this question by examining the cellular signaling events initiated by TCR engagements, a strategy referred to as a 'top-down' approach. On the other hand, based on the other correlation of CD4/CD8 co-receptor expression with its selected fate, other studies have addressed this question by gradually unraveling the sequential mechanisms that control the phenotypic outcome of this fate decision, a method known as the 'bottom-up' approach. Bridging these two approaches will contribute to a more comprehensive understanding of how TCR signals are coupled with developmental programs in the nucleus. Advances made during the last two decades seemed to make these two approaches more closely linked. For instance, identification of two transcription factors, ThPOK and Runx3, which play central roles in the development of helper and cytotoxic lineages, respectively, provided significant insights into the transcriptional network that controls a CD4/CD8 lineage choice. This review summarizes achievements made using the 'bottom-up' approach, followed by a perspective on future pathways toward coupling TCR signaling with nuclear programs.
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Affiliation(s)
- Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
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28
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Hsu FC, Shapiro MJ, Dash B, Chen CC, Constans MM, Chung JY, Romero Arocha SR, Belmonte PJ, Chen MW, McWilliams DC, Shapiro VS. An Essential Role for the Transcription Factor Runx1 in T Cell Maturation. Sci Rep 2016; 6:23533. [PMID: 27020276 PMCID: PMC4810436 DOI: 10.1038/srep23533] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/08/2016] [Indexed: 12/26/2022] Open
Abstract
The transcription factor Runx1 has essential roles throughout hematopoiesis. Here, we demonstrate that Runx1 is critical for T cell maturation. Peripheral naïve CD4(+) T cells from CD4-cre Runx1 cKO mice are phenotypically and functionally immature as shown by decreased production of TNF-α upon TCR stimulation. The loss of peripheral CD4(+) T cells in CD4-cre Runx1 cKO mice is not due to defects in homeostasis or decreased expression of IL-7Rα, as transgenic expression of IL-7Rα does not rescue the loss of CD4(+) T cells. Rather, immature Runx1-deficient CD4(+) T cells are eliminated in the periphery by the activation and fixation of the classical complement pathway. In the thymus, there is a severe block in all aspects of intrathymic T cell maturation, although both positive and negative selection are unaltered. Thus, loss of Runx1 leads to the earliest characterized block in post-positive selection intrathymic maturation of CD4 T cells.
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Affiliation(s)
- Fan-Chi Hsu
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | | | - Barsha Dash
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | - Chien-Chang Chen
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | - Megan M Constans
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | - Ji Young Chung
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | | | - Paul J Belmonte
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | - Meibo W Chen
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
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29
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Abstract
During blood cell development, hematopoietic stem cells generate diverse mature populations via several rounds of binary fate decisions. At each bifurcation, precursors adopt one fate and inactivate the alternative fate either stochastically or in response to extrinsic stimuli and stably maintain the selected fates. Studying of these processes would contribute to better understanding of etiology of immunodeficiency and leukemia, which are caused by abnormal gene regulation during the development of hematopoietic cells. The CD4(+) helper versus CD8(+) cytotoxic T-cell fate decision serves as an excellent model to study binary fate decision processes. These two cell types are derived from common precursors in the thymus. Positive selection of their TCRs by self-peptide presented on either MHC class I or class II triggers their fate decisions along with mutually exclusive retention and silencing of two coreceptors, CD4 and CD8. In the past few decades, extensive effort has been made to understand the T-cell fate decision processes by studying regulation of genes encoding the coreceptors and selection processes. These studies have identified several key transcription factors and gene regulatory networks. In this chapter, I will discuss recent advances in our understanding of the binary cell fate decision processes of T cells.
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Affiliation(s)
- Takeshi Egawa
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA.
