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Lima RS, Belchior-Bezerra M, Silva de Oliveira D, Rocha RDS, Medeiros NI, Mattos RT, Camile Dos Reis I, Marques AS, Rosário PW, Calsolari MR, Correa-Oliveira R, Dutra WO, Moreira PR, Gomes JA. Obesity Influences T CD4 Lymphocytes Subsets Profiles in Children and Adolescent's Immune Response. J Nutr 2024:S0022-3166(24)00386-9. [PMID: 39019165 DOI: 10.1016/j.tjnut.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/14/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND OBJECTIVES: Evidence shows that CD4+ T cells are altered in obesity and play a significant role in the systemic inflammation in adults with the disease. Because the profile of these cells is poorly understood in the pediatric population, this study aims to investigate the profile of CD4+ T lymphocytes and the plasma levels of cytokines in this population. METHODS Using flow cytometry, we compared the expression profile of lymphocyte markers, master transcription factors, cytokines, and molecules involved in the regulation of the immune response in CD4+ T cells from children and adolescents with obesity (OB group, n = 20) with those with eutrophy group (EU group, n = 16). Plasma levels of cytokines in both groups were determined by CBA. RESULTS The OB group presents a lower frequency of CD3+ T cells, as well as a decreased frequency of CD4+ T cells expressing CD28, IL-4, and FOXP3, but an increased frequency of CD4+IL-17A+ cells compared with the EU group. The frequency of CD28 is increased in Th2 and Treg cells in the OB group, whereas CTLA-4 is decreased in all subpopulations compared with the EU group. Furthermore, Th2, Th17, and Treg profiles can differentiate the EU and OB groups. IL-10 plasma levels are reduced in the OB group and negatively correlated with adiposity and inflammatory parameters. CONCLUSIONS CD4+ T cells have an altered pattern of expression in children and adolescents with obesity, contributing to the inflammatory state and clinical characteristics of these patients.
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Affiliation(s)
- Rafael Silva Lima
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mayara Belchior-Bezerra
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Daniela Silva de Oliveira
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Nayara I Medeiros
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Imunologia Celular e Molecular, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ, Belo Horizonte, Brazil
| | - Rafael T Mattos
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Isabelle Camile Dos Reis
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Aiessa Santos Marques
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Pedro Ws Rosário
- Centro de Especialidades Médicas (CEM), Hospital Santa Casa, Belo Horizonte, Brazil
| | | | - Rodrigo Correa-Oliveira
- Imunologia Celular e Molecular, Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ, Belo Horizonte, Brazil
| | - Walderez O Dutra
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paula Rocha Moreira
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Juliana As Gomes
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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2
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Gao ZX, He T, Zhang P, Hu X, Ge M, Xu YQ, Wang P, Pan HF. Epigenetic regulation of immune cells in systemic lupus erythematosus: insight from chromatin accessibility. Expert Opin Ther Targets 2024; 28:637-649. [PMID: 38943564 DOI: 10.1080/14728222.2024.2375372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/28/2024] [Indexed: 07/01/2024]
Abstract
INTRODUCTION Systemic Lupus Erythematosus (SLE) is a multi-dimensional autoimmune disease involving numerous tissues throughout the body. The chromatin accessibility landscapes in immune cells play a pivotal role in governing their activation, function, and differentiation. Aberrant modulation of chromatin accessibility in immune cells is intimately associated with the onset and progression of SLE. AREAS COVERED In this review, we described the chromatin accessibility landscapes in immune cells, summarized the recent evidence of chromatin accessibility related to the pathogenesis of SLE, and discussed the potential of chromatin accessibility as a valuable option to identify novel therapeutic targets for this disease. EXPERT OPINION Dynamic changes in chromatin accessibility are intimately related to the pathogenesis of SLE and have emerged as a new direction for exploring its epigenetic mechanisms. The differently accessible chromatin regions in immune cells often contain binding sites for transcription factors (TFs) and cis-regulatory elements such as enhancers and promoters, which may be potential therapeutic targets for SLE. Larger scale cohort studies and integrating epigenomic, transcriptomic, and metabolomic data can provide deeper insights into SLE chromatin biology in the future.
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Affiliation(s)
- Zhao-Xing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Tian He
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Peng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xiao Hu
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Man Ge
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yi-Qing Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Peng Wang
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
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3
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Hoshino A, Picard BH, Polychronopoulou S, Kelaidi C, Azarnoush S, Kracker S, Rieux-Laucat F, Boutboul D, Latour S. Loss-of-phosphorylation of IKZF1 results in gain-of-function associated with immune dysregulation. J Allergy Clin Immunol 2024; 154:229-236.e2. [PMID: 38438084 DOI: 10.1016/j.jaci.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 01/21/2024] [Accepted: 01/25/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Immune dysregulation often presents as autoimmunity, inflammation, and/or lymphoproliferation. Several germline genetic defects have been associated with immune dysregulation; they include heterozygous gain-of-function (GOF) mutations in IKZF1, an essential transcription factor for hematopoiesis containing zinc finger domains (ZFs). However, in a large percentage of patients, the genetic origin of their immunedysregulation remains undetermined. OBJECTIVE A family with 2 members presenting immune dysregulation signs was studied to identify the genetic cause of their disease. METHODS Whole exome sequencing, analysis of immunologic parameters, and functional assays (including Western blotting, electrophoretic mobility shift assay during the cell cycle, and TH cell differentiation) were performed. RESULTS The 2 patients carried a novel heterozygous mutation in IKZF1 (IKZF1T398M). IKZF1 heterozygous mutations have previously been shown to be responsible for several distinct human immunologic diseases by directly affecting the ability of ZFs to bind to DNA or to dimerize. Herein, we showed that the IKZF1T398M, which is outside the ZFs, caused impaired phosphorylation of IKZF1, resulting in enhanced DNA-binding ability at the S phase of the cell cycle, reduction of the G1-S phase transition, and decreased proliferation. Confirming these data, similar functional alterations were observed with IKZF1T398A, but not with IKZF1T398D, mimicking dephosphorylation and phosphorylation, respectively. In T lymphocytes, expression of IKZF1T398M led to TH cell differentiation skewed toward TH2 cells. Thus, our data indicate that IKZF1T398M behaves as a GOF variant underlying immune dysregulation. CONCLUSION Disturbed IKZF1 phosphorylation represents a novel GOF mechanism (GOF by loss of phosphorylation (termed as GOF-LOP) associated with immune dysregulation, highlighting the regulatory role of IKZF1 during cell cycle progression through phosphorylation.
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Affiliation(s)
- Akihiro Hoshino
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Benoît Heid Picard
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France; Université de Paris-Cité, Paris, France
| | - Sophia Polychronopoulou
- Department of Pediatric Hematology-Oncology, Aghia Sophia Children's Hospital, Goudi-Athens, Athens, Greece
| | - Charikleia Kelaidi
- Department of Pediatric Hematology-Oncology, Aghia Sophia Children's Hospital, Goudi-Athens, Athens, Greece
| | - Saba Azarnoush
- Department of Pediatric Immuno-Hematology, Hôpital Robert-Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sven Kracker
- Université de Paris-Cité, Paris, France; Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Frédéric Rieux-Laucat
- Université de Paris-Cité, Paris, France; Laboratory of Immunogenetics of Pediatric Autoimmunity, INSERM UMR 1163, Imagine Institute, Paris, France
| | - David Boutboul
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France; Université de Paris-Cité, Paris, France.
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Bharadwaj NS, Zumwalde NA, Kapur A, Patankar M, Gumperz JE. Human CD4 + memory phenotype T cells use mitochondrial metabolism to generate sensitive IFN-γ responses. iScience 2024; 27:109775. [PMID: 38726371 PMCID: PMC11079467 DOI: 10.1016/j.isci.2024.109775] [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: 01/10/2024] [Revised: 03/12/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
The transition of naive T lymphocytes into antigenically activated effector cells is associated with a metabolic shift from oxidative phosphorylation to aerobic glycolysis. This shift facilitates production of the key anti-tumor cytokine interferon (IFN)-γ; however, an associated loss of mitochondrial efficiency in effector T cells ultimately limits anti-tumor immunity. Memory phenotype (MP) T cells are a newly recognized subset that arises through homeostatic activation signals following hematopoietic transplantation. We show here that human CD4+ MP cell differentiation is associated with increased glycolytic and oxidative metabolic activity, but MP cells retain less compromised mitochondria compared to effector CD4+ T cells, and their IFN-γ response is less dependent on glucose and more reliant on glutamine. MP cells also produced IFN-γ more efficiently in response to weak T cell receptor (TCR) agonism than effectors and mediated stronger responses to transformed B cells. MP cells may thus be particularly well suited to carry out sustained immunosurveillance against neoplastic cells.
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Affiliation(s)
- Nikhila S. Bharadwaj
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health; Madison, WI 53706, USA
| | - Nicholas A. Zumwalde
- Department of Genetics, University of Wisconsin School of Medicine and Public Health; Madison, WI 53706, USA
| | - Arvinder Kapur
- QIAGEN Sciences Inc., 19300 Germantown Road, Germantown, MD 20874, USA
| | - Manish Patankar
- Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health; Madison, WI 53706, USA
| | - Jenny E. Gumperz
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health; Madison, WI 53706, USA
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5
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Forsyth KS, Toothacre NE, Jiwrajka N, Driscoll AM, Shallberg LA, Cunningham-Rundles C, Barmettler S, Farmer J, Verbsky J, Routes J, Beiting DP, Romberg N, May MJ, Anguera MC. NF-κB Signaling is Required for X-Chromosome Inactivation Maintenance Following T cell Activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.579505. [PMID: 38405871 PMCID: PMC10888971 DOI: 10.1101/2024.02.08.579505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
X Chromosome Inactivation (XCI) is a female-specific process which balances X-linked gene dosage between sexes. Unstimulated T cells lack cytological enrichment of Xist RNA and heterochromatic modifications on the inactive X chromosome (Xi), and these modifications become enriched at the Xi after cell stimulation. Here, we examined allele-specific gene expression and the epigenomic profiles of the Xi following T cell stimulation. We found that the Xi in unstimulated T cells is largely dosage compensated and is enriched with the repressive H3K27me3 modification, but not the H2AK119-ubiquitin (Ub) mark, even at promoters of XCI escape genes. Upon CD3/CD28-mediated T cell stimulation, the Xi accumulates H2AK119-Ub and H3K27me3 across the Xi. Next, we examined the T cell signaling pathways responsible for Xist RNA localization to the Xi and found that T cell receptor (TCR) engagement, specifically NF-κB signaling downstream of TCR, is required. Disruption of NF-κB signaling, using inhibitors or genetic deletions, in mice and patients with immunodeficiencies prevents Xist/XIST RNA accumulation at the Xi and alters expression of some X-linked genes. Our findings reveal a novel connection between NF-κB signaling pathways which impact XCI maintenance in female T cells.
