1
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Shin B, Chang SJ, MacNabb BW, Rothenberg EV. Transcriptional network dynamics in early T cell development. J Exp Med 2024; 221:e20230893. [PMID: 39167073 PMCID: PMC11338287 DOI: 10.1084/jem.20230893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/07/2024] [Accepted: 07/10/2024] [Indexed: 08/23/2024] Open
Abstract
The rate at which cells enter the T cell pathway depends not only on the immigration of hematopoietic precursors into the strong Notch signaling environment of the thymus but also on the kinetics with which each individual precursor cell reaches T-lineage commitment once it arrives. Notch triggers a complex, multistep gene regulatory network in the cells in which the steps are stereotyped but the transition speeds between steps are variable. Progenitor-associated transcription factors delay T-lineage differentiation even while Notch-induced transcription factors within the same cells push differentiation forward. Progress depends on regulator cross-repression, on breaching chromatin barriers, and on shifting, competitive collaborations between stage-specific and stably expressed transcription factors, as reviewed here.
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Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering California Institute of Technology , Pasadena, CA, USA
| | - Samantha J Chang
- Division of Biology and Biological Engineering California Institute of Technology , Pasadena, CA, USA
| | - Brendan W MacNabb
- Division of Biology and Biological Engineering California Institute of Technology , Pasadena, CA, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering California Institute of Technology , Pasadena, CA, USA
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2
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Steier Z, Kim EJY, Aylard DA, Robey EA. The CD4 Versus CD8 T Cell Fate Decision: A Multiomics-Informed Perspective. Annu Rev Immunol 2024; 42:235-258. [PMID: 38271641 DOI: 10.1146/annurev-immunol-083122-040929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The choice of developing thymocytes to become CD8+ cytotoxic or CD4+ helper T cells has been intensely studied, but many of the underlying mechanisms remain to be elucidated. Recent multiomics approaches have provided much higher resolution analysis of gene expression in developing thymocytes than was previously achievable, thereby offering a fresh perspective on this question. Focusing on our recent studies using CITE-seq (cellular indexing of transcriptomes and epitopes) analyses of mouse thymocytes, we present a detailed timeline of RNA and protein expression changes during CD8 versus CD4 T cell differentiation. We also revisit our current understanding of the links between T cell receptor signaling and expression of the lineage-defining transcription factors ThPOK and RUNX3. Finally, we propose a sequential selection model to explain the tight linkage between MHC-I versus MHC-II recognition and T cell lineage choice. This model incorporates key aspects of previously proposed kinetic signaling, instructive, and stochastic/selection models.
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Affiliation(s)
- Zoë Steier
- Department of Bioengineering and Center for Computational Biology, University of California, Berkeley, California, USA
- Graduate Program in Bioengineering, University of California, Berkeley, and University of California, San Francisco, Berkeley and San Francisco, California, USA
- Current affiliation: Institute for Medical Engineering and Science, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard; and Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Esther Jeong Yoon Kim
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Dominik A Aylard
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Ellen A Robey
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
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3
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Luchtel RA. ETS1 Function in Leukemia and Lymphoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:359-378. [PMID: 39017852 DOI: 10.1007/978-3-031-62731-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
ETS proto-oncogene 1 (ETS1) is a transcription factor (TF) critically involved in lymphoid cell development and function. ETS1 expression is tightly regulated throughout differentiation and activation in T-cells, natural killer (NK) cells, and B-cells. It has also been described as an oncogene in a range of solid and hematologic cancer types. Among hematologic malignancies, its role has been best studied in T-cell acute lymphoblastic leukemia (T-ALL), adult T-cell leukemia/lymphoma (ATLL), and diffuse large B-cell lymphoma (DLBCL). Aberrant expression of ETS1 in these malignancies is driven primarily by chromosomal amplification and enhancer-driven transcriptional regulation, promoting the ETS1 transcriptional program. ETS1 also facilitates aberrantly expressed or activated transcriptional complexes to drive oncogenic pathways. Collectively, ETS1 functions to regulate cell growth, differentiation, signaling, response to stimuli, and viral interactions in these malignancies. A tumor suppressor role has also been indicated for ETS1 in select lymphoma types, emphasizing the importance of cellular context in ETS1 function. Research is ongoing to further characterize the clinical implications of ETS1 dysregulation in hematologic malignancies, to further resolve binding complexes and transcriptional targets, and to identify effective therapeutic targeting approaches.
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Affiliation(s)
- Rebecca A Luchtel
- Division of Hematology and Oncology, Department of Medicine, Northwestern University, Chicago, IL, USA.
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4
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Garrett-Sinha LA. An update on the roles of transcription factor Ets1 in autoimmune diseases. WIREs Mech Dis 2023; 15:e1627. [PMID: 37565573 PMCID: PMC10842644 DOI: 10.1002/wsbm.1627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
Transcription factors are crucial to regulate gene expression in immune cells and in other cell types. In lymphocytes, there are a large number of different transcription factors that are known to contribute to cell differentiation and the balance between quiescence and activation. One such transcription factor is E26 oncogene homolog 1 (Ets1). Ets1 expression is high in quiescent B and T lymphocytes and its levels are decreased upon activation. The human ETS1 gene has been identified as a susceptibility locus for many autoimmune and inflammatory diseases. In accord with this, gene knockout of Ets1 in mice leads to development of a lupus-like autoimmune disease, with enhanced activation and differentiation of both B cells and T cells. Prior reviews have summarized functional roles for Ets1 based on studies of Ets1 knockout mice. In recent years, numerous additional studies have been published that further validate ETS1 as a susceptibility locus for human diseases where immune dysregulation plays a causative role. In this update, new information that further links Ets1 to human autoimmune diseases is organized and collated to serve as a resource. This update also describes recent studies that seek to understand molecularly how Ets1 regulates immune cell activation, either using human cells and tissues or mouse models. This resource is expected to be useful to investigators seeking to understand how Ets1 may regulate the human immune response, particularly in terms of its roles in autoimmunity and inflammation. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Lee Ann Garrett-Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York, USA
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5
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Lin SC, Yu G, Lee YC, Song JH, Song X, Zhang J, Panaretakis T, Logothetis CJ, Komatsu Y, Yu-Lee LY, Wang G, Lin SH. Endothelial-to-osteoblast transition in normal mouse bone development. iScience 2023; 26:105994. [PMID: 36798441 PMCID: PMC9926118 DOI: 10.1016/j.isci.2023.105994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/23/2022] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Metastatic prostate cancer (PCa) in bone induces bone-forming lesions. We have previously shown that PCa-induced bone originates from endothelial cells (ECs) that have undergone EC-to-osteoblast (OSB) transition. Here, we investigated whether EC-to-OSB transition also occurs during normal bone formation. We developed an EC and OSB dual-color reporter mouse (DRM) model that marks EC-OSB hybrid cells with red and green fluorescent proteins. We observed EC-to-OSB transition (RFP and GFP co-expression) in both endochondral and intramembranous bone formation during embryonic development and in adults. Co-expression was confirmed in cells isolated from DRM. Bone marrow- and lung-derived ECs underwent transition to OSBs and mineralization in osteogenic medium. RNA-sequencing revealed GATA family transcription factors were upregulated in EC-OSB hybrid cells and knockdown of GATA3 inhibited BMP4-induced mineralization. Our findings support that EC-to-OSB transition occurs during normal bone development and suggest a new paradigm regarding the endothelial origin of OSBs.
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Affiliation(s)
- Song-Chang Lin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guoyu Yu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yu-Chen Lee
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian H. Song
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Theocharis Panaretakis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher J. Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yoshihiro Komatsu
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Li-Yuan Yu-Lee
- Departments of Medicine and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Guocan Wang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sue-Hwa Lin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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6
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Fang D, Healy A, Zhu J. Differential regulation of lineage-determining transcription factor expression in innate lymphoid cell and adaptive T helper cell subsets. Front Immunol 2023; 13:1081153. [PMID: 36685550 PMCID: PMC9846361 DOI: 10.3389/fimmu.2022.1081153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
CD4 T helper (Th) cell subsets, including Th1, Th2 and Th17 cells, and their innate counterparts innate lymphoid cell (ILC) subsets consisting of ILC1s, ILC2s and ILC3s, display similar effector cytokine-producing capabilities during pro-inflammatory immune responses. These lymphoid cell subsets utilize the same set of lineage-determining transcription factors (LDTFs) for their differentiation, development and functions. The distinct ontogeny and developmental niches between Th cells and ILCs indicate that they may adopt different external signals for the induction of LDTF during lineage commitment. Increasing evidence demonstrates that many conserved cis-regulatory elements at the gene loci of LDTFs are often preferentially utilized for the induction of LDTF expression during Th cell differentiation and ILC development at different stages. In this review, we discuss the functions of lineage-related cis-regulatory elements in inducing T-bet, GATA3 or RORγt expression based on the genetic evidence provided in recent publications. We also review and compare the upstream signals involved in LDTF induction in Th cells and ILCs both in vitro and in vivo. Finally, we discuss the possible mechanisms and physiological importance of regulating LDTF dynamic expression during ILC development and activation.