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30
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Rupp LJ, Brady BL, Carpenter AC, De Obaldia ME, Bhandoola A, Bosselut R, Muljo SA, Bassing CH. The microRNA biogenesis machinery modulates lineage commitment during αβ T cell development. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 193:4032-42. [PMID: 25217159 PMCID: PMC4185242 DOI: 10.4049/jimmunol.1401359] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Differentiation of CD4(+) helper and CD8(+) cytotoxic αβ T cells from CD4(+)CD8(+) thymocytes involves upregulation of lineage-specifying transcription factors and transcriptional silencing of CD8 or CD4 coreceptors, respectively, in MHC class II or I (MHCII or I)-restricted thymocytes. In this study, we demonstrate that inactivation of the Dicer RNA endonuclease in murine thymocytes impairs initiation of Cd4 and Cd8 silencing, leading to development of positively selected MHCI- and MHCII-restricted mature CD4(+)CD8(+) thymocytes. Expression of the antiapoptotic BCL2 protein or inactivation of the p53 proapoptotic protein rescues these thymocytes from apoptosis, increasing their frequency and permitting accumulation of CD4(+)CD8(+) αβ T cells in the periphery. Dicer-deficient MHCI-restricted αβ T cells fail to normally silence Cd4 and display impaired induction of the CD8 lineage-specifying transcription factor Runx3, whereas Dicer-deficient MHCII-restricted αβ T cells show impaired Cd8 silencing and impaired induction of the CD4 lineage-specifying transcription factor Thpok. Finally, we show that the Drosha RNA endonuclease, which functions upstream of Dicer in microRNA biogenesis, also regulates Cd4 and Cd8 silencing. Our data demonstrate a previously dismissed function for the microRNA biogenesis machinery in regulating expression of lineage-specifying transcription factors and silencing of Cd4 and Cd8 during αβ T cell differentiation.
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Affiliation(s)
- Levi J Rupp
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Brenna L Brady
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Andrea C Carpenter
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Maria Elena De Obaldia
- Immunology Graduate Group, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Avinash Bhandoola
- Immunology Graduate Group, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Remy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Stefan A Muljo
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Craig H Bassing
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Immunology Graduate Group, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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31
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A ThPOK-LRF transcriptional node maintains the integrity and effector potential of post-thymic CD4+ T cells. Nat Immunol 2014; 15:947-56. [PMID: 25129370 PMCID: PMC4251968 DOI: 10.1038/ni.2960] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 07/15/2014] [Indexed: 12/15/2022]
Abstract
The transcription factor ThPOK promotes CD4+ T cell differentiation in the thymus. Here, using a mouse strain that allows post-thymic gene deletion, we show that ThPOK maintains CD4+ T lineage integrity and couples effector differentiation to environmental cues after antigenic stimulation. ThPOK preserved the integrity and amplitude of effector responses, and was required for proper TH1 and TH2 differentiation in vivo by restraining the expression and function of the transcriptional regulator of cytotoxic T cell differentiation, Runx3. The transcription factor LRF contributed in a redundant manner with ThPOK to prevent the trans-differentiation of mature CD4+ T cells into CD8+ T cells. As such, the ThPOK-LRF transcriptional module was essential for CD4+ T cell integrity and responses.
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32
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Cleveland SM, Goodings C, Tripathi RM, Elliott N, Thompson MA, Guo Y, Shyr Y, Davé UP. LMO2 induces T-cell leukemia with epigenetic deregulation of CD4. Exp Hematol 2014; 42:581-93.e5. [PMID: 24792354 PMCID: PMC4241760 DOI: 10.1016/j.exphem.2014.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 04/18/2014] [Accepted: 04/23/2014] [Indexed: 02/05/2023]
Abstract
In this study, we present a remarkable clonal cell line, 32080, derived from a CD2-Lmo2- transgenic T-cell leukemia with differentiation arrest at the transition from the intermediate single positive to double positive stages of T-cell development. We observed that 32080 cells had a striking variegated pattern in CD4 expression. There was cell-to-cell variability, with some cells expressing no CD4 and others expressing high CD4. The two populations were isogenic and yet differed in their rates of apoptosis and sensitivity to glucocorticoid. We sorted the 32080 line for CD4-positive or CD4-negative cells and observed them in culture. After 1 week, both sorted populations showed variegated CD4 expression, like the parental line, showing that the two populations could interconvert. We determined that cell replication was necessary to transit from CD4(+) to CD4(-) and CD4(-) to CD4(+). Lmo2 knockdown decreased CD4 expression, while inhibition of intracellular NOTCH1 or histone deacetylase activity induced CD4 expression. Enforced expression of RUNX1 repressed CD4 expression. We analyzed the CD4 locus by Histone 3 chromatin immunoprecipitation and found silencing marks in the CD4(-) cells and activating marks in the CD4(+) population. The 32080 cell line is a striking model of intermediate single positive to double positive T-cell plasticity and invokes a novel mechanism for LMO2's oncogenic functions.