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6
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Eggert J, Zinzow-Kramer WM, Hu Y, Kolawole EM, Tsai YL, Weiss A, Evavold BD, Salaita K, Scharer CD, Au-Yeung BB. Cbl-b mitigates the responsiveness of naive CD8 + T cells that experience extensive tonic T cell receptor signaling. Sci Signal 2024; 17:eadh0439. [PMID: 38319998 PMCID: PMC10897907 DOI: 10.1126/scisignal.adh0439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Naive T cells experience tonic T cell receptor (TCR) signaling in response to self-antigens presented by major histocompatibility complex (MHC) in secondary lymphoid organs. We investigated how relatively weak or strong tonic TCR signals influence naive CD8+ T cell responses to stimulation with foreign antigens. The heterogeneous expression of Nur77-GFP, a transgenic reporter of tonic TCR signaling, in naive CD8+ T cells suggests variable intensities or durations of tonic TCR signaling. Although the expression of genes associated with acutely stimulated T cells was increased in Nur77-GFPHI cells, these cells were hyporesponsive to agonist TCR stimulation compared with Nur77-GFPLO cells. This hyporesponsiveness manifested as diminished activation marker expression and decreased secretion of IFN-γ and IL-2. The protein abundance of the ubiquitin ligase Cbl-b, a negative regulator of TCR signaling, was greater in Nur77-GFPHI cells than in Nur77-GFPLO cells, and Cbl-b deficiency partially restored the responsiveness of Nur77-GFPHI cells. Our data suggest that the cumulative effects of previously experienced tonic TCR signaling recalibrate naive CD8+ T cell responsiveness. These changes include gene expression changes and negative regulation partially dependent on Cbl-b. This cell-intrinsic negative feedback loop may enable the immune system to restrain naive CD8+ T cells with higher self-reactivity.
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Affiliation(s)
- Joel Eggert
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University; Atlanta, 30322, USA
| | - Wendy M. Zinzow-Kramer
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University; Atlanta, 30322, USA
| | - Yuesong Hu
- Department of Chemistry, Emory University; Atlanta, 30322, USA
| | - Elizabeth M. Kolawole
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, 84112, USA
| | - Yuan-Li Tsai
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Departments of Medicine and of Microbiology and Immunology, University of California, San Francisco; San Francisco, 94143, USA
| | - Arthur Weiss
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Departments of Medicine and of Microbiology and Immunology, University of California, San Francisco; San Francisco, 94143, USA
| | - Brian D. Evavold
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, 84112, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University; Atlanta, 30322, USA
| | | | - Byron B. Au-Yeung
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University; Atlanta, 30322, USA
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7
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Rudloff MW, Zumbo P, Favret NR, Roetman JJ, Detrés Román CR, Erwin MM, Murray KA, Jonnakuti ST, Dündar F, Betel D, Philip M. Hallmarks of CD8 + T cell dysfunction are established within hours of tumor antigen encounter before cell division. Nat Immunol 2023; 24:1527-1539. [PMID: 37537361 PMCID: PMC10878719 DOI: 10.1038/s41590-023-01578-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/07/2023] [Indexed: 08/05/2023]
Abstract
Tumor-specific CD8+ T cells (TST) in patients with cancer are dysfunctional and unable to halt cancer progression. TST dysfunction, also known as exhaustion, is thought to be driven by chronic T cell antigen receptor (TCR) stimulation over days to weeks. However, we know little about the interplay between CD8+ T cell function, cell division and epigenetic remodeling within hours of activation. Here, we assessed early CD8+ T cell differentiation, cell division, chromatin accessibility and transcription in tumor-bearing mice and acutely infected mice. Surprisingly, despite robust activation and proliferation, TST had near complete effector function impairment even before undergoing cell division and had acquired hallmark chromatin accessibility features previously associated with later dysfunction/exhaustion. Moreover, continued tumor/antigen exposure drove progressive epigenetic remodeling, 'imprinting' the dysfunctional state. Our study reveals the rapid divergence of T cell fate choice before cell division in the context of tumors versus infection.
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Affiliation(s)
- Michael W Rudloff
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Natalie R Favret
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Jessica J Roetman
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Carlos R Detrés Román
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Megan M Erwin
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Kristen A Murray
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Sriya T Jonnakuti
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mary Philip
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA.
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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8
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Ktena YP, Dionysiou M, Gondek LP, Cooke KR. The impact of epigenetic modifications on allogeneic hematopoietic stem cell transplantation. Front Immunol 2023; 14:1188853. [PMID: 37325668 PMCID: PMC10264773 DOI: 10.3389/fimmu.2023.1188853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
The field of epigenetics studies the complex processes that regulate gene expression without altering the DNA sequence itself. It is well established that epigenetic modifications are crucial to cellular homeostasis and differentiation and play a vital role in hematopoiesis and immunity. Epigenetic marks can be mitotically and/or meiotically heritable upon cell division, forming the basis of cellular memory, and have the potential to be reversed between cellular fate transitions. Hence, over the past decade, there has been increasing interest in the role that epigenetic modifications may have on the outcomes of allogeneic hematopoietic transplantation and growing enthusiasm in the therapeutic potential these pathways may hold. In this brief review, we provide a basic overview of the types of epigenetic modifications and their biological functions, summarizing the current literature with a focus on hematopoiesis and immunity specifically in the context of allogeneic hematopoietic stem cell transplantation.
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Affiliation(s)
- Yiouli P. Ktena
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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9
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De Boer RJ, Yates AJ. Modeling T Cell Fate. Annu Rev Immunol 2023; 41:513-532. [PMID: 37126420 PMCID: PMC11100019 DOI: 10.1146/annurev-immunol-101721-040924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Many of the pathways that underlie the diversification of naive T cells into effector and memory subsets, and the maintenance of these populations, remain controversial. In recent years a variety of experimental tools have been developed that allow us to follow the fates of cells and their descendants. In this review we describe how mathematical models provide a natural language for describing the growth, loss, and differentiation of cell populations. By encoding mechanistic descriptions of cell behavior, models can help us interpret these new datasets and reveal the rules underpinning T cell fate decisions, both at steady state and during immune responses.
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Affiliation(s)
- Rob J De Boer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands;
| | - Andrew J Yates
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA;
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10
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Liu J, Zhu S, Hu W, Zhao X, Shan Q, Peng W, Xue HH. CTCF mediates CD8+ effector differentiation through dynamic redistribution and genomic reorganization. J Exp Med 2023; 220:e20221288. [PMID: 36752796 PMCID: PMC9948760 DOI: 10.1084/jem.20221288] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/12/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Differentiation of effector CD8+ T cells is instructed by stably and dynamically expressed transcription regulators. Here we show that naive-to-effector differentiation was accompanied by dynamic CTCF redistribution and extensive chromatin architectural changes. Upon CD8+ T cell activation, CTCF acquired de novo binding sites and anchored novel chromatin interactions, and these changes were associated with increased chromatin accessibility and elevated expression of cytotoxic program genes including Tbx21, Ifng, and Klrg1. CTCF was also evicted from its ex-binding sites in naive state, with concomitantly reduced chromatin interactions in effector cells, as observed at memory precursor-associated genes including Il7r, Sell, and Tcf7. Genetic ablation of CTCF indeed diminished cytotoxic gene expression, but paradoxically elevated expression of memory precursor genes. Comparative Hi-C analysis revealed that key memory precursor genes were harbored within insulated neighborhoods demarcated by constitutive CTCF binding, and their induction was likely due to disrupted CTCF-dependent insulation. CTCF thus promotes cytotoxic effector differentiation by integrating local chromatin accessibility control and higher-order genomic reorganization.
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Affiliation(s)
- Jia Liu
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
| | - Shaoqi Zhu
- Department of Physics, The George Washington University, Washington, DC, USA
| | - Wei Hu
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
| | - Xin Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
| | - Qiang Shan
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC, USA
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
- New Jersey Veterans Affairs Health Care System, East Orange, NJ, USA
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11
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Pandey P, Khan F, Upadhyay TK, Sharangi AB. Deciphering the Immunomodulatory Role of Cyclin-Dependent Kinase 4/6 Inhibitors in the Tumor Microenvironment. Int J Mol Sci 2023; 24:ijms24032236. [PMID: 36768557 PMCID: PMC9916547 DOI: 10.3390/ijms24032236] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Cancer is characterized by persistent cell proliferation driven by aberrant cell cycle regulation and stimulation of cyclin-dependent kinases (CDKs). A very intriguing and potential approach for the development of antitumor medicines is the suppression of CDKs that lead to induction of apoptosis and cell cycle arrest. The shift of the cell cycle from the G0/G1 phase to the S phase, which is characterized by active transcription and synthesis, depends on the development of the cyclin D-CDK4/6 complex. A precise balance between anticancer activity and general toxicity is demonstrated by CDK inhibitors, which can specifically block CDK4/6 and control the cell cycle by reducing the G1 to S phase transition. CDK4/6 inhibitors have recently been reported to exhibit significant cell growth inhibition via modulating the tumour microenvironment in cancerous cells. One significant new understanding is that these inhibitors serve important functions in the interaction among tumour cells and the host immune system in addition to being cytostatic. Herein, we discuss the biological significance of CDK4/6 inhibitors in cancer therapeutics, as well as their biological impact on T cells and other important immune cells. Furthermore, we explore the integration of preclinical findings of these pharmaceuticals' ability to enhance antitumor immunity.