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Affiliation(s)
- Difeng Fang
- *Correspondence: Difeng Fang, ; Jinfang Zhu,
| | | | - Jinfang Zhu
- *Correspondence: Difeng Fang, ; Jinfang Zhu,
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7
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Martinelli M, Aguilar G, Lee DS, Kromer A, Nguyen N, Wilkins BJ, Akimova T, Beier UH, Ghanem LR. The poly(C)-binding protein Pcbp2 is essential for CD4 + T cell activation and proliferation. iScience 2022; 26:105860. [PMID: 36632062 PMCID: PMC9826892 DOI: 10.1016/j.isci.2022.105860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
The RNA-binding protein Pcbp2 is widely expressed in the innate and adaptive immune systems and is essential for mouse development. To determine whether Pcbp2 is required for CD4+ T cell development and function, we derived mice with conditional Pcbp2 deletion in CD4+ T cells and assessed their overall phenotype and proliferative responses to activating stimuli. We found that Pcbp2 is essential for T conventional cell (Tconv) proliferation, working through regulation of co-stimulatory signaling. Pcbp2 deficiency in the CD4+ lineage did not impact Treg abundance in vivo or function in vitro. In addition, our data demonstrate a clear association between Pcbp2 control of Runx1 exon 6 splicing in CD4+ T cells and a specific role for Pcbp2 in the maintenance of peripheral CD4+ lymphocyte population size. Last, we show that Pcbp2 function is required for optimal in vivo Tconv cell activation in a T cell adoptive transfer colitis model system.
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Affiliation(s)
- Massimo Martinelli
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA,Department of Translational Medical Science, Section of Pediatrics, University of Naples “Federico II”, Naples 80131, Italy
| | - Gabrielle Aguilar
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David S.M. Lee
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Biomedical Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Kromer
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nhu Nguyen
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Benjamin J. Wilkins
- Division of Anatomic Pathology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA,Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tatiana Akimova
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ulf H. Beier
- Division of Nephrology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Louis R. Ghanem
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding author
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8
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Babaie F, Omraninava M, Gorabi AM, Khosrojerdi A, Aslani S, Yazdchi A, Torkamandi S, Mikaeili H, Sathyapalan T, Sahebkar A. Etiopathogenesis of Psoriasis from Genetic Perspective: An updated Review. Curr Genomics 2022; 23:163-174. [PMID: 36777004 PMCID: PMC9878828 DOI: 10.2174/1389202923666220527111037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/11/2022] [Accepted: 04/12/2022] [Indexed: 11/22/2022] Open
Abstract
Psoriasis is an organ-specific autoimmune disease characterized by the aberrant proliferation and differentiation of keratinocytes, leading to skin lesions. Abnormal immune responses mediated by T cells and dendritic cells and increased production of inflammatory cytokines have been suggested as underlying mechanisms in the pathogenesis of psoriasis. Emerging evidence suggests that there is a heritable basis for psoriatic disorders. Moreover, numerous gene variations have been associated with the disease risk, particularly those in innate and adaptive immune responses and antigen presentation pathways. Herein, this article discusses the genetic implications of psoriatic diseases' etiopathogenesis to develop novel investigative and management options.
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Affiliation(s)
- Farhad Babaie
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran;,Department of Medical Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Melodi Omraninava
- Department of Infectious Diseases, Faculty of Medical Sciences, Sari Branch, Islamic Azad University, Sari, Iran
| | - Armita Mahdavi Gorabi
- Research Center for Advanced Technologies in Cardiovascular Medicine, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Arezou Khosrojerdi
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeed Aslani
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Arsalan Yazdchi
- Student Research Committee, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahram Torkamandi
- Department of Medical Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran;,Address correspondence to these authors at the Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran, P.O. Box: 91779-48564, Iran; E-mail: ; Department of Medical Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran; E-mail: and Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; E-mail:
| | - Haleh Mikaeili
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran;,Address correspondence to these authors at the Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran, P.O. Box: 91779-48564, Iran; E-mail: ; Department of Medical Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran; E-mail: and Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; E-mail:
| | - Thozhukat Sathyapalan
- Department of Academic Diabetes, Endocrinology and Metabolism, Hull York Medical School, University of Hull, Hull, UK
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran;,Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran;,Department of Biotechnology, School of Pharmacy, Mashhad University of Western Australia, Mashhad, Iran,Address correspondence to these authors at the Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran, P.O. Box: 91779-48564, Iran; E-mail: ; Department of Medical Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran; E-mail: and Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; E-mail:
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9
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Igalouzene R, Hernandez-Vargas H, Benech N, Guyennon A, Bauché D, Barrachina C, Dubois E, Marie JC, Soudja SM. SMAD4 TGF-β–independent function preconditions naive CD8+ T cells to prevent severe chronic intestinal inflammation. J Clin Invest 2022; 132:151020. [PMID: 35426367 PMCID: PMC9012287 DOI: 10.1172/jci151020] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 03/08/2022] [Indexed: 12/13/2022] Open
Abstract
SMAD4, a mediator of TGF-β signaling, plays an important role in T cells to prevent inflammatory bowel disease (IBD). However, the precise mechanisms underlying this control remain elusive. Using both genetic and epigenetic approaches, we revealed an unexpected mechanism by which SMAD4 prevents naive CD8+ T cells from becoming pathogenic for the gut. Prior to the engagement of the TGF-β receptor, SMAD4 restrains the epigenetic, transcriptional, and functional landscape of the TGF-β signature in naive CD8+ T cells. Mechanistically, prior to TGF-β signaling, SMAD4 binds to promoters and enhancers of several TGF-β target genes, and by regulating histone deacetylation, suppresses their expression. Consequently, regardless of a TGF-β signal, SMAD4 limits the expression of TGF-β negative feedback loop genes, such as Smad7 and Ski, and likely conditions CD8+ T cells for the immunoregulatory effects of TGF-β. In addition, SMAD4 ablation conferred naive CD8+ T cells with both a superior survival capacity, by enhancing their response to IL-7, as well as an enhanced capacity to be retained within the intestinal epithelium, by promoting the expression of Itgae, which encodes the integrin CD103. Accumulation, epithelial retention, and escape from TGF-β control elicited chronic microbiota-driven CD8+ T cell activation in the gut. Hence, in a TGF-β–independent manner, SMAD4 imprints a program that preconditions naive CD8+ T cell fate, preventing IBD.
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Affiliation(s)
- Ramdane Igalouzene
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon (CRCL), INSERM U1052, CNRS UMR 5286, Centre Léon Bérard (CLB) and University of Lyon 1, Lyon, France
| | - Hector Hernandez-Vargas
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon (CRCL), INSERM U1052, CNRS UMR 5286, Centre Léon Bérard (CLB) and University of Lyon 1, Lyon, France
| | - Nicolas Benech
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon (CRCL), INSERM U1052, CNRS UMR 5286, Centre Léon Bérard (CLB) and University of Lyon 1, Lyon, France
| | - Alexandre Guyennon
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon (CRCL), INSERM U1052, CNRS UMR 5286, Centre Léon Bérard (CLB) and University of Lyon 1, Lyon, France
| | - David Bauché
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon (CRCL), INSERM U1052, CNRS UMR 5286, Centre Léon Bérard (CLB) and University of Lyon 1, Lyon, France
| | - Célia Barrachina
- Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Emeric Dubois
- Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Julien C. Marie
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon (CRCL), INSERM U1052, CNRS UMR 5286, Centre Léon Bérard (CLB) and University of Lyon 1, Lyon, France
| | - Saïdi M’Homa Soudja
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon (CRCL), INSERM U1052, CNRS UMR 5286, Centre Léon Bérard (CLB) and University of Lyon 1, Lyon, France
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10
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Tsao HW, Kaminski J, Kurachi M, Barnitz RA, DiIorio MA, LaFleur MW, Ise W, Kurosaki T, Wherry EJ, Haining WN, Yosef N. Batf-mediated epigenetic control of effector CD8 + T cell differentiation. Sci Immunol 2022; 7:eabi4919. [PMID: 35179948 DOI: 10.1126/sciimmunol.abi4919] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The response of naive CD8+ T cells to their cognate antigen involves rapid and broad changes to gene expression that are coupled with extensive chromatin remodeling, but the mechanisms governing these changes are not fully understood. Here, we investigated how these changes depend on the basic leucine zipper ATF-like transcription factor Batf, which is essential for the early phases of the process. Through genome scale profiling, we characterized the role of Batf in chromatin organization at several levels, including the accessibility of key regulatory regions, the expression of their nearby genes, and the interactions that these regions form with each other and with key transcription factors. We identified a core network of transcription factors that cooperated with Batf, including Irf4, Runx3, and T-bet, as indicated by their colocalization with Batf and their binding in regions whose accessibility, interactions, and expression of nearby genes depend on Batf. We demonstrated the synergistic activity of this network by overexpressing the different combinations of these genes in fibroblasts. Batf and Irf4, but not Batf alone, were sufficient to increase accessibility and transcription of key loci, normally associated with T cell function. Addition of Runx3 and T-bet further contributed to fine-tuning of these changes and was essential for establishing chromatin loops characteristic of T cells. These data provide a resource for studying the epigenomic and transcriptomic landscape of effector differentiation of cytotoxic T cells and for investigating the interdependency between transcription factors and its effects on the epigenome and transcriptome of primary cells.
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Affiliation(s)
- Hsiao-Wei Tsao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James Kaminski
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Makoto Kurachi
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - R Anthony Barnitz
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael A DiIorio
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martin W LaFleur
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.,Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Wataru Ise
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Pediatric Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, USA.,Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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11
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Wong WK, Yin B, Lam CYK, Huang Y, Yan J, Tan Z, Wong SHD. The Interplay Between Epigenetic Regulation and CD8 + T Cell Differentiation/Exhaustion for T Cell Immunotherapy. Front Cell Dev Biol 2022; 9:783227. [PMID: 35087832 PMCID: PMC8787221 DOI: 10.3389/fcell.2021.783227] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Effective immunotherapy treats cancers by eradicating tumourigenic cells by activated tumour antigen-specific and bystander CD8+ T-cells. However, T-cells can gradually lose cytotoxicity in the tumour microenvironment, known as exhaustion. Recently, DNA methylation, histone modification, and chromatin architecture have provided novel insights into epigenetic regulations of T-cell differentiation/exhaustion, thereby controlling the translational potential of the T-cells. Thus, developing strategies to govern epigenetic switches of T-cells dynamically is critical to maintaining the effector function of antigen-specific T-cells. In this mini-review, we 1) describe the correlation between epigenetic states and T cell phenotypes; 2) discuss the enzymatic factors and intracellular/extracellular microRNA imprinting T-cell epigenomes that drive T-cell exhaustion; 3) highlight recent advances in epigenetic interventions to rescue CD8+ T-cell functions from exhaustion. Finally, we express our perspective that regulating the interplay between epigenetic changes and transcriptional programs provides translational implications of current immunotherapy for cancer treatments.