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Affiliation(s)
- Susan M Cleveland
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Charnise Goodings
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Rati M Tripathi
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Natalina Elliott
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Mary Ann Thompson
- Vanderbilt University Medical Center, Department of Pathology, Microbiology, and Immunology, Nashville, Tennessee, USA
| | - Yan Guo
- Center for Quantitative Sciences, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Utpal P Davé
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA.
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33
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Liu X, Yin S, Cao W, Fan W, Yu L, Yin L, Wang L, Wang J. Runt-related transcription factor 3 is involved in the altered phenotype and function in ThPok-deficient invariant natural killer T cells. Cell Mol Immunol 2014; 11:232-44. [PMID: 24561456 DOI: 10.1038/cmi.2014.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/10/2014] [Accepted: 01/12/2014] [Indexed: 01/09/2023] Open
Abstract
The interplay between the CD4-lineage transcription factor ThPok and the CD8-lineage transcription factor, runt-related transcription factor 3 (Runx3), in T-cell development has been extensively documented. However, little is known about the roles of these transcription factors in invariant natural killer T (iNKT) cell development. CD1d-restricted iNKT cells are committed to the CD4(+)CD8(-) and CD4(-)CD8(-) sublineages, which respond to antigen stimulation with rapid and potent release of T helper (Th) 1 and Th2 cytokines. However, previous reports have demonstrated a new population of CD8(+) NKT cells in ThPok-deficient mice. In the current study, we sought to determine whether Runx3 was involved in the re-expression of CD8 and function of iNKT cells in the absence of ThPok. We used mice lacking Runx3, ThPok or both and verified that Runx3 was partially responsible for the appearance of CD8(+) iNKT cells in ThPok knockout mice. Additionally, Runx3 participated in the immune response mediated by iNKT cells in a model of α-galactosylceramide-induced acute hepatitis. These results indicate that Runx3 is crucial for the phenotypic and functional changes observed in ThPok-deficient iNKT cells.
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34
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The role of BTB-zinc finger transcription factors during T cell development and in the regulation of T cell-mediated immunity. Curr Top Microbiol Immunol 2014; 381:21-49. [PMID: 24850219 DOI: 10.1007/82_2014_374] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The proper regulation of the development and function of peripheral helper and cytotoxic T cell lineages is essential for T cell-mediated adaptive immunity. Progress made during the last 10-15 years led to the identification of several transcription factors and transcription factor networks that control the development and function of T cell subsets. Among the transcription factors identified are also several members of the so-called BTB/POZ domain containing zinc finger (ZF) transcription factor family (BTB-ZF), and important roles of BTB-ZF factors have been described. In this review, we will provide an up-to-date overview about the role of BTB-ZF factors during T cell development and in peripheral T cells.