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Affiliation(s)
- Pratibha Pandey
- Department of Biotechnology, Noida Institute of Engineering and Technology, 19, Knowledge Park-II, Institutional Area, Greater Noida 201306, India
| | - Fahad Khan
- Department of Biotechnology, Noida Institute of Engineering and Technology, 19, Knowledge Park-II, Institutional Area, Greater Noida 201306, India
- Correspondence:
| | - Tarun Kumar Upadhyay
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara 391760, India
| | - Amit Baran Sharangi
- Department of Plantation Spices Medicinal and Aromatic Crops, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur 741252, India
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12
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Ktena YP, Koldobskiy MA, Barbato MI, Fu HH, Luznik L, Llosa NJ, Haile A, Klein OR, Liu C, Gamper CJ, Cooke KR. Donor T cell DNMT3a regulates alloreactivity in mouse models of hematopoietic stem cell transplantation. J Clin Invest 2022; 132:e158047. [PMID: 35608905 PMCID: PMC9246380 DOI: 10.1172/jci158047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/19/2022] [Indexed: 11/17/2022] Open
Abstract
DNA methyltransferase 3a (DNMT3a) is an important part of the epigenetic machinery that stabilizes patterns of activated T cell responses. We hypothesized that donor T cell DNMT3a regulates alloreactivity after allogeneic blood and marrow transplantation (allo-BMT). T cell conditional Dnmt3a KO mice were used as donors in allo-BMT models. Mice receiving allo-BMT from KO donors developed severe acute graft-versus-host disease (aGVHD), with increases in inflammatory cytokine levels and organ histopathology scores. KO T cells migrated and proliferated in secondary lymphoid organs earlier and demonstrated an advantage in trafficking to the small intestine. Donor T cell subsets were purified after BMT for whole-genome bisulfite sequencing (WGBS) and RNA-Seq. KO T cells had global methylation similar to that of WT cells, with distinct, localized areas of hypomethylation. Using a highly sensitive computational method, we produced a comprehensive profile of the altered epigenome landscape. Hypomethylation corresponded with changes in gene expression in several pathways of T cell signaling and differentiation. Additionally, Dnmt3a-KO T cells resulted in superior graft-versus-tumor activity. Our findings demonstrate a critical role for DNMT3a in regulating T cell alloreactivity and reveal pathways that control T cell tolerance. These results also provide a platform for deciphering clinical data that associate donor DNMT3a mutations with increased GVHD, decreased relapse, and improved survival.
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Affiliation(s)
- Yiouli P. Ktena
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Michael A. Koldobskiy
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Michael I. Barbato
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Han-Hsuan Fu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Leo Luznik
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nicolas J. Llosa
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Azeb Haile
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Orly R. Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Chen Liu
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Christopher J. Gamper
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Kenneth R. Cooke
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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13
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Kong J, Ha D, Lee J, Kim I, Park M, Im SH, Shin K, Kim S. Network-based machine learning approach to predict immunotherapy response in cancer patients. Nat Commun 2022; 13:3703. [PMID: 35764641 PMCID: PMC9240063 DOI: 10.1038/s41467-022-31535-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 06/22/2022] [Indexed: 11/08/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have substantially improved the survival of cancer patients over the past several years. However, only a minority of patients respond to ICI treatment (~30% in solid tumors), and current ICI-response-associated biomarkers often fail to predict the ICI treatment response. Here, we present a machine learning (ML) framework that leverages network-based analyses to identify ICI treatment biomarkers (NetBio) that can make robust predictions. We curate more than 700 ICI-treated patient samples with clinical outcomes and transcriptomic data, and observe that NetBio-based predictions accurately predict ICI treatment responses in three different cancer types-melanoma, gastric cancer, and bladder cancer. Moreover, the NetBio-based prediction is superior to predictions based on other conventional ICI treatment biomarkers, such as ICI targets or tumor microenvironment-associated markers. This work presents a network-based method to effectively select immunotherapy-response-associated biomarkers that can make robust ML-based predictions for precision oncology.
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Affiliation(s)
- JungHo Kong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Doyeon Ha
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Juhun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Inhae Kim
- ImmunoBiome Inc., Pohang, 37666, Korea
| | - Minhyuk Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- ImmunoBiome Inc., Pohang, 37666, Korea
- Institute of Convergence Science, Yonsei University, Seoul, 03722, Korea
| | - Kunyoo Shin
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- Institute of Convergence Science, Yonsei University, Seoul, 03722, Korea
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea.
- Institute of Convergence Science, Yonsei University, Seoul, 03722, Korea.
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14
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Chen X, Sunkel B, Wang M, Kang S, Wang T, Gnanaprakasam JNR, Liu L, Cassel TA, Scott DA, Muñoz-Cabello AM, Lopez-Barneo J, Yang J, Lane AN, Xin G, Stanton B, Fan TWM, Wang R. Succinate dehydrogenase/complex II is critical for metabolic and epigenetic regulation of T cell proliferation and inflammation. Sci Immunol 2022; 7:eabm8161. [PMID: 35486677 PMCID: PMC9332111 DOI: 10.1126/sciimmunol.abm8161] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Effective T cell-mediated immune responses require the proper allocation of metabolic resources to sustain growth, proliferation, and cytokine production. Epigenetic control of the genome also governs T cell transcriptome and T cell lineage commitment and maintenance. Cellular metabolic programs interact with epigenetic regulation by providing substrates for covalent modifications of chromatin. By using complementary genetic, epigenetic, and metabolic approaches, we revealed that tricarboxylic acid (TCA) cycle flux fueled biosynthetic processes while controlling the ratio of succinate/α-ketoglutarate (α-KG) to modulate the activities of dioxygenases that are critical for driving T cell inflammation. In contrast to cancer cells, where succinate dehydrogenase (SDH)/complex II inactivation drives cell transformation and growth, SDH/complex II deficiency in T cells caused proliferation and survival defects when the TCA cycle was truncated, blocking carbon flux to support nucleoside biosynthesis. Replenishing the intracellular nucleoside pool partially relieved the dependence of T cells on SDH/complex II for proliferation and survival. SDH deficiency induced a proinflammatory gene signature in T cells and promoted T helper 1 and T helper 17 lineage differentiation. An increasing succinate/α-KG ratio in SDH-deficient T cells promoted inflammation by changing the pattern of the transcriptional and chromatin accessibility signatures and consequentially increasing the expression of the transcription factor, PR domain zinc finger protein 1. Collectively, our studies revealed a role of SDH/complex II in allocating carbon resources for anabolic processes and epigenetic regulation in T cell proliferation and inflammation.
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Affiliation(s)
- Xuyong Chen
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Benjamin Sunkel
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Meng Wang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Siwen Kang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Tingting Wang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - JN Rashida Gnanaprakasam
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Lingling Liu
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Teresa A. Cassel
- Center for Environmental and Systems Biochemistry, Dept. of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - David A. Scott
- Cancer Metabolism Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Ana M. Muñoz-Cabello
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario "Virgen del Rocío"/CSIC/Universidad de Sevilla, Spain
| | - Jose Lopez-Barneo
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario "Virgen del Rocío"/CSIC/Universidad de Sevilla, Spain
| | - Jun Yang
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Andrew N. Lane
- Center for Environmental and Systems Biochemistry, Dept. of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Gang Xin
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Benjamin Stanton
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Teresa W.-M. Fan
- Center for Environmental and Systems Biochemistry, Dept. of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Ruoning Wang
- Center for Childhood Cancer & Blood Diseases, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
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15
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Zhao J, Wei K, Chang C, Xu L, Jiang P, Guo S, Schrodi SJ, He D. DNA Methylation of T Lymphocytes as a Therapeutic Target: Implications for Rheumatoid Arthritis Etiology. Front Immunol 2022; 13:863703. [PMID: 35309322 PMCID: PMC8927780 DOI: 10.3389/fimmu.2022.863703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease that can cause joint damage and disability. Epigenetic variation, especially DNA methylation, has been shown to be involved in almost all the stages of the pathology of RA, from autoantibody production to various self-effector T cells and the defects of protective T cells that can lead to chronic inflammation and erosion of bones and joints. Given the critical role of T cells in the pathology of RA, the regulatory functions of DNA methylation in T cell biology remain unclear. In this review, we elaborate on the relationship between RA pathogenesis and DNA methylation in the context of different T cell populations. We summarize the relevant methylation events in T cell development, differentiation, and T cell-related genes in disease prediction and drug efficacy. Understanding the epigenetic regulation of T cells has the potential to profoundly translate preclinical results into clinical practice and provide a framework for the development of novel, individualized RA therapeutics.
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Affiliation(s)
- Jianan Zhao
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Kai Wei
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Cen Chang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Lingxia Xu
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Ping Jiang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Shicheng Guo
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Steven J Schrodi
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Dongyi He
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
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16
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Heritable changes in division speed accompany the diversification of single T cell fate. Proc Natl Acad Sci U S A 2022; 119:2116260119. [PMID: 35217611 PMCID: PMC8892279 DOI: 10.1073/pnas.2116260119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 11/18/2022] Open
Abstract
Rapid clonal expansion of antigen-specific T cells is a fundamental feature of adaptive immune responses. Here, we utilize continuous live-cell imaging in vitro to track the division speed and genealogical connections of all descendants derived from a single naive CD8+ T cell throughout up to ten divisions of activation-induced proliferation. Bayesian inference of tree-structured data reveals that clonal expansion is divided into a homogenously fast burst phase encompassing two to three divisions and a subsequent diversification phase during which T cells segregate into quickly dividing effector T cells and more slowly cycling memory precursors. Our work highlights cell cycle speed as a major heritable property that is regulated in parallel to key lineage decisions of activated T cells. Rapid clonal expansion of antigen-specific T cells is a fundamental feature of adaptive immune responses. It enables the outgrowth of an individual T cell into thousands of clonal descendants that diversify into short-lived effectors and long-lived memory cells. Clonal expansion is thought to be programmed upon priming of a single naive T cell and then executed by homogenously fast divisions of all of its descendants. However, the actual speed of cell divisions in such an emerging “T cell family” has never been measured with single-cell resolution. Here, we utilize continuous live-cell imaging in vitro to track the division speed and genealogical connections of all descendants derived from a single naive CD8+ T cell throughout up to ten divisions of activation-induced proliferation. This comprehensive mapping of T cell family trees identifies a short burst phase, in which division speed is homogenously fast and maintained independent of external cytokine availability or continued T cell receptor stimulation. Thereafter, however, division speed diversifies, and model-based computational analysis using a Bayesian inference framework for tree-structured data reveals a segregation into heritably fast- and slow-dividing branches. This diversification of division speed is preceded already during the burst phase by variable expression of the interleukin-2 receptor alpha chain. Later it is accompanied by selective expression of memory marker CD62L in slower dividing branches. Taken together, these data demonstrate that T cell clonal expansion is structured into subsequent burst and diversification phases, the latter of which coincides with specification of memory versus effector fate.