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Affiliation(s)
- Wai Ki Wong
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Bohan Yin
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Ching Ying Katherine Lam
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Yingying Huang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Jiaxiang Yan
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Zhiwu Tan
- AIDS Institute and Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Siu Hong Dexter Wong
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
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12
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Ets1 Promotes the Differentiation of Post-Selected iNKT Cells through Regulation of the Expression of Vα14Jα18 T Cell Receptor and PLZF. Int J Mol Sci 2021; 22:ijms222212199. [PMID: 34830080 PMCID: PMC8621504 DOI: 10.3390/ijms222212199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/03/2021] [Accepted: 11/06/2021] [Indexed: 12/23/2022] Open
Abstract
The transcription factor Ets1 is essential for the development/differentiation of invariant Natural Killer T (iNKT) cells at multiple stages. However, its mechanisms of action and target genes in iNKT cells are still elusive. Here, we show that Ets1 is required for the optimal expression of the Vα14Jα18 T cell receptor (TCR) in post-selected thymic iNKT cells and their immediate differentiation. Ets1 is also critical for maintaining the peripheral homeostasis of iNKT cells, which is a role independent of the expression of the Vα14Jα18 TCR. Genome-wide transcriptomic analyses of post-selected iNKT cells further reveal that Ets1 controls leukocytes activation, proliferation differentiation, and leukocyte-mediated immunity. In addition, Ets1 regulates the expression of ICOS and PLZF in iNKT cells. More importantly, restoring the expression of PLZF and the Vα14Jα18 TCR partially rescues the differentiation of iNKT cells in the absence of Ets1. Taken together, our results establish a detailed molecular picture of how Ets1 regulates the stepwise differentiation of iNKT cells.
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13
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Mei D, Qi Y, Xia Y, Ma J, Hu H, Ai J, Chen L, Wu N, Liao D. Microarray profile analysis identifies ETS1 as potential biomarker regulated by miR-23b and modulates TCF4 in gastric cancer. World J Surg Oncol 2021; 19:311. [PMID: 34686186 PMCID: PMC8540102 DOI: 10.1186/s12957-021-02417-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/03/2021] [Indexed: 12/30/2022] Open
Abstract
Background Gastric cancer (GC), a common malignancy of the human digestive system, represents the second leading cause of cancer-related deaths worldwide. Early detection of GC has a significant impact on clinical outcomes. The aim of this study was to identify potential GC biomarkers. Methods In this study, we conducted a multi-step analysis of expression profiles in GC clinical samples downloaded from TCGA database to identify differentially expressed miRNAs (DEMs) and differentially expressed mRNAs (DEGs). Potential prognostic biomarkers from the available DEMs were then established using the Cox regression method. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to investigate the biological role of the predicted target genes of the miRNA biomarkers. Then, the prognostic DEM-mediated regulatory network was constructed based on transcription factor (TF)–miRNA–target interaction. Subsequently, the consensus genes were further determined based on the overlap between DEGs and these target genes of DEMs. Besides, expression profile, co-expression analysis, immunity, and prognostic values of these prognostic genes were also investigated to further explore the roles in the mechanism of GC tumorigenesis. Results We got five miRNAs, including miR-23b, miR-100, miR-143, miR-145, and miR-409, which are associated with the overall survival of GC patients. Subsequently, enrichment analysis of the target genes of the miRNA biomarkers shown that the GO biological process terms were mainly enriched in mRNA catabolic process, nuclear chromatin, and RNA binding. In addition, the KEGG pathways were significantly enriched in fatty acid metabolism, extracellular matrix (ECM) receptor interaction, and proteoglycans in cancer pathways. The transcriptional regulatory network consisting of 68 TFs, 4 DEMs, and 58 targets was constructed based on the interaction of TFs, miRNAs, and targets. The downstream gene ETS1 of miR-23b and TCF4 regulated by ETS1 were obtained by the regulatory network construction and co-expression analysis. High expression of ETS1 and TCF4 indicated poor prognosis in GC patients, particularly in the advanced stages. The expression of ETS1 and TCF4 was correlated with CD4+ T cells, CD8+ T cells, and B cells. Conclusions miR-23b, ETS1, and TCF4 were identified as the prognostic biomarkers. ETS1 and TCF4 had potential immune function in GC, which provided a theoretical basis for molecular-targeted combined immunotherapy in the future.
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Affiliation(s)
- Dinglian Mei
- The Department of Oncology, Beijing Mentougou District Hospital, Beijing, 102300, People's Republic of China
| | - Yalong Qi
- The Department of Oncology, Beijing Mentougou District Hospital, Beijing, 102300, People's Republic of China
| | - Yuanyuan Xia
- The Department of Oncology, Beijing Mentougou District Hospital, Beijing, 102300, People's Republic of China
| | - Jun Ma
- The Department of Oncology, Beijing Mentougou District Hospital, Beijing, 102300, People's Republic of China
| | - Hao Hu
- The Department of Oncology, Beijing Mentougou District Hospital, Beijing, 102300, People's Republic of China
| | - Jun Ai
- The Department of Oncology, Beijing Mentougou District Hospital, Beijing, 102300, People's Republic of China
| | - Liqiang Chen
- The Department of Oncology, Beijing Mentougou District Hospital, Beijing, 102300, People's Republic of China
| | - Ning Wu
- Department of Oncology, Shanghai Pudong New Area Gongli Hospital, Shanghai, 200135, People's Republic of China
| | - Daixiang Liao
- The Department of Oncology, Beijing Mentougou District Hospital, Beijing, 102300, People's Republic of China.
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14
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Itoh A, Adams D, Huang W, Wu Y, Kachapati K, Bednar KJ, Leung PSC, Zhang W, Flavell RA, Gershwin ME, Ridgway WM. Enoxacin Up-Regulates MicroRNA Biogenesis and Down-Regulates Cytotoxic CD8 T-Cell Function in Autoimmune Cholangitis. Hepatology 2021; 74:835-846. [PMID: 33462854 DOI: 10.1002/hep.31724] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/01/2020] [Accepted: 12/23/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS Primary biliary cholangitis (PBC) is a prototypical organ-specific autoimmune disease that is mediated by autoreactive T-cell attack and destruction of cholangiocytes. Despite the clear role of autoimmunity in PBC, immune-directed therapies have failed to halt PBC, including biologic therapies effective in other autoimmune diseases. MicroRNA (miRNA) dysregulation is implicated in the pathogenesis (PBC). In the dominant-negative TGF-β receptor type II (dnTGFβRII) mouse model of PBC, autoreactive CD8 T cells play a major pathogenic role and demonstrate a striking pattern of miRNA down-regulation. Enoxacin is a small molecule fluoroquinolone that enhances miRNA biogenesis, partly by stabilizing the interaction of transactivation response RNA-binding protein with Argonaute (Ago) 2. APPROACH AND RESULTS We hypothesized that correcting aberrant T-cell miRNA expression with enoxacin in dnTGFβRII mice could modulate autoreactive T-cell function and prevent PBC. Here, we show that liver-infiltrating dnTGFβRII CD8 T cells have significantly decreased levels of the miRNA biogenesis molecules prolyl 4-hydroxylase subunit alpha 1 (P4HA1) and Ago2 along with significantly increased levels of granzyme B and perforin. Enoxacin treatment significantly up-regulated miRNAs in dnTGFβRII CD8 T cells and effectively treated autoimmune cholangitis in dnTGFβRII mice. Enoxacin treatment directly altered T cells both ex vivo and in vitro, resulting in altered memory subset numbers, decreased proliferation, and decreased interferon-γ production. Enoxacin significantly decreased CD8 T-cell expression of the transcription factor, Runx3, and significantly decreased perforin expression at both the mRNA and protein levels. CONCLUSIONS Enoxacin increases miRNA expression in dnTGFβRII CD8 T cells, reduces CD8 T-cell pathogenicity, and effectively halted progression of autoimmune biliary disease. Targeting the miRNA pathway is a therapeutic approach to autoimmunity that corrects pathological miRNA abnormalities in autoreactive T cells.