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35
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Transcriptional regulatory network analysis of the over-expressed genes in adipose tissue. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0145-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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36
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Transcriptional control of CD4 and CD8 coreceptor expression during T cell development. Cell Mol Life Sci 2013; 70:4537-53. [PMID: 23793512 PMCID: PMC3827898 DOI: 10.1007/s00018-013-1393-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/27/2013] [Accepted: 05/29/2013] [Indexed: 11/24/2022]
Abstract
The differentiation and function of peripheral helper and cytotoxic T cell lineages is coupled with the expression of CD4 and CD8 coreceptor molecules, respectively. This indicates that the control of coreceptor gene expression is closely linked with the regulation of CD4/CD8 lineage decision of DP thymocytes. Research performed during the last two decades revealed comprehensive mechanistic insight into the developmental stage- and subset/lineage-specific regulation of Cd4, Cd8a and Cd8b1 (Cd8) gene expression. These studies provided important insight into transcriptional control mechanisms during T cell development and into the regulation of cis-regulatory networks in general. Moreover, the identification of transcription factors involved in the regulation of CD4 and CD8 significantly advanced the knowledge of the transcription factor network regulating CD4/CD8 cell-fate choice of DP thymocytes. In this review, we provide an overview of the identification and characterization of CD4/CD8 cis-regulatory elements and present recent progress in our understanding of how these cis-regulatory elements control CD4/CD8 expression during T cell development and in peripheral T cells. In addition, we describe the transcription factors implicated in the regulation of coreceptor gene expression and discuss how these factors are integrated into the transcription factor network that regulates CD4/CD8 cell-fate choice of DP thymocytes.
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37
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Martínez-Sosa P, Mendoza L. The regulatory network that controls the differentiation of T lymphocytes. Biosystems 2013; 113:96-103. [PMID: 23743337 DOI: 10.1016/j.biosystems.2013.05.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 02/13/2013] [Accepted: 05/21/2013] [Indexed: 12/22/2022]
Abstract
There is a vast amount of molecular information regarding the differentiation of T lymphocytes, in particular regarding in vitro experimental treatments that modify their differentiation process. This publicly available information was used to infer the regulatory network that controls the differentiation of T lymphocytes into CD4(+) and CD8(+) cells. Hereby we present a network that consists of 50 nodes and 97 regulatory interactions, representing the main signaling circuits established among molecules and molecular complexes regulating the differentiation of T cells. The network was converted into a continuous dynamical system in the form of a set of coupled ordinary differential equations, and its dynamical behavior was studied. With the aid of numerical methods, nine fixed point attractors were found for the dynamical system. These attractors correspond to the activation patterns observed experimentally for the following cell types: CD4(-)CD8(-), CD4(+)CD8(+), CD4(+) naive, Th1, Th2, Th17, Treg, CD8(+) naive, and CTL. Furthermore, the model is able to describe the differentiation process from the precursor CD4(-)CD8(-) to any of the effector types due to a specific series of extracellular signals.
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Affiliation(s)
- Pablo Martínez-Sosa
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70228, Ciudad Universitaria, CP04510 México, D.F., Mexico
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38
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Enders A, Stankovic S, Teh C, Uldrich AP, Yabas M, Juelich T, Altin JA, Frankenreiter S, Bergmann H, Roots CM, Kyparissoudis K, Goodnow CC, Godfrey DI. ZBTB7B (Th-POK) regulates the development of IL-17-producing CD1d-restricted mouse NKT cells. THE JOURNAL OF IMMUNOLOGY 2012; 189:5240-9. [PMID: 23105140 DOI: 10.4049/jimmunol.1201486] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CD1d-dependent NKT cells represent a heterogeneous family of effector T cells including CD4(+)CD8(-) and CD4(-)CD8(-) subsets that respond to glycolipid Ags with rapid and potent cytokine production. NKT cell development is regulated by a unique combination of factors, however very little is known about factors that control the development of NKT subsets. In this study, we analyze a novel mouse strain (helpless) with a mis-sense mutation in the BTB-POZ domain of ZBTB7B and demonstrate that this mutation has dramatic, intrinsic effects on development of NKT cell subsets. Although NKT cell numbers are similar in Zbtb7b mutant mice, these cells are hyperproliferative and most lack CD4 and instead express CD8. Moreover, the majority of ZBTB7B mutant NKT cells in the thymus are retinoic acid-related orphan receptor γt positive, and a high frequency produce IL-17 while very few produce IFN-γ or other cytokines, sharply contrasting the profile of normal NKT cells. Mice heterozygous for the helpless mutation also have reduced numbers of CD4(+) NKT cells and increased production of IL-17 without an increase in CD8(+) cells, suggesting that ZBTB7B acts at multiple stages of NKT cell development. These results reveal ZBTB7B as a critical factor genetically predetermining the balance of effector subsets within the NKT cell population.