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17
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Li L, Muftuoglu M, Liang S, Basyal M, Lv J, Akdogan ME, Chen K, Andreeff M, Parmar S. In-depth analysis of SARS-CoV-2-specific T cells reveals diverse differentiation hierarchies in vaccinated individuals. JCI Insight 2022; 7:156559. [PMID: 35230977 PMCID: PMC9057595 DOI: 10.1172/jci.insight.156559] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/23/2022] [Indexed: 11/29/2022] Open
Abstract
SARS-CoV-2 vaccines pose as the most effective approach for mitigating the COVID-19 pandemic. High-degree efficacy of SARS-CoV-2 vaccines in clinical trials indicates that vaccination invariably induces an adaptive immune response. However, the emergence of breakthrough infections in vaccinated individuals suggests that the breadth and magnitude of vaccine-induced adaptive immune response may vary. We assessed vaccine-induced SARS-CoV-2 T cell response in 21 vaccinated individuals and found that SARS-CoV-2–specific T cells, which were mainly CD4+ T cells, were invariably detected in all individuals but the response was varied. We then investigated differentiation states and cytokine profiles to identify immune features associated with superior recall function and longevity. We identified SARS-CoV-2–specific CD4+ T cells were polyfunctional and produced high levels of IL-2, which could be associated with superior longevity. Based on the breadth and magnitude of vaccine-induced SARS-CoV-2 response, we identified 2 distinct response groups: individuals with high abundance versus low abundance of SARS-CoV-2–specific T cells. The fractions of TNF-α– and IL-2–producing SARS-CoV-2 T cells were the main determinants distinguishing high versus low responders. Last, we identified that the majority of vaccine-induced SARS-CoV-2 T cells were reactive against non-mutated regions of mutant S-protein, suggesting that vaccine-induced SARS-CoV-2 T cells could provide continued protection against emerging variants of concern.
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Affiliation(s)
- Li Li
- Department of Lymphoma and Myeloma, The Univerisity of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Muharrem Muftuoglu
- Department of Leukemia, The Univerisity of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The Univerisity of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Mahesh Basyal
- Department of Leukemia, The Univerisity of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Jiangxing Lv
- Department of Lymphoma and Myeloma, The Univerisity of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Mehmet E Akdogan
- Department of Electrical and Computer Engineering, The University of Texas San Antonio, San Antonio, United States of America
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The Univerisity of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Michael Andreeff
- Department of Leukemia, The Univerisity of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Simrit Parmar
- Department of Lymphoma and Myeloma, The Univerisity of Texas MD Anderson Cancer Center, Houston, United States of America
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18
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Kim MS, Park D, Lee S, Park S, Kim KE, Kim TS, Park HJ, Cho D. Erythroid Differentiation Regulator 1 Strengthens TCR Signaling by Enhancing PLCγ1 Signal Transduction Pathway. Int J Mol Sci 2022; 23:ijms23020844. [PMID: 35055028 PMCID: PMC8776247 DOI: 10.3390/ijms23020844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/27/2021] [Accepted: 01/11/2022] [Indexed: 02/05/2023] Open
Abstract
Erythroid differentiation regulator 1 (Erdr1) has previously been reported to control thymocyte selection via TCR signal regulation, but the effect of Erdr1 as a TCR signaling modulator was not studied in peripheral T cells. In this report, it was determined whether Erdr1 affected TCR signaling strength in CD4 T cells. Results revealed that Erdr1 significantly enhanced the anti-TCR antibody-mediated activation and proliferation of T cells while failing to activate T cells in the absence of TCR stimulation. In addition, Erdr1 amplified Ca2+ influx and the phosphorylation of PLCγ1 in CD4 T cells with the TCR stimuli. Furthermore, NFAT1 translocation into nuclei in CD4 T cells was also significantly promoted by Erdr1 in the presence of TCR stimulation. Taken together, our results indicate that Erdr1 positively modulates TCR signaling strength via enhancing the PLCγ1/Ca2+/NFAT1 signal transduction pathway.
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Affiliation(s)
- Myun Soo Kim
- Kine Sciences, 525, Seolleung-ro, Gangnam-gu, Seoul 06149, Korea; (M.S.K.); (D.P.); (S.L.); (S.P.); (H.J.P.)
| | - Dongmin Park
- Kine Sciences, 525, Seolleung-ro, Gangnam-gu, Seoul 06149, Korea; (M.S.K.); (D.P.); (S.L.); (S.P.); (H.J.P.)
| | - Sora Lee
- Kine Sciences, 525, Seolleung-ro, Gangnam-gu, Seoul 06149, Korea; (M.S.K.); (D.P.); (S.L.); (S.P.); (H.J.P.)
| | - Sunyoung Park
- Kine Sciences, 525, Seolleung-ro, Gangnam-gu, Seoul 06149, Korea; (M.S.K.); (D.P.); (S.L.); (S.P.); (H.J.P.)
| | - Kyung Eun Kim
- Department of Cosmetic Sciences, Sookmyung Women’s University, Cheongpa-ro 47-gil 100 (Cheongpa-dong 2ga), Yongsan-gu, Seoul 04310, Korea;
| | - Tae Sung Kim
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, 5-ga, Anam-dong, Seongbuk-gu, Seoul 02841, Korea;
| | - Hyun Jeong Park
- Kine Sciences, 525, Seolleung-ro, Gangnam-gu, Seoul 06149, Korea; (M.S.K.); (D.P.); (S.L.); (S.P.); (H.J.P.)
| | - Daeho Cho
- Kine Sciences, 525, Seolleung-ro, Gangnam-gu, Seoul 06149, Korea; (M.S.K.); (D.P.); (S.L.); (S.P.); (H.J.P.)
- Institute of Convergence Science, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02841, Korea
- Correspondence: ; Tel.: +82-2-3290-3739; Fax: +82-2-928-8273
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19
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Argenty J, Rouquié N, Bories C, Mélique S, Duplan-Eche V, Saoudi A, Fazilleau N, Lesourne R. A selective LIS1 requirement for mitotic spindle assembly discriminates distinct T-cell division mechanisms within the T-cell lineage. eLife 2022; 11:80277. [PMID: 36519536 PMCID: PMC9797186 DOI: 10.7554/elife.80277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
The ability to proliferate is a common feature of most T-cell populations. However, proliferation follows different cell-cycle dynamics and is coupled to different functional outcomes according to T-cell subsets. Whether the mitotic machineries supporting these qualitatively distinct proliferative responses are identical remains unknown. Here, we show that disruption of the microtubule-associated protein LIS1 in mouse models leads to proliferative defects associated with a blockade of T-cell development after β-selection and of peripheral CD4+ T-cell expansion after antigen priming. In contrast, cell divisions in CD8+ T cells occurred independently of LIS1 following T-cell antigen receptor stimulation, although LIS1 was required for proliferation elicited by pharmacological activation. In thymocytes and CD4+ T cells, LIS1 deficiency did not affect signaling events leading to activation but led to an interruption of proliferation after the initial round of division and to p53-induced cell death. Proliferative defects resulted from a mitotic failure, characterized by the presence of extra-centrosomes and the formation of multipolar spindles, causing abnormal chromosomes congression during metaphase and separation during telophase. LIS1 was required to stabilize dynein/dynactin complexes, which promote chromosome attachment to mitotic spindles and ensure centrosome integrity. Together, these results suggest that proliferative responses are supported by distinct mitotic machineries across T-cell subsets.
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Affiliation(s)
- Jérémy Argenty
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Nelly Rouquié
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Cyrielle Bories
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Suzanne Mélique
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Valérie Duplan-Eche
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Abdelhadi Saoudi
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Nicolas Fazilleau
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Renaud Lesourne
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
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20
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Mehrotra A, Bhushan B, Kumar A, Panigrahi M, Chauhan A, Kumari S, Saini BL, Dutt T, Mishra BP. Characterisation and comparison of immune response mechanisms in an indigenous and a commercial pig breed after classical swine fever vaccination. Anim Genet 2021; 53:68-79. [PMID: 34729794 DOI: 10.1111/age.13152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/29/2021] [Accepted: 10/14/2021] [Indexed: 01/27/2023]
Abstract
The live attenuated classical swine fever (CSF) vaccine has been successfully used to prevent and control CSF outbreaks for 6 decades. However, the immune response mechanisms against the vaccine remain poorly understood. Moreover, very few reports exist regarding the breed differences in the response to CSF vaccine. In this study, we generated the peripheral blood mononuclear cell transcriptomes of indigenous Ghurrah and commercial Landrace pig breeds, before and 7 days after CSF vaccination. Subsequently, between and within-breed differential gene expression analyses were carried out. Results revealed large differences in pre-vaccination peripheral blood mononuclear cell transcriptome profiles of the two breeds, which were homogenised 7 days after vaccination. Before vaccination, gene set enrichment analysis showed that pathways related to antigen sensing and innate immune response were enriched in Ghurrah, while pathways related to adaptive immunity were enriched in Landrace. Ghurrah exhibited greater immunomodulation compared to Landrace following the vaccination. In Ghurrah, cell-cycle processes and T-cell response pathways were upregulated after vaccination. However, no pathways were upregulated in Landrace after vaccination. Pathways related to inflammation were downregulated in both the breeds after vaccination. Key regulators of inflammation such as IL1A, IL1B, NFKBIA and TNF genes were strongly downregulated in both the breeds after vaccination. Overall, our results have elucidated the mechanisms of host immune response against CSF vaccination in two distinct breeds and revealed common key genes instrumental in the global immune response to the vaccine.
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Affiliation(s)
- A Mehrotra
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - B Bhushan
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - A Kumar
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - M Panigrahi
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - A Chauhan
- Division of Livestock Production and Management, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - S Kumari
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - B L Saini
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - T Dutt
- Division of Livestock Production and Management, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
| | - B P Mishra
- Animal Biotechnology, ICAR - Indian Veterinary Research Institute, Izatnangar, Bareilly, UP, 243122, India
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21
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Chen J, Meng J, Jin C, Mo F, Ding Y, Gao X, Zhang L, Zhang M, Liang C. 4-Methylumbelliferone treatment and hyaluronan inhibition as a therapeutic strategy for chronic prostatitis. Prostate 2021; 81:1078-1090. [PMID: 34320251 DOI: 10.1002/pros.24205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 06/05/2021] [Accepted: 07/12/2021] [Indexed: 01/21/2023]
Abstract
BACKGROUND Hyaluronan (HA), an extracellular matrix component, accumulates in most chronic inflammatory tissues. Here, we studied the impact of HA on the pathogenesis of chronic prostatitis. MATERIALS AND METHODS First, we sorted demographic characteristics and peripheral blood serum samples from patients with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) to assess the relationship between the levels of HA in peripheral blood serum and the severity of inflammation in patients. Second, we induced an experimental autoimmune prostatitis (EAP) mouse model and treated the mice with 4-methylumbelliferone (4-MU) (200 mg/kg/day). After the mice were sacrificed, RNA from Th1 cells of the mouse spleens was extracted for RNA sequencing. We used weighted gene co-expression network analysis (WGCNA) to identify co-expressed gene modules and hub-gene related to the pathogenesis of EAP. The expression of critical genes associated with the identified pathway was confirmed by using western blot analysis. RESULTS HA was significantly more highly expressed in CP/CPPS patients than in healthy volunteers and positively correlated with the severity of pain, urination symptoms, and quality of life. Besides, the protein expression of HA was significantly higher in prostate tissues derived from EAP models than in those derived from controls. 4-MU, an oral inhibitor of HA synthesis, relieved immunocyte infiltration to the prostate and significantly reduced the proportion of Th1 cells. Based on the WGCNA, we identified 18 co-expression modules and identified that the Grey60 and brown modules were positively associated with the EAP and negatively associated with the Control and 4-MU-treated groups. Pathway enrichment analyses and western blot assays proved that HA potentially activated the cell cycle pathway, increasing the proportion of Th1 cells promoting chronic prostatitis pathogenesis, while these processes were reversed by 4-MU treatment. CONCLUSIONS Our results suggest that HA is elevated in patients with CP/CPPS compared with healthy controls and that targeting HA through 4-MU suppresses the activity of the cell cycle-related pathway, potentially by decreasing the proportion of Th1 cells and relieving chronic prostatitis. Our findings might inspire the clinical treatment of chronic prostatitis.