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Affiliation(s)
- Arata Itoh
- Division of Immunology, Allergy and RheumatologyUniversity of Cincinnati College of MedicineCincinnatiOH
| | - David Adams
- Division of Immunology, Allergy and RheumatologyUniversity of Cincinnati College of MedicineCincinnatiOH
| | - Wenting Huang
- Division of Immunology, Allergy and RheumatologyUniversity of Cincinnati College of MedicineCincinnatiOH
| | - Yuehong Wu
- Division of Immunology, Allergy and RheumatologyUniversity of Cincinnati College of MedicineCincinnatiOH
| | - Kritika Kachapati
- Division of Immunology, Allergy and RheumatologyUniversity of Cincinnati College of MedicineCincinnatiOH
| | - Kyle J Bednar
- Division of Immunology, Allergy and RheumatologyUniversity of Cincinnati College of MedicineCincinnatiOH
| | - Patrick S C Leung
- Division of Rheumatology, Allergy and Clinical ImmunologyUniversity of California, DavisDavisCA
| | - Weici Zhang
- Division of Rheumatology, Allergy and Clinical ImmunologyUniversity of California, DavisDavisCA
| | - Richard A Flavell
- Department of Internal MedicineYale University School of MedicineNew HavenCT
| | - M Eric Gershwin
- Division of Rheumatology, Allergy and Clinical ImmunologyUniversity of California, DavisDavisCA
| | - William M Ridgway
- Division of Immunology, Allergy and RheumatologyUniversity of Cincinnati College of MedicineCincinnatiOH.,Division of Rheumatology, Allergy and Clinical ImmunologyUniversity of California, DavisDavisCA
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15
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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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16
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Dybska E, Adams AT, Duclaux-Loras R, Walkowiak J, Nowak JK. Waiting in the wings: RUNX3 reveals hidden depths of immune regulation with potential implications for inflammatory bowel disease. Scand J Immunol 2021; 93:e13025. [PMID: 33528856 DOI: 10.1111/sji.13025] [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: 09/12/2020] [Revised: 01/11/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Complex interactions between the environment and the mucosal immune system underlie inflammatory bowel disease (IBD). The involved cytokine signalling pathways are modulated by a number of transcription factors, one of which is runt-related transcription factor 3 (RUNX3). OBJECTIVE To systematically review the immune roles of RUNX3 in immune regulation, with a focus on the context of IBD. METHODS Relevant articles and reviews were identified through a Scopus search in April 2020. Information was categorized by immune cell types, analysed and synthesized. IBD transcriptome data sets and FANTOM5 regulatory networks were processed in order to complement the literature review. RESULTS The available evidence on the immune roles of RUNX3 allowed for its description in twelve cell types: intraepithelial lymphocyte, Th1, Th2, Th17, Treg, double-positive T, cytotoxic T, B, dendritic, innate lymphoid, natural killer and macrophages. In the gut, the activity of RUNX3 is multifaceted and context-dependent: it may promote homeostasis or exacerbated reactions via cytokine signalling and regulation of receptor expression. RUNX3 is mostly engaged in pathways involving ThPOK, T-bet, IFN-γ, TGF-β/IL-2Rβ, GATA/CBF-β, SMAD/p300 and a number of miRNAs. RUNX3 targets relevant to IBD may include RAG1, OSM and IL-17B. Moreover, in IBD RUNX3 expression correlates positively with GZMM, and negatively with IFNAR1, whereas in controls, it strongly associates with TGFBR3. CONCLUSIONS Dysregulation of RUNX3, mostly in the form of deficiency, likely contributes to IBD pathogenesis. More clinical research is needed to examine RUNX3 in IBD.
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Affiliation(s)
- Emilia Dybska
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Alex T Adams
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Rémi Duclaux-Loras
- INSERM U1111, Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Lyon, France
| | - Jarosław Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Jan K Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
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17
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Chopp LB, Gopalan V, Ciucci T, Ruchinskas A, Rae Z, Lagarde M, Gao Y, Li C, Bosticardo M, Pala F, Livak F, Kelly MC, Hannenhalli S, Bosselut R. An Integrated Epigenomic and Transcriptomic Map of Mouse and Human αβ T Cell Development. Immunity 2020; 53:1182-1201.e8. [PMID: 33242395 PMCID: PMC8641659 DOI: 10.1016/j.immuni.2020.10.024] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/25/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022]
Abstract
αβ lineage T cells, most of which are CD4+ or CD8+ and recognize MHC I- or MHC II-presented antigens, are essential for immune responses and develop from CD4+CD8+ thymocytes. The absence of in vitro models and the heterogeneity of αβ thymocytes have hampered analyses of their intrathymic differentiation. Here, combining single-cell RNA and ATAC (chromatin accessibility) sequencing, we identified mouse and human αβ thymocyte developmental trajectories. We demonstrated asymmetric emergence of CD4+ and CD8+ lineages, matched differentiation programs of agonist-signaled cells to their MHC specificity, and identified correspondences between mouse and human transcriptomic and epigenomic patterns. Through computational analysis of single-cell data and binding sites for the CD4+-lineage transcription factor Thpok, we inferred transcriptional networks associated with CD4+- or CD8+-lineage differentiation, and with expression of Thpok or of the CD8+-lineage factor Runx3. Our findings provide insight into the mechanisms of CD4+ and CD8+ T cell differentiation and a foundation for mechanistic investigations of αβ T cell development.
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Affiliation(s)
- Laura B Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Immunology Graduate Group, University of Pennsylvania Medical School, Philadelphia, PA, USA
| | - Vishaka Gopalan
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Ciucci
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison Ruchinskas
- Cancer Research Technology Program, Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Zachary Rae
- Cancer Research Technology Program, Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Manon Lagarde
- 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
| | - Caiyi Li
- Laboratory of Genomic Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ferenc Livak
- Laboratory of Genomic Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael C Kelly
- Cancer Research Technology Program, Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, 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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18
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Insights into Thymus Development and Viral Thymic Infections. Viruses 2019; 11:v11090836. [PMID: 31505755 PMCID: PMC6784209 DOI: 10.3390/v11090836] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/16/2022] Open
Abstract
T-cell development in the thymus is a complex and highly regulated process, involving a wide variety of cells and molecules which orchestrate thymocyte maturation into either CD4+ or CD8+ single-positive (SP) T cells. Here, we briefly review the process regulating T-cell differentiation, which includes the latest advances in this field. In particular, we highlight how, starting from a pool of hematopoietic stem cells in the bone marrow, the sequential action of transcriptional factors and cytokines dictates the proliferation, restriction of lineage potential, T-cell antigen receptors (TCR) gene rearrangements, and selection events on the T-cell progenitors, ultimately leading to the generation of mature T cells. Moreover, this review discusses paradigmatic examples of viral infections affecting the thymus that, by inducing functional changes within this lymphoid gland, consequently influence the behavior of peripheral mature T-lymphocytes.
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19
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Ran D, Cai M, Zhang X. Genetics of psoriasis: a basis for precision medicine. PRECISION CLINICAL MEDICINE 2019; 2:120-130. [PMID: 35693758 PMCID: PMC9026189 DOI: 10.1093/pcmedi/pbz011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/25/2019] [Accepted: 05/29/2019] [Indexed: 12/24/2022] Open
Abstract
Psoriasis is an inflammatory skin disease with a background of polygenic inheritance.
Both environmental and genetic factors are involved in the etiology of the disease. In the
last two decades, numerous studies have been conducted through linkage analysis,
genome-wide association study (GWAS), and direct sequencing to explore the role of genetic
variation in disease pathogenesis and progression. To date, >80 psoriasis
susceptibility genes have been identified, including HLA-Cw6,
IL12B, IL23R, and LCE3B/3C. Some
genetic markers have been applied in disease prediction, clinical diagnosis, treatment,
and new drug development, which could further explain the pathogenesis of psoriasis and
promote the development of precision medicine. This review summarizes related research on
genetic variation in psoriasis and explores implications of the findings in clinical
application and the promotion of a personalized medicine project.
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Affiliation(s)
- Delin Ran
- Institute of Dermatology and Department of Dermatology of the First Affiliated Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Minglong Cai
- Institute of Dermatology and Department of Dermatology of the First Affiliated Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology of the First Affiliated Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
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20
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Tian S, Huang P, Gu Y, Yang J, Wu R, Zhao J, Liu AJ, Zhang W. Systems Biology Analysis of the Effect and Mechanism of Qi-Jing-Sheng-Bai Granule on Leucopenia in Mice. Front Pharmacol 2019; 10:408. [PMID: 31105563 PMCID: PMC6494967 DOI: 10.3389/fphar.2019.00408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/01/2019] [Indexed: 12/23/2022] Open
Abstract
Qi-Jing-Sheng-Bai granule (QJSB) is a newly developed traditional Chinese medicine (TCM) formula. Clinically, it has been used for the treatment of leucopenia. However, its pharmacological mechanism needs more investigation. In this study, we firstly tested the effects of QJSB on leucopenia using mice induced by cyclophosphamide. Our results suggested that QJSB significantly raised the number of peripheral white blood cells, platelets and nucleated bone marrow cells. Additionally, it markedly enhanced the cell viability and promoted the colony formation of bone marrow mononuclear cells. Furthermore, it reversed the serum cytokines IL-6 and G-CSF disorders. Then, using transcriptomics datasets and metabonomic datasets, we integrated transcriptomics-based network pharmacology and metabolomics technologies to investigate the mechanism of action of QJSB. We found that QJSB regulated a series of biological processes such as hematopoietic cell lineage, homeostasis of number of cells, lymphocyte differentiation, metabolic processes (including lipid, amino acid, and nucleotide metabolism), B cell receptor signaling pathway, T cell activation and NOD-like receptor signaling pathway. In a summary, QJSB has protective effects to leucopenia in mice probably through accelerating cell proliferation and differentiation, regulating metabolism response pathways and modulating immunologic function at a system level.
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Affiliation(s)
- Saisai Tian
- School of Pharmacy, The Second Military Medical University, Shanghai, China
| | - Pengli Huang
- Institute of Interdisciplinary Complex Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yu Gu
- Institute of Interdisciplinary Complex Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jian Yang
- School of Pharmacy, The Second Military Medical University, Shanghai, China
| | - Ran Wu
- Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Jing Zhao
- Institute of Interdisciplinary Complex Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ai-Jun Liu
- School of Pharmacy, The Second Military Medical University, Shanghai, China.,Department of Pharmacy, Shanghai Pulmonary Hospital, Shanghai, China
| | - Weidong Zhang
- School of Pharmacy, The Second Military Medical University, Shanghai, China.,Institute of Interdisciplinary Complex Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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21
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Liquitaya-Montiel AJ, Mendoza L. Dynamical Analysis of the Regulatory Network Controlling Natural Killer Cells Differentiation. Front Physiol 2018; 9:1029. [PMID: 30116200 PMCID: PMC6082967 DOI: 10.3389/fphys.2018.01029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/11/2018] [Indexed: 12/22/2022] Open
Abstract
Many disease fighting strategies have focused on the generation of NK cells, since they constitute the main immune barrier against cancer and intracellular pathogens such as viruses. Therefore, a predictive model for the development of NK cells would constitute a useful tool to test several hypotheses regarding the production of these cells during both physiological and pathological conditions. Here, we present a boolean network model that reproduces experimental results reported on the literature regarding the progressive stages of the development of NK cells in wild-type and mutant backgrounds. The model allows for the simulation of different conditions, including extracellular micro-environment as well as the simulation of genetic alterations. It also describes how NK cell differentiation depends on a molecular regulatory network that controls the specification of lymphoid lineages, such as T and B cells, which share a common progenitor with NKs. Furthermore, the study shows that the structure of the regulatory network strongly determines the stability of the expression patterns against perturbations.