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Affiliation(s)
- Anselm Enders
- Ramaciotti Immunization Genomics Laboratory, Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 0200, Australia
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39
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The transcription factors Thpok and LRF are necessary and partly redundant for T helper cell differentiation. Immunity 2012; 37:622-33. [PMID: 23041065 DOI: 10.1016/j.immuni.2012.06.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 06/21/2012] [Indexed: 12/24/2022]
Abstract
T helper (Th) cells are critical for defenses against infection and recognize peptides bound to class II major histocompatibility complex (MHC II) molecules. Although transcription factors have been identified that direct Th cells into specific effector fates, whether a "master" regulator controls the developmental program common to all Th cells remains unclear. Here, we showed that the two transcription factors Thpok and LRF share this function. Although disruption of both factors did not prevent the generation of MHC II-specific T cells, these cells failed to express Th cell genes or undergo Th cell differentiation in vivo. In contrast, T cells lacking Thpok, which only displayed LRF-dependent functions, contributed to multiple effector responses, both in vitro and in vivo, with the notable exception of Th2 cell responses that control extracellular parasites. These findings identify the Thpok-LRF pair as a core node of Th cell differentiation and function.
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40
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Satpathy AT, KC W, Albring JC, Edelson BT, Kretzer NM, Bhattacharya D, Murphy TL, Murphy KM. Zbtb46 expression distinguishes classical dendritic cells and their committed progenitors from other immune lineages. ACTA ACUST UNITED AC 2012; 209:1135-52. [PMID: 22615127 PMCID: PMC3371733 DOI: 10.1084/jem.20120030] [Citation(s) in RCA: 454] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The zinc finger transcription factor Zbtb46 specifically marks cDCs and their committed precursors and, when overexpressed in BM progenitors, promotes cDC development at the expense of granulocytes. Distinguishing dendritic cells (DCs) from other cells of the mononuclear phagocyte system is complicated by the shared expression of cell surface markers such as CD11c. In this study, we identified Zbtb46 (BTBD4) as a transcription factor selectively expressed by classical DCs (cDCs) and their committed progenitors but not by plasmacytoid DCs (pDCs), monocytes, macrophages, or other lymphoid or myeloid lineages. Using homologous recombination, we replaced the first coding exon of Zbtb46 with GFP to inactivate the locus while allowing detection of Zbtb46 expression. GFP expression in Zbtb46gfp/+ mice recapitulated the cDC-specific expression of the native locus, being restricted to cDC precursors (pre-cDCs) and lymphoid organ– and tissue-resident cDCs. GFP+ pre-cDCs had restricted developmental potential, generating cDCs but not pDCs, monocytes, or macrophages. Outside the immune system, Zbtb46 was expressed in committed erythroid progenitors and endothelial cell populations. Zbtb46 overexpression in bone marrow progenitor cells inhibited granulocyte potential and promoted cDC development, and although cDCs developed in Zbtb46gfp/gfp (Zbtb46 deficient) mice, they maintained expression of granulocyte colony-stimulating factor and leukemia inhibitory factor receptors, which are normally down-regulated in cDCs. Thus, Zbtb46 may help enforce cDC identity by restricting responsiveness to non-DC growth factors and may serve as a useful marker to identify rare cDC progenitors and distinguish between cDCs and other mononuclear phagocyte lineages.
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Affiliation(s)
- Ansuman T Satpathy
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
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41
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Xiong Y, Bosselut R. CD4-CD8 differentiation in the thymus: connecting circuits and building memories. Curr Opin Immunol 2012; 24:139-45. [PMID: 22387323 PMCID: PMC3773541 DOI: 10.1016/j.coi.2012.02.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 01/22/2012] [Accepted: 02/06/2012] [Indexed: 10/28/2022]
Abstract
The proper choice of the CD4-helper or CD8-cytotoxic lineages by developing T cells is crucial for the generation of an antigen-responsive and functionally fit T cell repertoire. Here we present a brief overview of the transcriptional control of this process, with emphasis on two issues. The study of Cd4 expression, that had previously generated important paradigms for transcriptional regulation in eukaryotic cells, now brings new twists to the concept of 'epigenetic memory'. And connections are emerging between transcriptional regulators critical for commitment to either lineage. The present review attempts to integrate these findings and discusses the still elusive mechanisms that match CD4-CD8 lineage differentiation to MHC specificity.