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Affiliation(s)
- Jing Chen
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Chen Jin
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Fan Mo
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Yang Ding
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Xiaomei Gao
- The Graduate School of Anhui Medical University, Hefei, Anhui, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Meng Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
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22
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Ariafar A, Habibagahi M, Jaberipour M, Khezri A, Hadi Khezri M, Bozorgi H, Hosseini A, Razmkhah M. Upregulation of Cytotoxic T-Lymphocyte-Associated Protein 4 and Forkhead Box P3 Transcripts in Peripheral Blood of Patients with Bladder Cancer. IRANIAN JOURNAL OF MEDICAL SCIENCES 2021; 46:339-346. [PMID: 34539008 PMCID: PMC8438340 DOI: 10.30476/ijms.2020.84462.1426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 07/26/2020] [Accepted: 07/30/2020] [Indexed: 11/19/2022]
Abstract
Background Regulatory T cells (Tregs) play a key role in the progression of tumors. These cells express forkhead box P3 (FOXP3) and cytotoxic T-lymphocyte-associated protein 4 (CTLA4), which are the potential targets for cancer immunotherapy. The present study aimed to evaluate FOXP3 and CTLA4 transcripts in patients with bladder cancer (BC) compared with healthy individuals. Methods Transcripts of CTLA4 and FOXP3 genes in the peripheral blood mononuclear cells (PBMCs) of 50 patients with histologically confirmed BC and 50 healthy individuals were assessed at the Institute for Cancer Research, Shiraz University of Medical Sciences (Shiraz, Iran) during 2014-2016. RNA was extracted from PBMCs, then cDNA was synthesized and subjected to quantitative real-time PCR (qRT-PCR) using appropriate primers. Statistical analysis was performed using SPSS software (version 21.0). Results Significantly higher amounts of CTLA4 and FOXP3 gene transcripts were found in the peripheral blood of BC patients compared with healthy individuals. The expression of both genes was significantly higher in patients with non-invasive and grade I/II BC. The median of CTLA4 and FOXP3 transcript expressions was 3.74 and 5.39, respectively, in non-invasive BC patients, which was significant compared with the control group (P=0.0016 and P=0.009, respectively). The median of target gene mRNA expression in grade I/II BC patients was 2.9 for CTLA4 and 6.61 for FOXP3, which was significant compared with the controls (P=0.013 and P=0.0037, respectively). Conclusion This study highlights the functional activity of Tregs in early stages of bladder cancer and showed the importance of CTLA4 and FOXP3, when it comes to screening BC.
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Affiliation(s)
- Ali Ariafar
- Department of Urology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mojtaba Habibagahi
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mansooreh Jaberipour
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdolaziz Khezri
- Department of Urology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hadi Khezri
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hale Bozorgi
- Department of Urology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Hosseini
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahboobeh Razmkhah
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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23
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Mansurov A, Lauterbach A, Budina E, Alpar AT, Hubbell JA, Ishihara J. Immunoengineering approaches for cytokine therapy. Am J Physiol Cell Physiol 2021; 321:C369-C383. [PMID: 34232748 DOI: 10.1152/ajpcell.00515.2020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Since the discovery of cytokines, much effort has been put forth to achieve therapeutic translation for treatment of various diseases, including cancer and autoimmune diseases. Despite these efforts, very few cytokines have cleared regulatory approval, and those that were approved are not commonly used due to their challenging toxicity profile and/or limited therapeutic efficacy. The main limitation in translation has been that wild-type cytokines have unfavorable pharmacokinetic and pharmacodynamic profiles, either eliciting unwanted systemic side effects or insufficient residence in secondary lymphoid organs. In this review, we address protein-engineering approaches that have been applied to both proinflammatory and anti-inflammatory cytokines to enhance their therapeutic indices, and we highlight diseases in which administration of engineered cytokines is especially relevant.
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Affiliation(s)
- Aslan Mansurov
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Abigail Lauterbach
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Erica Budina
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Aaron T Alpar
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Jeffrey A Hubbell
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Jun Ishihara
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois.,Department of Bioengineering, Imperial College London, London, United Kingdom
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24
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Onodera A, González-Avalos E, Lio CWJ, Georges RO, Bellacosa A, Nakayama T, Rao A. Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells. Genome Biol 2021; 22:186. [PMID: 34158086 PMCID: PMC8218415 DOI: 10.1186/s13059-021-02384-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND TET enzymes mediate DNA demethylation by oxidizing 5-methylcytosine (5mC) in DNA to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Since these oxidized methylcytosines (oxi-mCs) are not recognized by the maintenance methyltransferase DNMT1, DNA demethylation can occur through "passive," replication-dependent dilution when cells divide. A distinct, replication-independent ("active") mechanism of DNA demethylation involves excision of 5fC and 5caC by the DNA repair enzyme thymine DNA glycosylase (TDG), followed by base excision repair. RESULTS Here by analyzing inducible gene-disrupted mice, we show that DNA demethylation during primary T cell differentiation occurs mainly through passive replication-dependent dilution of all three oxi-mCs, with only a negligible contribution from TDG. In addition, by pyridine borane sequencing (PB-seq), a simple recently developed method that directly maps 5fC/5caC at single-base resolution, we detect the accumulation of 5fC/5caC in TDG-deleted T cells. We also quantify the occurrence of concordant demethylation within and near enhancer regions in the Il4 locus. In an independent system that does not involve cell division, macrophages treated with liposaccharide accumulate 5hmC at enhancers and show altered gene expression without DNA demethylation; loss of TET enzymes disrupts gene expression, but loss of TDG has no effect. We also observe that mice with long-term (1 year) deletion of Tdg are healthy and show normal survival and hematopoiesis. CONCLUSIONS We have quantified the relative contributions of TET and TDG to cell differentiation and DNA demethylation at representative loci in proliferating T cells. We find that TET enzymes regulate T cell differentiation and DNA demethylation primarily through passive dilution of oxi-mCs. In contrast, while we observe a low level of active, replication-independent DNA demethylation mediated by TDG, this process does not appear to be essential for immune cell activation or differentiation.
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Affiliation(s)
- Atsushi Onodera
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
- Institute for Global Prominent Research, Chiba University, 1-33, Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Edahí González-Avalos
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Chan-Wang Jerry Lio
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Present address: Department of Microbial Infection and Immunity, Ohio State University, 460 W 12th Ave, Columbus, OH, 43210, USA
| | - Romain O Georges
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Alfonso Bellacosa
- Cancer Signaling and Epigenetics Program & Cancer Epigenetics Institute, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
- AMED-CREST, AMED, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA.
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25
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Abstract
T lymphocytes undergo carefully orchestrated programming during development in the thymus and subsequently during differentiation in the periphery. This intricate specification allows for cell-type and context-specific transcriptional programs that regulate immune responses to infection and malignancy. Epigenetic changes, including histone modifications and covalent modification of DNA itself through DNA methylation, are now recognized to play a critical role in these cell-fate decisions. DNA methylation is mediated primarily by the actions of the DNA methyltransferase (DNMT) and ten-eleven-translocation (TET) families of epigenetic enzymes. In this review, we discuss the role of DNA methylation and its enzymatic regulators in directing the development and differentiation of CD4+ and CD8+ T-cells.
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Affiliation(s)
- Luis O Correa
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI
| | - Martha S Jordan
- Department of Pathology and Laboratory Medicine; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Shannon A Carty
- Department of Internal Medicine, Division of Hematology and Oncology; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
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26
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Bhattacharyya ND, Counoupas C, Daniel L, Zhang G, Cook SJ, Cootes TA, Stifter SA, Bowen DG, Triccas JA, Bertolino P, Britton WJ, Feng CG. TCR Affinity Controls the Dynamics but Not the Functional Specification of the Antimycobacterial CD4 + T Cell Response. THE JOURNAL OF IMMUNOLOGY 2021; 206:2875-2887. [PMID: 34049970 DOI: 10.4049/jimmunol.2001271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/02/2021] [Indexed: 11/19/2022]
Abstract
The quality of T cell responses depends on the lymphocytes' ability to undergo clonal expansion, acquire effector functions, and traffic to the site of infection. Although TCR signal strength is thought to dominantly shape the T cell response, by using TCR transgenic CD4+ T cells with different peptide:MHC binding affinity, we reveal that TCR affinity does not control Th1 effector function acquisition or the functional output of individual effectors following mycobacterial infection in mice. Rather, TCR affinity calibrates the rate of cell division to synchronize the distinct processes of T cell proliferation, differentiation, and trafficking. By timing cell division-dependent IL-12R expression, TCR affinity controls when T cells become receptive to Th1-imprinting IL-12 signals, determining the emergence and magnitude of the Th1 effector pool. These findings reveal a distinct yet cooperative role for IL-12 and TCR binding affinity in Th1 differentiation and suggest that the temporal activation of clones with different TCR affinity is a major strategy to coordinate immune surveillance against persistent pathogens.