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Affiliation(s)
- Adhemar J. Liquitaya-Montiel
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Programa de Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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22
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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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23
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Prinz JC. Autoimmune aspects of psoriasis: Heritability and autoantigens. Autoimmun Rev 2017; 16:970-979. [PMID: 28705779 DOI: 10.1016/j.autrev.2017.07.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 06/10/2017] [Indexed: 12/28/2022]
Abstract
Chronic immune-mediated disorders (IMDs) constitute a major health burden. Understanding IMD pathogenesis is facing two major constraints: Missing heritability explaining familial clustering, and missing autoantigens. Pinpointing IMD risk genes and autoimmune targets, however, is of fundamental importance for developing novel causal therapies. The strongest association of all IMDs is seen with human leukocyte antigen (HLA) alleles. Using psoriasis as an IMD model this article reviews the pathogenic role HLA molecules may have within the polygenic predisposition of IMDs. It concludes that disease-associated HLA alleles account for both missing heritability and autoimmune mechanisms by facilitating tissue-specific autoimmune responses through autoantigen presentation.
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Affiliation(s)
- Jörg Christoph Prinz
- Department of Dermatology, University Clinics, Ludwig-Maximilian-University of Munich, Munich, Germany.
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24
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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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25
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Cauchy P, Maqbool MA, Zacarias-Cabeza J, Vanhille L, Koch F, Fenouil R, Gut M, Gut I, Santana MA, Griffon A, Imbert J, Moraes-Cabé C, Bories JC, Ferrier P, Spicuglia S, Andrau JC. Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation. Nucleic Acids Res 2015; 44:3567-85. [PMID: 26673693 PMCID: PMC4856961 DOI: 10.1093/nar/gkv1475] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/03/2015] [Indexed: 12/20/2022] Open
Abstract
Ets1 is a sequence-specific transcription factor that plays an important role during hematopoiesis, and is essential for the transition of CD4−/CD8− double negative (DN) to CD4+/CD8+ double positive (DP) thymocytes. Using genome-wide and functional approaches, we investigated the binding properties, transcriptional role and chromatin environment of Ets1 during this transition. We found that while Ets1 binding at distal sites was associated with active genes at both DN and DP stages, its enhancer activity was attained at the DP stage, as reflected by levels of the core transcriptional hallmarks H3K4me1/3, RNA Polymerase II and eRNA. This dual, stage-specific ability reflected a switch from non-T hematopoietic toward T-cell specific gene expression programs during the DN-to-DP transition, as indicated by transcriptome analyses of Ets1−/− thymic cells. Coincidentally, Ets1 associates more specifically with Runx1 in DN and with TCF1 in DP cells. We also provide evidence that Ets1 predominantly binds distal nucleosome-occupied regions in DN and nucleosome-depleted regions in DP. Finally and importantly, we demonstrate that Ets1 induces chromatin remodeling by displacing H3K4me1-marked nucleosomes. Our results thus provide an original model whereby the ability of a transcription factor to bind nucleosomal DNA changes during differentiation with consequences on its cognate enhancer activity.
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Affiliation(s)
- Pierre Cauchy
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Muhammad A Maqbool
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919 Route de Mende, Montpellier F-34293, France
| | - Joaquin Zacarias-Cabeza
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Laurent Vanhille
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Frederic Koch
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Romain Fenouil
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Marta Gut
- Centre Nacional D'Anàlisi Genòmica, Parc Científic de Barcelona, Baldiri i Reixac 4, Barcelona ES-08028, Spain
| | - Ivo Gut
- Centre Nacional D'Anàlisi Genòmica, Parc Científic de Barcelona, Baldiri i Reixac 4, Barcelona ES-08028, Spain
| | - Maria A Santana
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Aurélien Griffon
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Jean Imbert
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Carolina Moraes-Cabé
- INSERM UMR 1126 Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris F-75475, France
| | - Jean-Christophe Bories
- INSERM UMR 1126 Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris F-75475, France
| | - Pierre Ferrier
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Salvatore Spicuglia
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919 Route de Mende, Montpellier F-34293, France
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Riaz T, Sollid LM, Olsen I, de Souza GA. Quantitative Proteomics of Gut-Derived Th1 and Th1/Th17 Clones Reveal the Presence of CD28+ NKG2D- Th1 Cytotoxic CD4+ T cells. Mol Cell Proteomics 2015; 15:1007-16. [PMID: 26637539 DOI: 10.1074/mcp.m115.050138] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Indexed: 12/13/2022] Open
Abstract
T-helper cells are differentiated from CD4+ T cells and are traditionally characterized by inflammatory or immunosuppressive responses in contrast to cytotoxic CD8+ T cells. Mass-spectrometry studies on T-helper cells are rare. In this study, we aimed to identify the proteomes of human Th1 and Th1/Th17 clones derived from intestinal biopsies of Crohn's disease patients and to identify differentially expressed proteins between the two phenotypes. Crohn's disease is an inflammatory bowel disease, with predominantly Th1- and Th17-mediated response where cells of the "mixed" phenotype Th1/Th17 have also been commonly found. High-resolution mass spectrometry was used for protein identification and quantitation. In total, we identified 7401 proteins from Th1 and Th1/Th17 clones, where 334 proteins were differentially expressed. Major differences were observed in cytotoxic proteins that were overrepresented in the Th1 clones. The findings were validated by flow cytometry analyses using staining with anti-granzyme B and anti-perforin and by a degranulation assay, confirming higher cytotoxic features of Th1 compared with Th1/Th17 clones. By testing a larger panel of T-helper cell clones from seven different Crohn's disease patients, we concluded that only a subgroup of the Th1 cell clones had cytotoxic features, and these expressed the surface markers T-cell-specific surface glycoprotein CD28 and were negative for expression of natural killer group 2 member D.
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Affiliation(s)
- Tahira Riaz
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway;
| | - Ludvig Magne Sollid
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
| | - Ingrid Olsen
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway; Section for Immunology, Norwegian Veterinary Institute, Ullevaalsveien 68, 0454 Oslo, Norway
| | - Gustavo Antonio de Souza
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
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Liu M, Gao W, van Velkinburgh JC, Wu Y, Ni B, Tian Y. Role of Ets Proteins in Development, Differentiation, and Function of T-Cell Subsets. Med Res Rev 2015; 36:193-220. [PMID: 26301869 DOI: 10.1002/med.21361] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 07/12/2015] [Accepted: 07/23/2015] [Indexed: 12/18/2022]
Abstract
Through positive selection, double-positive cells in the thymus differentiate into CD4(+) or CD8(+) T single-positive cells that subsequently develop into different types of effective T cells, such as T-helper and cytotoxic T lymphocyte cells, that play distinctive roles in the immune system. Development, differentiation, and function of thymocytes and CD4(+) and CD8(+) T cells are controlled by a multitude of secreted and intracellular factors, ranging from cytokine signaling modules to transcription factors and epigenetic modifiers. Members of the E26 transformation specific (Ets) family of transcription factors, in particular, are potent regulators of these CD4(+) or CD8(+) T-cell processes. In this review, we summarize and discuss the functions and underlying mechanisms of the Ets family members that have been characterized as involved in these processes. Ongoing research of these factors is expected to identify practical applications for the Ets family members as novel therapeutic targets for inflammation-related diseases.
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Affiliation(s)
- Mian Liu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China.,Battalion 10 of Cadet Brigade, Third Military Medical University, Chongqing, 400038, P.R. China
| | - Weiwu Gao
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
| | | | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
| | - Bing Ni
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
| | - Yi Tian
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
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28
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O'Rielly DD, Rahman P. Genetic, Epigenetic and Pharmacogenetic Aspects of Psoriasis and Psoriatic Arthritis. Rheum Dis Clin North Am 2015; 41:623-42. [PMID: 26476223 DOI: 10.1016/j.rdc.2015.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There is a strong familial component to psoriatic disease as well as a complex array of genetic, immunologic, and environmental factors. The dominant genetic effect is located on chromosome 6p21.3 within the major histocompatibility complex region, accounting for one-third of genetic contribution. Genome-wide association studies (GWAS) identified additional genes, including skin barrier function, innate immune response, and adaptive immune response genes. To better understand disease susceptibility and progression requires replication in larger cohorts, fine-mapping efforts, new technologies, and functional studies of genetic variants, gene-gene interactions and gene-environmental interactions. New technologies available include next-generation sequencing, copy number variation analysis, and epigenetics.
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Affiliation(s)
- Darren D O'Rielly
- Faculty of Medicine, Health Sciences Centre, Memorial University of Newfoundland, 300 Prince Philip Drive, Room 1J440, St. John's, Newfoundland and Labrador A1B 3V6, Canada
| | - Proton Rahman
- St. Clare's Mercy Hospital, Memorial University of Newfoundland, 154 Le Marchant Road, St. John's, Newfoundland and Labrador A1C 5B8, Canada.