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Affiliation(s)
- Yumei Xiong
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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42
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Roles of VWRPY motif-mediated gene repression by Runx proteins during T-cell development. Immunol Cell Biol 2012; 90:827-30. [PMID: 22370763 DOI: 10.1038/icb.2012.6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Runx transcription factor family proteins have essential roles during T-cell development by either activating or repressing target genes. For instance, lineage- and stage-specific expression of Cd4 and ThPOK is controlled by a transcriptional silencer embedded in each locus, whose activity requires bindings of Runx complexes. The evolutionarily conserved VWRPY penta-peptide sequences in Runx proteins have been shown to be responsible for repressive function as a platform to recruit Groucho/TLE transcriptional corepressors. However, it remains elusive whether requirement for the VWRPY motif differs among Runx target genes. By examining mice lacking VWRPY motifs in both Runx1 and Runx3 proteins, here, we show a full and partial derepression of Cd4 and ThPOK in CD8-linegae T cells, respectively. Thus, whereas Cd4 silencing completely depends on the VWRPY motif, both VWRPY-dependent and -independent mechanisms operate to repress ThPOK gene. These results indicate that Runx proteins utilize different modes to repress expression of different target genes.
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43
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Aliahmad P, Kadavallore A, de la Torre B, Kappes D, Kaye J. TOX is required for development of the CD4 T cell lineage gene program. THE JOURNAL OF IMMUNOLOGY 2011; 187:5931-40. [PMID: 22021617 DOI: 10.4049/jimmunol.1101474] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The factors that regulate thymic development of the CD4(+) T cell gene program remain poorly defined. The transcriptional regulator ThPOK is a dominant factor in CD4(+) T cell development, which functions primarily to repress the CD8 lineage fate. Previously, we showed that nuclear protein TOX is also required for murine CD4(+) T cell development. In this study, we sought to investigate whether the requirement for TOX was solely due to a role in ThPOK induction. In apparent support of this proposition, ThPOK upregulation and CD8 lineage repression were compromised in the absence of TOX, and enforced ThPOK expression could restore some CD4 development. However, these "rescued" CD4 cells were defective in many aspects of the CD4(+) T cell gene program, including expression of Id2, Foxo1, and endogenous Thpok, among others. Thus, TOX is necessary to establish the CD4(+) T cell lineage gene program, independent of its influence on ThPOK expression.
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Affiliation(s)
- Parinaz Aliahmad
- Research Division of Immunology, Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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44
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Wang L, Xiong Y, Bosselut R. Maintaining CD4-CD8 lineage integrity in T cells: where plasticity serves versatility. Semin Immunol 2011; 23:360-7. [PMID: 21963088 PMCID: PMC3740965 DOI: 10.1016/j.smim.2011.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 08/19/2011] [Indexed: 01/10/2023]
Abstract
The divergence of the two αβ T cell subsets defined by the mutually exclusive expression of CD4 and CD8 glycoproteins is an important event during the intrathymic differentiation of T lymphocytes. This reviews briefly summarizes the mechanisms that promote commitment to the CD4 or CD8 lineage in the thymus, and discusses the transcription factor circuits and epigenetic mechanisms that concur to maintain lineage integrity in post-thymic cells and yet allow effector cell differentiation.