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Affiliation(s)
- Nayan D Bhattacharyya
- Immunology and Host Defense Group, Department of Infectious Diseases and Immunology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia.,Tuberculosis Research Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Claudio Counoupas
- Microbial Pathogenesis and Immunity Group, Department of Infectious Diseases and Immunology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia.,Tuberculosis Research Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Lina Daniel
- Immunology and Host Defense Group, Department of Infectious Diseases and Immunology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia.,Tuberculosis Research Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Guoliang Zhang
- Immunology and Host Defense Group, Department of Infectious Diseases and Immunology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia.,Tuberculosis Research Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Stuart J Cook
- Immune Imaging Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Taylor A Cootes
- Immunology and Host Defense Group, Department of Infectious Diseases and Immunology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia.,Tuberculosis Research Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Sebastian A Stifter
- Immunology and Host Defense Group, Department of Infectious Diseases and Immunology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia.,Tuberculosis Research Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - David G Bowen
- Liver Immunology Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,AW Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia; and
| | - James A Triccas
- Microbial Pathogenesis and Immunity Group, Department of Infectious Diseases and Immunology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia.,Tuberculosis Research Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia
| | - Patrick Bertolino
- Liver Immunology Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,AW Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia; and
| | - Warwick J Britton
- Tuberculosis Research Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Carl G Feng
- Immunology and Host Defense Group, Department of Infectious Diseases and Immunology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia; .,Tuberculosis Research Program, Centenary Institute, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia
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27
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Yan J, Pandey SP, Barnes BJ, Turner JR, Abraham C. T Cell-Intrinsic IRF5 Regulates T Cell Signaling, Migration, and Differentiation and Promotes Intestinal Inflammation. Cell Rep 2021; 31:107820. [PMID: 32610123 PMCID: PMC7409536 DOI: 10.1016/j.celrep.2020.107820] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 04/17/2020] [Accepted: 06/03/2020] [Indexed: 02/06/2023] Open
Abstract
IRF5 polymorphisms are associated with multiple immune-mediated diseases, including ulcerative colitis. IRF5 contributions are attributed to its role in myeloid lineages. How T cell-intrinsic IRF5 contributes to inflammatory outcomes is not well understood. We identify a previously undefined key role for T cell-intrinsic IRF5. In mice, IRF5 in CD4+ T cells promotes Th1- and Th17-associated cytokines and decreases Th2-associated cytokines. IRF5 is required for the optimal assembly of the TCR-initiated signaling complex and downstream signaling at early times, and at later times binds to promoters of Th1- and Th17-associated transcription factors and cytokines. IRF5 also regulates chemokine receptor-initiated signaling and, in turn, T cell migration. In vivo, IRF5 in CD4+ T cells enhances the severity of experimental colitis. Importantly, human CD4+ T cells from high IRF5-expressing disease-risk genetic carriers demonstrate increased chemokine-induced migration and Th1/Th17 cytokines and reduced Th2-associated and anti-inflammatory cytokines. These data demonstrate key roles for T cell-intrinsic IRF5 in inflammatory outcomes.
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Affiliation(s)
- Jie Yan
- Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Surya P Pandey
- Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Betsy J Barnes
- Center for Autoimmune and Musculoskeletal Diseases, The Feinstein Institute for Medical Research, Manhasset, NY, USA
| | - Jerrold R Turner
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Clara Abraham
- Department of Internal Medicine, Yale University, New Haven, CT, USA.
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28
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Opstelten R, Amsen D. Separating the wheat from the chaff: Making sense of Treg heterogeneity for better adoptive cellular therapy. Immunol Lett 2021; 239:96-112. [PMID: 33676975 DOI: 10.1016/j.imlet.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023]
Abstract
Regulatory T (Treg) cells are essential for immunological tolerance and can be used to suppress unwanted or excessive immune responses through adoptive cellular therapy. It is increasingly clear that many subsets of Treg cells exist, which have different functions and reside in different locations. Treg cell therapies may benefit from tailoring the selected subset to the tissue that must be protected as well as to characteristics of the immune response that must be suppressed, but little attention is given to this topic in current therapies. Here, we will discuss how three major axes of heterogeneity can be discerned among the Treg cell population, which determine function and lineage fidelity. A first axis relates to the developmental route, as Treg cells can be generated from immature T cells in the thymus or from already mature Tconv cells in the immunological periphery. Heterogeneity furthermore stems from activation history (naïve or effector) and location (lymphoid or peripheral tissues). Each of these axes bestows specific properties on Treg cells, which are further refined by additional processes leading to yet further variation. A critical aspect impacting on Treg cell heterogeneity is TCR specificity, which determines when and where Treg cells are generated as well as where they exhibit their effector functions. We will discuss the implications of this heterogeneity and the role of the TCR for the design of next generation adoptive cellular therapy with Treg cells.
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Affiliation(s)
- Rianne Opstelten
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Derk Amsen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
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29
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Frias AB, Boi SK, Lan X, Youngblood B. Epigenetic regulation of T cell adaptive immunity. Immunol Rev 2021; 300:9-21. [PMID: 33644866 DOI: 10.1111/imr.12943] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/24/2022]
Abstract
The conceptualization of adaptive immunity, founded on the observation of immunological memory, has served as the basis for modern vaccination and immunotherapy approaches. This fundamental concept has allowed immunologists to explore mechanisms that enable humoral and cellular lymphocytes to tailor immune response functions to a wide array of environmental insults and remain poised for future pathogenic encounters. Until recently, for T cells it has remained unclear how memory differentiation acquires and sustains a gene expression program that grants a cell with a capacity for a heightened recall response. Recent investigations into this critical question have identified epigenetic programs as a causal molecular mechanism governing T cell subset specification and immunological memory. Here, we outline the studies that have illustrated this concept and posit on how insights into T cell adaptive immunity can be applied to improve upon existing immunotherapies.
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Affiliation(s)
- Adolfo B Frias
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shannon K Boi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Lan
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.,College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
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30
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Chan WF, Coughlan HD, Zhou JHS, Keenan CR, Bediaga NG, Hodgkin PD, Smyth GK, Johanson TM, Allan RS. Pre-mitotic genome re-organisation bookends the B cell differentiation process. Nat Commun 2021; 12:1344. [PMID: 33637722 PMCID: PMC7910489 DOI: 10.1038/s41467-021-21536-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 02/02/2021] [Indexed: 01/08/2023] Open
Abstract
During cellular differentiation chromosome conformation is intricately remodelled to support the lineage-specific transcriptional programs required for initiating and maintaining lineage identity. When these changes occur in relation to cell cycle, division and time in response to cellular activation and differentiation signals has yet to be explored, although it has been proposed to occur during DNA synthesis or after mitosis. Here, we elucidate the chromosome conformational changes in B lymphocytes as they differentiate and expand from a naive, quiescent state into antibody secreting plasma cells. We find gene-regulatory chromosome reorganization in late G1 phase before the first division, and that this configuration is remarkably stable as the cells massively and rapidly clonally expand. A second wave of conformational change occurs as cells terminally differentiate into plasma cells, coincident with increased time in G1 phase. These results provide further explanation for how lymphocyte fate is imprinted prior to the first division. They also suggest that chromosome reconfiguration occurs prior to DNA replication and mitosis, and is linked to a gene expression program that controls the differentiation process required for the generation of immunity.
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Affiliation(s)
- Wing Fuk Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Hannah D Coughlan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Jie H S Zhou
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Christine R Keenan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Naiara G Bediaga
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Philip D Hodgkin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
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31
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Rao A. Scientific divagations: from signaling and transcription to chromatin changes in T cells. Nat Immunol 2021; 21:1473-1476. [PMID: 33173218 DOI: 10.1038/s41590-020-00823-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.
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32
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Sekiya T, Kagawa S, Masaki K, Fukunaga K, Yoshimura A, Takaki S. Regulation of peripheral Th/Treg differentiation and suppression of airway inflammation by Nr4a transcription factors. iScience 2021; 24:102166. [PMID: 33665581 PMCID: PMC7907427 DOI: 10.1016/j.isci.2021.102166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/08/2021] [Accepted: 02/04/2021] [Indexed: 12/24/2022] Open
Abstract
Helper T (Th) and regulatory T (Treg) cell differentiation programs promote the eradication of pathogens, while minimizing adverse immune reactions. Here, we found that Nr4a family of nuclear receptors supports Treg cell induction and represses Th1 and Th2 cell differentiation from naive CD4+ T cells. Nr4a factors are transiently induced in CD4+ T cells immediately after antigen stimulation, thereby mediating epigenetic changes. In differentiating Treg cells, Nr4a factors mainly upregulated the early responsive genes in the Treg cell-specifying gene set, either directly or in cooperation with Ets family transcription factors. In contrast, Nr4a factors repressed AP-1 activity by interrupting a positive feedback loop for Batf factor expression, thus suppressing Th2 cell-associated genes. In an allergic airway inflammation model, Nr4a factors suppressed the pathogenesis, mediating oral tolerance. Lastly, pharmacological activation of an engineered Nr4a molecule prevented allergic airway inflammation, indicating that Nr4a factors may be novel therapeutic targets for inflammatory diseases. Among “Treg signature genes”, Nr4a factors mainly induce early responsive ones Nr4a activate target genes directly or by supporting Ets factors' function Nr4a factors repress Th2-driving positive feedback loop for Batf factor expression Pharmacological activation of Nr4a factors' activity prevented airway inflammation
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Affiliation(s)
- Takashi Sekiya
- Section of Immune Response Modification, Department of Immune Regulation, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan.,Department of Immune Regulation, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan
| | - Shizuko Kagawa
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Katsunori Masaki
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Satoshi Takaki
- Department of Immune Regulation, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan
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33
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Subbannayya Y, Haug M, Pinto SM, Mohanty V, Meås HZ, Flo TH, Prasad TK, Kandasamy RK. The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function. Int J Mol Sci 2020; 22:E275. [PMID: 33383959 PMCID: PMC7795831 DOI: 10.3390/ijms22010275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/14/2022] Open
Abstract
CD4+ T cells (T helper cells) are cytokine-producing adaptive immune cells that activate or regulate the responses of various immune cells. The activation and functional status of CD4+ T cells is important for adequate responses to pathogen infections but has also been associated with auto-immune disorders and survival in several cancers. In the current study, we carried out a label-free high-resolution FTMS-based proteomic profiling of resting and T cell receptor-activated (72 h) primary human CD4+ T cells from peripheral blood of healthy donors as well as SUP-T1 cells. We identified 5237 proteins, of which significant alterations in the levels of 1119 proteins were observed between resting and activated CD4+ T cells. In addition to identifying several known T-cell activation-related processes altered expression of several stimulatory/inhibitory immune checkpoint markers between resting and activated CD4+ T cells were observed. Network analysis further revealed several known and novel regulatory hubs of CD4+ T cell activation, including IFNG, IRF1, FOXP3, AURKA, and RIOK2. Comparison of primary CD4+ T cell proteomic profiles with human lymphoblastic cell lines revealed a substantial overlap, while comparison with mouse CD+ T cell data suggested interspecies proteomic differences. The current dataset will serve as a valuable resource to the scientific community to compare and analyze the CD4+ proteome.