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Maccani JZ, Maccani MA. Altered placental DNA methylation patterns associated with maternal smoking: current perspectives. ADVANCES IN GENOMICS AND GENETICS 2015; 2015:205-214. [PMID: 26203295 PMCID: PMC4507353 DOI: 10.2147/agg.s61518] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The developmental origins of health and disease hypothesis states that adverse early life exposures can have lasting, detrimental effects on lifelong health. Exposure to maternal cigarette smoking during pregnancy is associated with morbidity and mortality in offspring, including increased risks for miscarriage, stillbirth, low birth weight, preterm birth, asthma, obesity, altered neurobehavior, and other conditions. Maternal cigarette smoking during pregnancy interferes with placental growth and functioning, and it has been proposed that this may occur through the disruption of normal and necessary placental epigenetic patterns. Epigenome-wide association studies have identified a number of differentially methylated placental genes that are associated with maternal smoking during pregnancy, including RUNX3, PURA, GTF2H2, GCA, GPR135, and HKR1. The placental methylation status of RUNX3 and NR3C1 has also been linked to adverse infant outcomes, including preterm birth and low birth weight, respectively. Candidate gene analyses have also found maternal smoking-associated placental methylation differences in the NR3C1, CYP1A1, HTR2A, and HSD11B2 genes, as well as in the repetitive elements LINE-1 and AluYb8. The differential methylation patterns of several genes have been confirmed to also exhibit altered gene expression patterns, including CYP1A1, CYP19A1, NR3C1, and HTR2A. Placental methylation patterns associated with maternal smoking during pregnancy may be largely gene-specific and tissue-specific and, to a lesser degree, involve global changes. It is important for future research to investigate the mechanistic roles that these differentially methylated genes may play in mediating the association between maternal smoking during pregnancy and disease in later life, as well as to elucidate the potential influence of emerging tobacco product use during pregnancy, including the use of electronic cigarettes, on placental epigenetics.
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Affiliation(s)
- Jennifer Zj Maccani
- Penn State Tobacco Center of Regulatory Science, College of Medicine, Department of Public Health Sciences, Hershey, PA, USA
| | - Matthew A Maccani
- Penn State Tobacco Center of Regulatory Science, College of Medicine, Department of Public Health Sciences, Hershey, PA, USA
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30
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Guerrero AD, Dong MB, Zhao Y, Lau-Kilby A, Tarbell KV. Interleukin-2-mediated inhibition of dendritic cell development correlates with decreased CD135 expression and increased monocyte/macrophage precursors. Immunology 2015; 143:640-50. [PMID: 24954893 DOI: 10.1111/imm.12345] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 06/06/2014] [Accepted: 06/18/2014] [Indexed: 11/27/2022] Open
Abstract
We have previously shown that interleukin-2 (IL-2) inhibits dendritic cell (DC) development from mouse bone marrow (BM) precursors stimulated with the ligand for FMS-like tyrosine kinase 3 receptor (Flt3L), and have provided evidence that this inhibition occurs at the monocyte DC precursor stage of DC development. Here, we explored the mechanism of IL-2-mediated inhibition of DC development. First, we showed that these in vitro cultures accurately model DCs that develop in vivo by comparing gene and protein expression of the three main Flt3L-induced DC subsets from the BM, CD11b(+) and CD24(+) conventional DCs (cDCs) and plasmacytoid DCs (pDCs) with their respective ex vivo spleen DC subsets (CD11b(+), CD8(+) and pDCs). Next, gene expression changes were quantified in Flt3L DC subsets that developed in the presence of IL-2. These changes included increased expression of Bcl2l11, which encodes the apoptosis-inducing protein Bim, and decreased expression of Flt3 (CD135), the receptor that initiates DC development. Interleukin-2 also significantly reduced Flt3 protein expression on all three Flt3L DC subsets, and attenuated Flt3L-induced STAT3 phosphorylation in DCs. Based on these data, we hypothesized that decreased Flt3 signalling may divert BM precursors down monocyte and macrophage lineages. Indeed, addition of IL-2 led to increases in Flt3(-) cells, including cKit(+) Ly6C(+) CD11b(-) populations consistent with the recently identified committed monocyte/macrophage progenitor. Therefore, IL-2 can inhibit DC development via decreased signalling through Flt3 and increased monocyte/macrophage development.
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Affiliation(s)
- Alan D Guerrero
- Immune Tolerance Section, Diabetes, Endocrinology and Obesity Branch, National Institute of Diabetes, and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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The CD4/CD8 lineages: central decisions and peripheral modifications for T lymphocytes. Curr Top Microbiol Immunol 2014; 373:113-29. [PMID: 23612990 DOI: 10.1007/82_2013_323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
CD4(+) helper and CD8(+) cytotoxic T cells, two major subsets of αβTCR expressing lymphocytes, are differentiated from common precursor CD4(+)CD8(+) double-positive (DP) thymocytes. Bifurcation of the CD4(+)/CD8(+) lineages in the thymus is a multilayered process and is thought to culminate in a loss of developmental plasticity between these functional subsets. Advances in the last decade have deepened our understanding of the transcription control mechanisms governing CD4 versus CD8 lineage commitment. Reciprocal expression and antagonistic interplay between two transcription factors, ThPOK and Runx3, is crucial for driving thymocyte decisions between these two cell fates. Here, we first focus on the regulation of ThPOK expression and its role in directing helper T cell development. We then discuss a novel aspect of the ThPOK/Runx3 axis in modifying CD4(+) T cell function upon exposure to gut microenvironment.
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Abstract
Spondyloarthritis (SpA) is a group of inflammatory rheumatic diseases whose main clinical feature is inflammation of the axial spine. Articular, periarticular, and extra-articular manifestations can also occur, depending on the type of spondyloarthritis. The most common clinical subsets of SpA are ankylosing spondylitis (AS) and psoriatic arthritis (PsA). SpA is a major health challenge given the propensity to affect young adults and the potential requirement for lifelong treatment. Although the precise etiology of SpA is unknown, there is mounting evidence that these diseases are a result of complex interplay of genetic, environmental, and immunological factors. In this review on SpA, we will discuss genetic variants with genome-wide significance, highlight potential clinical application of genetic variants, and discuss challenges in further elucidating the genetic basis of SpA.
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NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers. Proc Natl Acad Sci U S A 2013; 111:705-10. [PMID: 24374627 DOI: 10.1073/pnas.1315023111] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The main oncogenic driver in T-lymphoblastic leukemia is NOTCH1, which activates genes by forming chromatin-associated Notch transcription complexes. Gamma-secretase-inhibitor treatment prevents NOTCH1 nuclear localization, but most genes with NOTCH1-binding sites are insensitive to gamma-secretase inhibitors. Here, we demonstrate that fewer than 10% of NOTCH1-binding sites show dynamic changes in NOTCH1 occupancy when T-lymphoblastic leukemia cells are toggled between the Notch-on and -off states with gamma-secretase inhibiters. Dynamic NOTCH1 sites are functional, being highly associated with Notch target genes, are located mainly in distal enhancers, and frequently overlap with RUNX1 binding. In line with the latter association, we show that expression of IL7R, a gene with key roles in normal T-cell development and in T-lymphoblastic leukemia, is coordinately regulated by Runx factors and dynamic NOTCH1 binding to distal enhancers. Like IL7R, most Notch target genes and associated dynamic NOTCH1-binding sites cooccupy chromatin domains defined by constitutive binding of CCCTC binding factor, which appears to restrict the regulatory potential of dynamic NOTCH1 sites. More remarkably, the majority of dynamic NOTCH1 sites lie in superenhancers, distal elements with exceptionally broad and high levels of H3K27ac. Changes in Notch occupancy produces dynamic alterations in H3K27ac levels across the entire breadth of superenhancers and in the promoters of Notch target genes. These findings link regulation of superenhancer function to NOTCH1, a master regulatory factor and potent oncoprotein in the context of immature T cells, and delineate a generally applicable roadmap for identifying functional Notch sites in cellular genomes.
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Maccani JZJ, Koestler DC, Houseman EA, Marsit CJ, Kelsey KT. Placental DNA methylation alterations associated with maternal tobacco smoking at the RUNX3 gene are also associated with gestational age. Epigenomics 2013; 5:619-30. [PMID: 24283877 PMCID: PMC3982305 DOI: 10.2217/epi.13.63] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
AIMS The developmental origins of health and disease hypothesis states that later-life disease may be influenced by the quality of the in utero environment. Environmental toxicants can have detrimental effects on fetal development, potentially through effects on placental development and function. Maternal smoking during pregnancy is associated with low birth weight, preterm birth and other complications, and exposure to cigarette smoke in utero has been linked to gross pathologic and molecular changes to the placenta, including differential DNA methylation in placental tissue. The aim of this study was to investigate the relationship between maternal smoking during pregnancy, methylation changes in the placenta and gestational age. MATERIALS & METHODS We used Illumina(®)'s (CA, USA) Human Methylation27 BeadChip technology platform to investigate the methylation status of 21,551 autosomal, non-SNP-associated CpG loci in DNA extracted from 206 human placentas and examined loci whose variation in methylation was associated with maternal smoking during pregnancy. RESULTS We found that methylation patterns of a number of loci within the RUNX3 gene were significantly associated with smoking during pregnancy, and one of these loci was associated with decreased gestational age (p = 0.04). CONCLUSION Our findings, demonstrating maternal smoking-induced changes in DNA methylation at specific loci, suggest a mechanism by which in utero tobacco smoke exposure could exert its detrimental effects upon the health of the fetus.