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Affiliation(s)
- Lie Wang
- Laboratory of Immune Cell Biology, Center for Cancer Research (CCR), NCI, NIH, Bethesda, MD 20892-4259, USA
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45
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Collins A, Hewitt S, Chaumeil J, Sellars M, Micsinai M, Allinne J, Parisi F, Nora EP, Bolland D, Corcoran A, Kluger Y, Bosselut R, Ellmeier W, Chong M, Littman D, Skok J. RUNX transcription factor-mediated association of Cd4 and Cd8 enables coordinate gene regulation. Immunity 2011; 34:303-14. [PMID: 21435585 PMCID: PMC3101577 DOI: 10.1016/j.immuni.2011.03.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 09/07/2010] [Accepted: 12/21/2010] [Indexed: 01/24/2023]
Abstract
T cell fate is associated with mutually exclusive expression of CD4 or CD8 in helper and cytotoxic T cells, respectively. How expression of one locus is temporally coordinated with repression of the other has been a long-standing enigma, though we know RUNX transcription factors activate the Cd8 locus, silence the Cd4 locus, and repress the Zbtb7b locus (encoding the transcription factor ThPOK), which is required for CD4 expression. Here we found that nuclear organization was altered by interplay among members of this transcription factor circuitry: RUNX binding mediated association of Cd4 and Cd8 whereas ThPOK binding kept the loci apart. Moreover, targeted deletions within Cd4 modulated CD8 expression and pericentromeric repositioning of Cd8. Communication between Cd4 and Cd8 thus appears to enable long-range epigenetic regulation to ensure that expression of one excludes the other in mature CD4 or CD8 single-positive (SP) cells.
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Affiliation(s)
- Amélie Collins
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Susannah L. Hewitt
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Julie Chaumeil
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - MacLean Sellars
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Mariann Micsinai
- New York University Center for Health Informatics and Bioinformatics, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
- NYU Cancer Institute, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
- Department of Pathology and Yale Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Jeanne Allinne
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Fabio Parisi
- Department of Pathology and Yale Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Elphège P. Nora
- Institut Curie, CNRS UMR3215, INSERM U934, 75724 Paris Cedex 05, France
| | - Dan J. Bolland
- The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Anne E. Corcoran
- The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Yuval Kluger
- Department of Pathology and Yale Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Remy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research (CCR), NCI, NIH, Bethesda, MD 20892-4259, USA
| | - Wilfried Ellmeier
- Division of Immunobiology, Institute of Immunology, Medical University of Vienna, Lazarettgasse 19, A-1090 Vienna, Austria
| | - Mark M.W. Chong
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Dan R. Littman
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
- Howard Hughes Medical Institute
| | - Jane A. Skok
- Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
- Division of Infection and Immunity, The Department of Immunology and Molecular Pathology, University College London, London W1T 4JF, UK
- Corresponding author
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46
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Abstract
The role of the zinc finger transcription factor ThPOK (T-helper-inducing POZ-Kruppel-like factor) in promoting commitment of αβ T cells to the CD4 lineage is now well established. New results indicate that ThPOK is also important for the development and/or acquisition of effector functions by other T cell subsets, including several not marked by CD4 expression, i.e. double-negative invariant natural killer T (iNKT) cells, γδ cells, and even memory CD8(+) T cells. There is compelling evidence that ThPOK expression in most or all of these cases is dependent on T-cell receptor signaling and that differences in relative TCR signal strength/length may induce different levels of ThPOK expression. The developmental consequences of ThPOK expression vary according to cell type, which may partly reflect differences in ThPOK levels and/or in transcriptional networks between cell types.
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Affiliation(s)
- Dietmar J Kappes
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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47
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Balasubramani A, Mukasa R, Hatton RD, Weaver CT. Regulation of the Ifng locus in the context of T-lineage specification and plasticity. Immunol Rev 2011; 238:216-32. [PMID: 20969595 DOI: 10.1111/j.1600-065x.2010.00961.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Study of the development of distinct CD4(+) T-cell subsets from naive precursors continues to provide excellent opportunities for dissection of mechanisms that control lineage-specific gene expression or repression. Whereas it had been thought that the induction of transcription networks that control T-lineage commitment were highly stable, reinforced by epigenetic processes that confer heritability of functional phenotypes by the progeny of mature T cells, recent findings support a more dynamic view of T-lineage commitment. Here, we highlight advances in the mapping and functional characterization of cis elements in the Ifng locus that have provided new insights into the control of the chromatin structure and transcriptional activity of this signature T-helper 1 cell gene. We also examine epigenetic features of the Ifng locus that have evolved to enable its reprogramming for expression by other T-cell subsets, particularly T-helper 17 cells, and contrast features of the Ifng locus with those of the Il17a-Il17f locus, which appears less promiscuous.