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Affiliation(s)
- Yashwanth Subbannayya
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
| | - Markus Haug
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
| | - Sneha M. Pinto
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
| | - Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India; (V.M.); (T.S.K.P.)
| | - Hany Zakaria Meås
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
| | - Trude Helen Flo
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
| | - T.S. Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India; (V.M.); (T.S.K.P.)
| | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; (Y.S.); (M.H.); (S.M.P.); (H.Z.M.); (T.H.F.)
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34
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Moeini Shad T, Yousefi B, Amirifar P, Delavari S, Rae W, Kokhaei P, Abolhassani H, Aghamohammadi A, Yazdani R. Variable Abnormalities in T and B Cell Subsets in Ataxia Telangiectasia. J Clin Immunol 2020; 41:76-88. [PMID: 33052516 DOI: 10.1007/s10875-020-00881-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/29/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND Ataxia-telangiectasia (AT) is a rare genetic condition, caused by biallelic deleterious variants in the ATM gene, and has variable immunological abnormalities. This study aimed to examine immunologic parameters reflecting cell development, activation, proliferation, and class switch recombination (CSR) and determine their relationship to the clinical phenotype in AT patients. METHODS In this study, 40 patients with a confirmed diagnosis of AT from the Iranian immunodeficiency registry center and 28 age-sex matched healthy controls were enrolled. We compared peripheral B and T cell subsets and T cell proliferation response to CD3/CD28 stimulation in AT patients with and without CSR defects using flow cytometry. RESULTS A significant decrease in naïve, transitional, switched memory, and IgM only memory B cells, along with a sharp increase in the marginal zone-like and CD21low B cells was observed in the patients. We also found CD4+ and CD8+ naïve, central memory, and terminally differentiated effector memory CD4+ (TEMRA) T cells were decreased. CD4+ and CD8+ effector memory, CD8+ TEMRA, and CD4+ regulatory T cells were significantly elevated in our patients. CD4+ T cell proliferation was markedly impaired compared to the healthy controls. Moreover, immunological investigations of 15 AT patients with CSR defect revealed a significant reduction in the marginal zone, switched memory, and more intense defects in IgM only memory B cells, CD4+ naïve and central memory T cells. CONCLUSION The present study revealed that patients with AT have a broad spectrum of cellular and humoral deficiencies. Therefore, a detailed evaluation of T and B cell subsets increases understanding of the disease in patients and the risk of infection.
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Affiliation(s)
- Tannaz Moeini Shad
- Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahman Yousefi
- Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Parisa Amirifar
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Delavari
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - William Rae
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Parviz Kokhaei
- Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran.,Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital Solna and Karolinska Institutet, Stockholm, Sweden
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Primary Immunodeficiencies, Iran University of Medical Sciences, Tehran, Iran.,Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Reza Yazdani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
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35
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Hojyo S, Tumes D, Murata A, Tokoyoda K. Multiple developmental pathways lead to the generation of CD4 T-cell memory. Int Immunol 2020; 32:589-595. [PMID: 32766843 DOI: 10.1093/intimm/dxaa051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
Long-term immunological memory mediated by CD4 T cells provides a rapid protection against previously encountered pathogens or antigens. However, it is still controversial how memory CD4 T cells are generated and maintained. Unclear definitions of T-cell memory may be partially responsible for this controversy. It is becoming clear that diverse pathways are responsible for the differentiation and long-term persistence of memory T cells. We herein discuss the diversity of memory cell generation, describing a novel population of resting memory CD4 T cells and their precursors.
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Affiliation(s)
- Shintaro Hojyo
- Deutsches Rheuma-Forschungszentrum Berlin, a Leibniz Institute, Berlin, Germany.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Damon Tumes
- Centre for Cancer Biology, SA Pathology and The University of South Australia, Adelaide, South Australia, Australia
| | - Akihiko Murata
- Department of Immunology, School of Life Science, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
| | - Koji Tokoyoda
- Deutsches Rheuma-Forschungszentrum Berlin, a Leibniz Institute, Berlin, Germany.,Department of Immunology, School of Life Science, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
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36
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Tortola L, Jacobs A, Pohlmeier L, Obermair FJ, Ampenberger F, Bodenmiller B, Kopf M. High-Dimensional T Helper Cell Profiling Reveals a Broad Diversity of Stably Committed Effector States and Uncovers Interlineage Relationships. Immunity 2020; 53:597-613.e6. [PMID: 32735846 DOI: 10.1016/j.immuni.2020.07.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 12/27/2022]
Abstract
CD4+ T helper (Th) cells are fundamental players in immunity. Based on the expression of signature cytokines and transcription factors, several Th subsets have been defined. Th cells are thought to be far more heterogeneous and multifunctional than originally believed, but characterization of the full diversity has been hindered by technical limitations. Here, we employ mass cytometry to analyze the diversity of Th cell responses generated in vitro and in animal disease models, revealing a vast heterogeneity of effector states with distinct cytokine footprints. The diversities of cytokine responses established during primary antigen encounters in Th1- and Th2-cell-polarizing conditions are largely maintained after secondary challenge, regardless of the new inflammatory environment, highlighting many of the identified states as stable Th cell sublineages. We also find that Th17 cells tend to upregulate Th2-cell-associated cytokines upon challenge, indicating a closer developmental connection between Th17 and Th2 cells than previously anticipated.
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Affiliation(s)
- Luigi Tortola
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland.
| | - Andrea Jacobs
- Department of Quantitative Biomedicine, University of Zurich, 8057 Zurich, Switzerland
| | - Lea Pohlmeier
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | | | | | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, 8057 Zurich, Switzerland
| | - Manfred Kopf
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland.
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37
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de Graaf NPJ, Bontkes HJ, Roffel S, Kleverlaan CJ, Rustemeyer T, Gibbs S, Feilzer AJ. Non-heat inactivated autologous serum increases accuracy of in vitro CFSE lymphocyte proliferation test (LPT) for nickel. Clin Exp Allergy 2020; 50:722-732. [PMID: 32215995 PMCID: PMC7317482 DOI: 10.1111/cea.13603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 02/08/2020] [Accepted: 03/04/2020] [Indexed: 01/08/2023]
Abstract
Background Skin patch testing is still seen as the gold standard for the diagnosis of allergic hypersensitivity. For several metals and for patients with a suspected adverse reaction to their medical device implant material, patch testing can be unreliable. The current alternative to metal allergy patch testing is the in vitro lymphocyte proliferation test (LPT) using tritiated thymidine. This method is well‐established but requires handling of radioactive material, often uses heat‐inactivated allogenic human pooled serum and cannot determine T cell subsets. Objective To develop a radioactive free LPT by using carboxyfluorescein succinimidyl ester (CFSE) and to evaluate the influence of serum source (heat‐inactivated human pooled serum [HI HPS] vs autologous serum) on the sensitivity and specificity of the nickel‐specific LPT. Methods Peripheral blood mononuclear cells derived from nickel‐allergic patients and healthy controls were collected, labelled with CFSE and cultured in medium containing 10% HI HPS or 10% autologous serum with or without additional T cell skewing cytokine cocktails (Th1: IL‐7/IL‐12, Th2: IL‐7/IL‐4 or Th17: IL‐7/IL‐23/IL‐1β) in the absence or presence of NiSO4. The stimulation index (SI) was calculated as the ratio of divided cells, that is the percentage of CFSElow/neg CD3+CD4+ T‐lymphocytes upon nickel stimulation compared to the percentage of CFSElow/neg CD3+CD4+ T‐lymphocytes without antigen. These results were compared with the history of Ni allergy, patch test results and the MELISA test. Results Autologous serum positively influenced Ni‐specific proliferation while HI HPS negatively influenced Ni‐specific proliferation. The test protocol analysing CD4+ cells and autologous serum without skewing cytokines scored the best diagnostic values (sensitivity 95%; specificity 93%; and overall accuracy 94%) compared to the parallel test using HI HPS (accuracy 60%). Cytokine supplements did not further improve the test protocol which used autologous serum. The protocol using HI HPS could be further improved by addition of the cytokine skewing cocktails. Conclusions Here, we describe an optimized and highly accurate flow cytometric LPT which comprises of CFSE‐labelled cells cultured in autologous serum (not heat inactivated) and without the presence of T cell skewing cytokines. Clinical relevance The sensitivity and specificity of LPT is enhanced, compared to HI HPS, when autologous serum without skewing cytokines is used.
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Affiliation(s)
- Niels P J de Graaf
- Department of Dermatology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Dental Materials Science, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Hetty J Bontkes
- Department of Clinical Chemistry, Medical Immunology Laboratory, Amsterdam Infection & Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sanne Roffel
- Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam, MOVE Research Institute Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Cornelis J Kleverlaan
- Department of Dental Materials Science, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Thomas Rustemeyer
- Department of Dermatology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sue Gibbs
- Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam, MOVE Research Institute Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Molecular Cell Biology and Immunology, Amsterdam Infection & Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Albert J Feilzer
- Department of Dental Materials Science, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Adoue V, Joffre O. [Endogenous retroviruses: friend or foe of the immune system?]. Med Sci (Paris) 2020; 36:253-260. [PMID: 32228844 DOI: 10.1051/medsci/2020022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Upon priming by dendritic cells, naïve CD4 T lymphocytes are exposed to distinct molecular environments depending on the nature of the pathological stimulus. In response, they mobilize different gene networks that establish lineage-specific developmental programs, and coordinate the acquisition of specific phenotype and functions. Accordingly, CD4 T cells are capable of differentiation into a large variety of functionally-distinct T helper (Th) cell subsets. In this review, we describe the molecular events that control CD4 T cell differentiation at the level of the chromatin. We insist on recent works that have highlighted the key role of H3K9me3-dependent epigenetic mechanisms in the regulation of T cell identity. Interestingly, these pathways shape and control the developmental programs at least in part through the regulation of endogenous retroviruses-derived sequences that have been exapted into cis-regulatory modules of Th genes.