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Affiliation(s)
- Jennifer ZJ Maccani
- Department of Pathology & Laboratory Medicine, Brown University, Providence, RI, USA
| | - Devin C Koestler
- Section of Biostatistics & Epidemiology, Department of Community & Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | | | - Carmen J Marsit
- Section of Biostatistics & Epidemiology, Department of Community & Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Pharmacology & Toxicology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Karl T Kelsey
- Department of Pathology & Laboratory Medicine, Brown University, Providence, RI, USA
- Department of Epidemiology, Brown University, Providence, RI, USA
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Lotem J, Levanon D, Negreanu V, Leshkowitz D, Friedlander G, Groner Y. Runx3-mediated transcriptional program in cytotoxic lymphocytes. PLoS One 2013; 8:e80467. [PMID: 24236182 PMCID: PMC3827420 DOI: 10.1371/journal.pone.0080467] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 10/02/2013] [Indexed: 12/03/2022] Open
Abstract
The transcription factor Runx3 is highly expressed in CD8+ T and NK cytotoxic lymphocytes and is required for their effective activation and proliferation but molecular insights into the transcription program regulated by Runx3 in these cells are still missing. Using Runx3-ChIP-seq and transcriptome analysis of wild type vs. Runx3-/- primary cells we have now identified Runx3-regulated genes in the two cell types at both resting and IL-2-activated states. Runx3-bound genomic regions in both cell types were distantly located relative to gene transcription start sites and were enriched for RUNX and ETS motifs. Bound genomic regions significantly overlapped T-bet and p300-bound enhancer regions in Runx3-expressing Th1 helper cells. Compared to resting cells, IL-2-activated CD8+ T and NK cells contain three times more Runx3-regulated genes that are common to both cell types. Functional annotation of shared CD8+ T and NK Runx3-regulated genes revealed enrichment for immune-associated terms including lymphocyte activation, proliferation, cytotoxicity, migration and cytokine production, highlighting the role of Runx3 in CD8+ T and NK activated cells.
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MESH Headings
- Animals
- Core Binding Factor Alpha 3 Subunit/genetics
- Enhancer Elements, Genetic
- Gene Expression Profiling
- Gene Expression Regulation/drug effects
- Histones/metabolism
- Interleukin-2/metabolism
- Interleukin-2/pharmacology
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lymphocyte Activation/genetics
- Lymphocyte Activation/immunology
- Mice
- Mice, Knockout
- Nucleotide Motifs
- Position-Specific Scoring Matrices
- Protein Binding
- Resting Phase, Cell Cycle/genetics
- T-Lymphocytes, Cytotoxic/drug effects
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Transcription Factor AP-1/metabolism
- Transcription Initiation Site
- Transcription, Genetic
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Affiliation(s)
- Joseph Lotem
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ditsa Levanon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Varda Negreanu
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dena Leshkowitz
- Israel National Center for Personalized Medicine Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Gilgi Friedlander
- Israel National Center for Personalized Medicine Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Yoram Groner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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NFAT5 induction by the pre-T-cell receptor serves as a selective survival signal in T-lymphocyte development. Proc Natl Acad Sci U S A 2013; 110:16091-6. [PMID: 24043824 DOI: 10.1073/pnas.1215934110] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Rel-like transcription factors nuclear factor kappa B (NF-κB) and the calcineurin-dependent nuclear factor of activated T cells (NFATc) control specific points of thymocyte maturation. Thymocytes also express a distinct member of the Rel family, the calcineurin-independent, osmostress response regulator NFAT5. Here we show that IKKβ regulates the expression of NFAT5 in thymocytes, which in turn contributes to the survival of T-cell receptor αβ thymocytes and the transition from the β-selection checkpoint to the double-positive stage in an osmostress-independent manner. NFAT5-deficient thymocytes had normal expression and proximal signaling of the pre-T-cell receptor but exhibited a partial defect in β-chain allelic exclusion and increased apoptosis. Further analysis showed that NFAT5 regulated the expression of the prosurvival factors A1 and Bcl2 and attenuated the proapoptotic p53/Noxa axis. These findings position NFAT5 as a target of the IKKβ/NF-κB pathway in thymocytes and as a downstream effector of the prosurvival role of the pre-T-cell receptor.
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Xiong Y, Castro E, Yagi R, Zhu J, Lesourne R, Love PE, Feigenbaum L, Bosselut R. Thpok-independent repression of Runx3 by Gata3 during CD4+ T-cell differentiation in the thymus. Eur J Immunol 2013; 43:918-28. [PMID: 23310955 DOI: 10.1002/eji.201242944] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 11/27/2012] [Accepted: 01/07/2013] [Indexed: 11/06/2022]
Abstract
CD4(+) helper T cells are essential for immune responses and differentiate in the thymus from CD4(+) CD8(+) "double-positive" (DP) thymocytes. The transcription factor Runx3 inhibits CD4(+) T-cell differentiation by repressing Cd4 gene expression; accordingly, Runx3 is not expressed in DP thymocytes or developing CD4(+) T cells. The transcription factor Thpok is upregulated in CD4-differentiating thymocytes and required to repress Runx3. However, how Runx3 is controlled at early stages of CD4(+) T-cell differentiation, before the onset of Thpok expression, remains unknown. Here we show that Gata3, a transcription factor preferentially and transiently upregulated by CD4(+) T-cell precursors, represses Runx3 and binds the Runx3 locus in vivo. Accordingly, we show that high-level Gata3 expression and expression of Runx3 are mutually exclusive. Furthermore, whereas Runx3 represses Cd4, we show that Gata3 promotes Cd4 expression in Thpok-deficient thymocytes. Thus, in addition to its previously documented role in promoting CD4-lineage gene-expression, Gata3 represses CD8-lineage gene expression. These findings identify Gata3 as a critical pivot of CD4-CD8 lineage differentiation.
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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 20892-4259, MD, USA
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Review of Ets1 structure, function, and roles in immunity. Cell Mol Life Sci 2013; 70:3375-90. [PMID: 23288305 DOI: 10.1007/s00018-012-1243-7] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 11/20/2012] [Accepted: 12/11/2012] [Indexed: 10/27/2022]
Abstract
The Ets1 transcription factor is a member of the Ets gene family and is highly conserved throughout evolution. Ets1 is known to regulate a number of important biological processes in normal cells and in tumors. In particular, Ets1 has been associated with regulation of immune cell function and with an aggressive behavior in tumors that express it at high levels. Here we review and summarize the general features of Ets1 and describe its roles in immunity and autoimmunity, with a focus on its roles in B lymphocytes. We also review evidence that suggests that Ets1 may play a role in malignant transformation of hematopoietic malignancies including B cell malignancies.
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40
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Ma D, Wei Y, Liu F. Regulatory mechanisms of thymus and T cell development. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 39:91-102. [PMID: 22227346 DOI: 10.1016/j.dci.2011.12.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 12/22/2011] [Accepted: 12/22/2011] [Indexed: 05/31/2023]
Abstract
The thymus is a central hematopoietic organ which produces mature T lymphocytes with diverse antigen specificity. During development, the thymus primordium is derived from the third pharyngeal endodermal pouch, and then differentiates into cortical and medullary thymic epithelial cells (TECs). TECs represent the primary functional cell type that forms the unique thymic epithelial microenvironment which is essential for intrathymic T-cell development, including positive selection, negative selection and emigration out of the thymus. Our understanding of thymopoiesis has been greatly advanced by using several important animal models. This review will describe progress on the molecular mechanisms involved in thymus and T cell development with particular focus on the signaling and transcription factors involved in this process in mouse and zebrafish.
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Affiliation(s)
- Dongyuan Ma
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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41
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Tsoi LC, Spain SL, Knight J, Ellinghaus E, Stuart PE, Capon F, Ding J, Li Y, Tejasvi T, Gudjonsson JE, Kang HM, Allen MH, McManus R, Novelli G, Samuelsson L, Schalkwijk J, Ståhle M, Burden AD, Smith CH, Cork MJ, Estivill X, Bowcock AM, Krueger GG, Weger W, Worthington J, Tazi-Ahnini R, Nestle FO, Hayday A, Hoffmann P, Winkelmann J, Wijmenga C, Langford C, Edkins S, Andrews R, Blackburn H, Strange A, Band G, Pearson RD, Vukcevic D, Spencer CCA, Deloukas P, Mrowietz U, Schreiber S, Weidinger S, Koks S, Kingo K, Esko T, Metspalu A, Lim HW, Voorhees JJ, Weichenthal M, Wichmann HE, Chandran V, Rosen CF, Rahman P, Gladman DD, Griffiths CEM, Reis A, Kere J, Nair RP, Franke A, Barker JNWN, Abecasis GR, Elder JT, Trembath RC. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity. Nat Genet 2012; 44:1341-8. [PMID: 23143594 PMCID: PMC3510312 DOI: 10.1038/ng.2467] [Citation(s) in RCA: 741] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 10/17/2012] [Indexed: 02/08/2023]
Abstract
To gain further insight into the genetic architecture of psoriasis, we conducted a meta-analysis of 3 genome-wide association studies (GWAS) and 2 independent data sets genotyped on the Immunochip, including 10,588 cases and 22,806 controls. We identified 15 new susceptibility loci, increasing to 36 the number associated with psoriasis in European individuals. We also identified, using conditional analyses, five independent signals within previously known loci. The newly identified loci shared with other autoimmune diseases include candidate genes with roles in regulating T-cell function (such as RUNX3, TAGAP and STAT3). Notably, they included candidate genes whose products are involved in innate host defense, including interferon-mediated antiviral responses (DDX58), macrophage activation (ZC3H12C) and nuclear factor (NF)-κB signaling (CARD14 and CARM1). These results portend a better understanding of shared and distinctive genetic determinants of immune-mediated inflammatory disorders and emphasize the importance of the skin in innate and acquired host defense.