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Affiliation(s)
- Anand Balasubramani
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
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48
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Xiong Y, Bosselut R. The enigma of CD4-lineage specification. Eur J Immunol 2011; 41:568-74. [PMID: 21341258 PMCID: PMC3388806 DOI: 10.1002/eji.201041098] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Revised: 11/10/2010] [Accepted: 12/15/2010] [Indexed: 01/20/2023]
Abstract
CD4(+) T cells are essential for defenses against pathogens and affect the functions of most cells involved in the immune response. Although CD4(+) T cells generally recognize peptide antigens bound to MHC-II molecules, important subsets are restricted by other MHC or MHC-like molecules, including CD1d-restricted "invariant" iNK T cells. This review discusses recently identified nodes in the transcriptional circuits that are involved in controlling CD4(+) T-cell differentiation, notably the commitment factor Thpok and its interplay with Runx transcriptional regulators, and focuses on how transcription factors acting upstream of Thpok, including Gata3, Tox and E-box proteins, promote the emergence of CD4-lineage-specific gene expression patterns.
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Affiliation(s)
- Yumei Xiong
- Laboratory of Immune Cell Biology, Center for Cancer Research (CCR), NCI, NIH, Bethesda, MD 20892-4259, USA
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49
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Abstract
The helper versus cytotoxic-lineage choice of CD4(+)CD8(+) DP thymocytes correlates with MHC restriction of their T cell receptors and the termination of either CD8 or CD4 coreceptor expression. It has been hypothesized that transcription factors regulating the expression of the Cd4/Cd8 coreceptor genes must play a role in regulating the lineage decision of DP thymocytes. Indeed, progress made during the past decade led to the identification of several transcription factors that regulate CD4/CD8 expression that are as well important regulators of helper/cytotoxic cell fate choice. These studies provided insight into the molecular link between the regulation of coreceptor expression and lineage decision. However, studies initiated by the identification of ThPOK, a central transcription factor for helper T cell development, have offered another perspective on the cross-regulation between these two processes. Here, we review advances in our understanding of regulatory circuits composed of transcription factors and their link to epigenetic mechanisms, which play essential roles in specifying and sealing cell lineage identity during the CD4/CD8 commitment process of DP thymocytes.
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Affiliation(s)
- Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, Research Center for Allergy and Immunology, RIKEN, Suehiro-cho, Turumi-ku, Yokohama, Kanagawa, Japan
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50
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Wong WF, Kohu K, Chiba T, Sato T, Satake M. Interplay of transcription factors in T-cell differentiation and function: the role of Runx. Immunology 2010; 132:157-64. [PMID: 21091910 DOI: 10.1111/j.1365-2567.2010.03381.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Over the past years, increasing numbers of distinct subsets have been discovered and identified for a T lymphocytes' entity. Differentiation and function of each T cell subset are controlled by a specific master transcription factor. Importantly, Runt-related transcription factors, particularly Runx1 and Runx3, interplay with these master regulators in various aspects of T cells' immunity. In this review article, we first explain roles of Th-Pok and Runx3 in differentiation of CD4 versus CD8 single positive cells, and later focus on cross-regulation of Th-Pok and Runx3 and their relationship with other factors such as TCR strength. Next, we provide evidences for the direct interplay of Runx1/3 with T-bet and GATA3 during Th1 versus Th2 commitment to activate or silence transcription of signature cytokine genes, IFNγ and IL4. Lastly, we explain feed-forward relationship between Runx1 and Foxp3 and discuss roles of Runx1 in regulatory T cells' suppressive activity. This review highlights an essential importance of Runx molecules in controlling various T cell subsets' differentiation and functions through molecular interplay with the master transcription factors in terms of protein-protein interaction as well as regulation of gene expression.
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Affiliation(s)
- Won Fen Wong
- Institute of Development, Aging and Cancer, Tohoku University, Sendai, Isehara, Japan
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