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Affiliation(s)
- Lam C Tsoi
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Jo Knight
- Neuroscience Research, Centre for Addiction and Mental Health, Toronto, ON, Canada M5T 1R8
- National Institute for Health Research (NIHR), Biomedical Research Centre, Guy’s and St. Thomas’ NHS Foundation Trust
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Capon
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Jun Ding
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Yanming Li
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Hyun M Kang
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Michael H Allen
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Ross McManus
- Department of Clinical Medicine Trinity College Dublin, Ireland
- Institute of Molecular Medicine, Trinity College Dublin, Ireland
| | - Giuseppe Novelli
- National Agency for Evaluation of Universities and Research Institutes (ANVUR)
- Research Center San Pietro Hospital, Rome, Italy
| | - Lena Samuelsson
- Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Joost Schalkwijk
- Department of Dermatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Mona Ståhle
- Dermatology Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Catherine H Smith
- St John’s Institute of Dermatology, King’s College London, London, UK
| | - Michael J Cork
- Academic Unit of Dermatology Research, Department of Infection and Immunity, The University of Sheffield, Sheffield, UK
| | - Xavier Estivill
- Genes and Disease Programme, Centre for Genomic Regulation (CRG) and UPF, Hospital del Mar Research Institute (CRG) and Public Health and Epidemiology Network Biomedical Research Centre (CIBERESP), Barcelona, Spain
| | - Anne M Bowcock
- Division of Human Genetics, Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | | | - Wolfgang Weger
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachid Tazi-Ahnini
- Academic Unit of Dermatology Research, Department of Infection and Immunity, The University of Sheffield, Sheffield, UK
| | - Frank O Nestle
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Adrian Hayday
- Division of Immunology, Infection and Inflammatory Disease; King’s College London, London, UK
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, 54127 Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, 54127 Bonn, Germany
| | - Juliane Winkelmann
- Department of Neurology, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Munich, Germany
| | - Cisca Wijmenga
- Genetics Department, University Medical Center and University of Groningen, Groningen, The Netherlands
| | | | - Sarah Edkins
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Amy Strange
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Richard D Pearson
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Damjan Vukcevic
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Chris CA Spencer
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | | | - Ulrich Mrowietz
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
- PopGen biobank, University Hospital S.-H., Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Sulev Koks
- Department of Physiology, Centre of Translational Medicine and Centre for Translational Genomics, University of Tartu, 50409 Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology and Venerology, University of Tartu, 50409 Tartu, Estonia
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, MI, 48202, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael Weichenthal
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - H. Erich Wichmann
- Institute of Epidemiology I, Helmholtz Centre Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University, 81377 Munich, Germany
- Klinikum Grosshadern, 81377 Munich, Germany
| | - Vinod Chandran
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8, Canada
| | - Cheryl F Rosen
- Department of Medicine, Division of Dermatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8
| | - Proton Rahman
- Department of Medicine, Memorial University, St. John’s, Newfoundland A1C 5B8, Canada
| | - Dafna D Gladman
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8, Canada
| | - Christopher EM Griffiths
- Dermatological Sciences, Salford Royal NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Andre Reis
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Finland
| | | | | | | | | | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Jonathan NWN Barker
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
- St John’s Institute of Dermatology, King’s College London, London, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
- Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London, UK
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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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43
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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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44
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Wurster AL, Precht P, Becker KG, Wood WH, Zhang Y, Wang Z, Pazin MJ. IL-10 transcription is negatively regulated by BAF180, a component of the SWI/SNF chromatin remodeling enzyme. BMC Immunol 2012; 13:9. [PMID: 22336179 PMCID: PMC3313858 DOI: 10.1186/1471-2172-13-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 02/15/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND SWI/SNF chromatin remodeling enzymes play a critical role in the development of T helper lymphocytes, including Th2 cells, and directly program chromatin structure at Th2 cytokine genes. Different versions of SWI/SNF complexes, including BAF and PBAF, have been described based on unique subunit composition. However, the relative role of BAF and PBAF in Th cell function and cytokine expression has not been reported. RESULTS Here we examine the role of the PBAF SWI/SNF complex in Th cell development and gene expression using mice deficient for a PBAF-specific component, BAF180. We find that T cell development in the thymus and lymphoid periphery is largely normal when the BAF180 gene is deleted late in thymic development. However, BAF180-deficient Th2 cells express high levels of the immunoregulatory cytokine IL-10. BAF180 binds directly to regulatory elements in the Il-10 locus but is replaced by BAF250 BAF complexes in the absence of BAF180, resulting in increased histone acetylation and CBP recruitment to the IL-10 locus. CONCLUSIONS These results demonstrate that BAF180 is a repressor of IL-10 transcription in Th2 cells and suggest that the differential recruitment of different SWI/SNF subtypes can have direct consequences on chromatin structure and gene transcription.
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Affiliation(s)
- Andrea L Wurster
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, USA
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45
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Fisher IB, Ostrowski M, Muthusamy N. Role for Ets-2(Thr-72) transcription factor in stage-specific thymocyte development and survival. J Biol Chem 2011; 287:5199-210. [PMID: 22128184 DOI: 10.1074/jbc.m111.242602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Interference of Ras signaling deregulates thymocyte development in mouse models. However, the role of Ets-2, a transcription factor that is phosphorylated on a critical threonine residue (Thr-72) by the Ras/MAPK pathway in thymocyte development, has not been defined. Transgenic mice overexpressing a phosphomutant Ets-2 (T72A) in the thymus displayed reduced thymus size associated with a 60-80% reduction in thymocyte populations. The transgenic mice exhibited a 20-fold increase in a c-Kit(+) CD4(+) CD8(+) CD3(-) population and a 5-fold increase in a unique CD5(low) population associated with a partial developmental block at the DN2-DN3 stage of thymocytes. Transgenic thymocytes exhibited increased apoptosis, and overexpression of Bcl-2 rescued the hypocellularity and associated thymocyte developmental block in double transgenic mice. The observed defects in these mice are not dependent on Ets-1 expression. These studies implicate for the first time a stage-specific Ets-1-independent regulatory role for Ets-2 in early thymocyte development and survival.
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Affiliation(s)
- Ian B Fisher
- Molecular Cellular Developmental Biology Program, Division of Hematology, Ohio State University, Columbus, Ohio 43210, USA
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46
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Thompson PK, Zúñiga-Pflücker JC. On becoming a T cell, a convergence of factors kick it up a Notch along the way. Semin Immunol 2011; 23:350-9. [PMID: 21981947 DOI: 10.1016/j.smim.2011.08.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 08/19/2011] [Indexed: 12/18/2022]
Abstract
The thymus is seeded by bone marrow-derived progenitors, which undergo a series of differentiation and proliferation events in order to generate functional T lymphocytes. The Notch signaling pathway, together with multiple transcription factors, act in concert to commit progenitors to a T-lineage fate, extinguishing non-T cell potential, inducing thymocyte differentiation and supporting proliferation and survival along the way to becoming a mature T cell. This review focuses on recent evidence regarding the complex interplay between the Notch pathway and other key transcription factors at specific lineage-decision points during the program of T cell development.
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Affiliation(s)
- Patrycja K Thompson
- Department of Immunology, University of Toronto, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
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47
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An J, Golech S, Klaewsongkram J, Zhang Y, Subedi K, Huston GE, Wood WH, Wersto RP, Becker KG, Swain SL, Weng N. Krüppel-like factor 4 (KLF4) directly regulates proliferation in thymocyte development and IL-17 expression during Th17 differentiation. FASEB J 2011; 25:3634-45. [PMID: 21685331 PMCID: PMC3177573 DOI: 10.1096/fj.11-186924] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/02/2011] [Indexed: 11/11/2022]
Abstract
Krüppel-like factor 4 (KLF4), a transcription factor, plays a key role in the pluripotency of stem cells. We sought to determine the function of KLF4 in T-cell development and differentiation by using T-cell-specific Klf4-knockout (KO) mice. We found that KLF4 was highly expressed in thymocytes and mature T cells and was rapidly down-regulated in mature T cells after activation. In Klf4-KO mice, we observed a modest reduction of thymocytes (27%) due to the reduced proliferation of double-negative (DN) thymocytes. We demonstrated that a direct repression of Cdkn1b by KLF4 was a cause of decreased DN proliferation. During in vitro T-cell differentiation, we observed significant reduction of IL-17-expressing CD4(+) T cells (Th17; 24%) but not in other types of Th differentiation. The reduction of Th17 cells resulted in a significant attenuation of the severity (35%) of experimental autoimmune encephalomyelitis in vivo in Klf4-KO mice as compared with the Klf4 wild-type littermates. Finally, we demonstrated that KLF4 directly binds to the promoter of Il17a and positively regulates its expression. In summary, these findings identify KLF4 as a critical regulator in T-cell development and Th17 differentiation.
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Affiliation(s)
- Jie An
- Laboratory of Molecular Biology and Immunology
| | | | | | | | | | - Gail E. Huston
- Trudeau Institute, Saranac Lake, New York, New York, USA; and
| | | | - Robert P. Wersto
- Flow Cytometry Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | | | - Susan L. Swain
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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48
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Leng RX, Pan HF, Chen GM, Feng CC, Fan YG, Ye DQ, Li XP. The dual nature of Ets-1: Focus to the pathogenesis of systemic lupus erythematosus. Autoimmun Rev 2011; 10:439-43. [DOI: 10.1016/j.autrev.2011.01.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 01/29/2011] [Indexed: 12/21/2022]
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49
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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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50
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Arita K, Endo S, Kaifu T, Kitaguchi K, Nakamura A, Ohmori H, Kohu K, Satake M, Takai T. Transcriptional Activation of thePirbGene in B Cells by PU.1 and Runx3. THE JOURNAL OF IMMUNOLOGY 2011; 186:7050-9. [DOI: 10.4049/jimmunol.1001302] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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