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Affiliation(s)
- Véronique Adoue
- Centre de Physiopathologie Toulouse Purpan, Inserm U1043 - BP 3028, 31024 Toulouse Cedex 3, France
| | - Olivier Joffre
- Centre de Physiopathologie Toulouse Purpan, Inserm U1043 - BP 3028, 31024 Toulouse Cedex 3, France
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39
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Al-Ghezi ZZ, Singh N, Mehrpouya-Bahrami P, Busbee PB, Nagarkatti M, Nagarkatti PS. AhR Activation by TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) Attenuates Pertussis Toxin-Induced Inflammatory Responses by Differential Regulation of Tregs and Th17 Cells Through Specific Targeting by microRNA. Front Microbiol 2019; 10:2349. [PMID: 31681214 PMCID: PMC6813193 DOI: 10.3389/fmicb.2019.02349] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022] Open
Abstract
The Aryl Hydrocarbon Receptor (AhR) is a transcription factor that, when activated by ligand-binding, has been shown to regulate the immune response. Pertussis Toxin (PTX) is a virulence factor found in Bordetella pertussis, a human respiratory pathogen that causes whooping cough. PTX promotes colonization and disease promotion by triggering a heightened inflammatory response. The role of AhR in the regulation of PTX-mediated inflammation has not previously been studied. In the current study, we investigate if AhR activation by 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), a well characterized ligand, can attenuate PTX-mediated systemic inflammation. To that end, C57BL/6 mice were injected intraperitoneally (IP) with PTX twice and treated with TCDD or vehicle (VEH). The PTX+VEH group showed elevated levels of pro-inflammatory cytokines (IL-17A, IL-6, and IFNγ) in serum and increased proportions of CD4+ Th1 and Th17 cells in their spleens. In contrast, the PTX+TCDD group showed significantly lower levels of these inflammatory cytokines and decreased proportions of Th1 and Th17 cells, but increased proportions of Th2 and FoxP3+Tregs when compared to the PTX+VEH group. PTX+TCDD treated mice also showed elevated levels of IL-10, and TFG-b, potent anti-inflammatory cytokines. MicroRNAs (miRs) analysis of CD4+ T cells from the spleens of the PTX+TCDD treated mice revealed significant alterations in their expression and several of these miRs targeted cytokines and signaling molecules involved in inflammation. Specifically, the PTX+TCDD group had a significantly enhanced expression of miR-3082-5p that targeted IL-17, and a decreased expression of miR-1224-5p, which targeted FoxP3. Transfection studies with these miR mimics and inhibitors confirmed the specificity of the target genes. The current study suggests that AhR activation by TCDD suppresses PTX-induced inflammation through miR regulation that triggers reciprocal polarization of Tregs and Th17 cells and also suggests that AhR activation may serve as a treatment modality to suppress heightened inflammation induced during B. pertussis infection.
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Affiliation(s)
- Zinah Zamil Al-Ghezi
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Narendra Singh
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Pegah Mehrpouya-Bahrami
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Philip Brandon Busbee
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Prakash S Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
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40
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41
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DNA (Hydroxy)Methylation in T Helper Lymphocytes. Trends Biochem Sci 2019; 44:589-598. [DOI: 10.1016/j.tibs.2019.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/24/2022]
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42
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Wang P, Xu Y, Zhang J, Shi L, Lei T, Hou Y, Lu Z, Zhao Y. The amino acid sensor general control nonderepressible 2 (GCN2) controls T H9 cells and allergic airway inflammation. J Allergy Clin Immunol 2019; 144:1091-1105. [PMID: 31121187 DOI: 10.1016/j.jaci.2019.04.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 04/11/2019] [Accepted: 04/17/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND TH9 cells have emerged as important mediators of allergic airway inflammation. There is evidence that general control nonderepressible 2 (GCN2) affects the immune response under some stress conditions. However, whether GCN2 regulates CD4+ T-cell differentiation during allergic inflammation remains unknown. OBJECTIVE We sought to clarify the regulatory roles of GCN2 in CD4+ T-cell subset differentiation and its significance in patients with allergic airway inflammation. METHODS The effects of GCN2 in differentiation of TH cell subsets were detected by using the in vitro induction system. GCN2 knockout mice, ovalbumin-induced allergic airway inflammation, and adoptive transfer mouse models were used to determine the significance of GCN2 in TH9 differentiation and allergic airway inflammation in vivo. RNA sequencing, real-time PCR, Western blotting, and other molecular approaches were used to identify the molecular mechanisms relevant to regulation of GCN2 in TH9 cell differentiation. RESULTS GCN2 deficiency significantly inhibited differentiation of TH9 cells but not TH1, TH2, and regulatory T cells. GCN2 knockout mice and recombination-activating gene 2 knockout (Rag2KO) mice that received adoptively transferred GCN2-deficient CD4+ T cells exhibited reduced TH9 differentiation and less severe allergic airway inflammation. Furthermore, the isolated GCN2-deficient TH9 cells also mediated less severe allergic airway inflammation on adoptive transfer. Mechanistically, GCN2 deficiency inhibits TH9 cell differentiation through a hypoxia-inducible factor 1α-dependent glycolytic pathway. CONCLUSION Our results reveal a novel role of GCN2 in TH9 cell differentiation. Our findings indicate that new strategies to inhibit GCN2 activity might provide novel approaches to attenuate allergic airway inflammation.
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Affiliation(s)
- Peng Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; Department of Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yana Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jiayu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Lu Shi
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tong Lei
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangxiao Hou
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhongbing Lu
- University of Chinese Academy of Sciences, Beijing, China.
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
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Lio CWJ, Shukla V, Samaniego-Castruita D, González-Avalos E, Chakraborty A, Yue X, Schatz DG, Ay F, Rao A. TET enzymes augment activation-induced deaminase (AID) expression via 5-hydroxymethylcytosine modifications at the Aicda superenhancer. Sci Immunol 2019; 4:eaau7523. [PMID: 31028100 PMCID: PMC6599614 DOI: 10.1126/sciimmunol.aau7523] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/19/2019] [Indexed: 12/15/2022]
Abstract
TET enzymes are dioxygenases that promote DNA demethylation by oxidizing the methyl group of 5-methylcytosine to 5-hydroxymethylcytosine (5hmC). Here, we report a close correspondence between 5hmC-marked regions, chromatin accessibility and enhancer activity in B cells, and a strong enrichment for consensus binding motifs for basic region-leucine zipper (bZIP) transcription factors at TET-responsive genomic regions. Functionally, Tet2 and Tet3 regulate class switch recombination (CSR) in murine B cells by enhancing expression of Aicda, which encodes the activation-induced cytidine deaminase (AID) enzyme essential for CSR. TET enzymes deposit 5hmC, facilitate DNA demethylation, and maintain chromatin accessibility at two TET-responsive enhancer elements, TetE1 and TetE2, located within a superenhancer in the Aicda locus. Our data identify the bZIP transcription factor, ATF-like (BATF) as a key transcription factor involved in TET-dependent Aicda expression. 5hmC is not deposited at TetE1 in activated Batf-deficient B cells, indicating that BATF facilitates TET recruitment to this Aicda enhancer. Our study emphasizes the importance of TET enzymes for bolstering AID expression and highlights 5hmC as an epigenetic mark that captures enhancer dynamics during cell activation.
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Affiliation(s)
- Chan-Wang J Lio
- Division of Signaling and Gene Expression, La Jolla Institute, San Diego, CA, USA.
| | - Vipul Shukla
- Division of Signaling and Gene Expression, La Jolla Institute, San Diego, CA, USA
| | | | | | | | - Xiaojing Yue
- Division of Signaling and Gene Expression, La Jolla Institute, San Diego, CA, USA
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ferhat Ay
- Division of Vaccine Discovery, La Jolla Institute, San Diego, CA, USA
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute, San Diego, CA, USA.
- Sanford Consortium for Regenerative Medicine, San Diego, CA, USA
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California, San Diego, San Diego, CA, USA
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Laphanuwat P, Jirawatnotai S. Immunomodulatory Roles of Cell Cycle Regulators. Front Cell Dev Biol 2019; 7:23. [PMID: 30863749 PMCID: PMC6399147 DOI: 10.3389/fcell.2019.00023] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 02/08/2019] [Indexed: 01/11/2023] Open
Abstract
Core cell cycle regulators, including cyclin-dependent kinases (CDKs), cyclins, and cyclin-dependent kinase inhibitors (CKIs), are known for their well-characterized roles in cell division. Several recent studies have shed light on the roles of these proteins in immune modulation. The development and activation of cells in the immune system take place not only during embryonic development but throughout the life of a multicellular organism. Cell cycle regulators are involved in the development of immune cells, partly as the machinery controlling the expansion and differentiation of the populations of immune cells. In addition, these proteins serve non-cell cycle functions. In this review, we summarize the emerging roles of cell cycle regulators in modulating functions of the immune system and discuss how they may be exploited as therapeutic targets.
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Affiliation(s)
- Phatthamon Laphanuwat
- Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Siriraj Center of Research for Excellence for Systems Pharmacology, Mahidol University, Bangkok, Thailand
| | - Siwanon Jirawatnotai
- Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Siriraj Center of Research for Excellence for Systems Pharmacology, Mahidol University, Bangkok, Thailand
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Vincenzetti L, Leoni C, Chirichella M, Kwee I, Monticelli S. The contribution of active and passive mechanisms of 5mC and 5hmC removal in human T lymphocytes is differentiation- and activation-dependent. Eur J Immunol 2019; 49:611-625. [PMID: 30698829 DOI: 10.1002/eji.201847967] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/15/2019] [Accepted: 01/29/2019] [Indexed: 12/11/2022]
Abstract
In mammals, the 5'-methylcytosine (5mC) modification in the genomic DNA contributes to the dynamic control of gene expression. 5mC erasure is required for the activation of developmental programs and occurs either by passive dilution through DNA replication, or by enzymatic oxidation of the methyl mark to 5-hydroxymethylcytosine (5hmC), which can persist as such or undergo further oxidation and enzymatic removal. The relative contribution of each mechanism to epigenetic control in dynamic biological systems still remains a compelling question. To explore this critical issue, we used primary human T lymphocytes, in which two cellular states can be clearly identified, namely quiescent naïve T cells, which are slowly or rarely proliferating, and rapidly proliferating activated T cells. We found that active mechanisms of methylation removal were selectively at work in naïve T cells, while memory T lymphocytes entirely relied on passive, replication-dependent dilution, suggesting that proliferative capacity influences the choice of the preferential demethylation mechanism. Active processes of demethylation appear to be critical in quiescent naïve T lymphocytes for the maintenance of regulatory regions poised for rapid responses to physiological stimuli.
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Affiliation(s)
- Lucia Vincenzetti
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Cristina Leoni
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Michele Chirichella
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Ivo Kwee
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Silvia Monticelli
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
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Abstract
Interferon gamma, referred to here as IFN-γ, is a major component in immunological cell signaling and is a critical regulatory protein for overall immune system function. First discovered in 1965 (Wheelock Science 149: (3681)310-311, 1965), IFN-γ is the only Type II interferon identified. Its expression is both positively and negatively controlled by different factors. In this chapter, we will review the transcriptional and post-transcriptional control of IFN-γ expression. In the transcriptional control part, the regular activators and suppressors are summarized, we will also focus on the epigenetic control, such as chromosome access, DNA methylation, and histone acetylation. The more we learn about the control of this regulatory protein will allow us to apply this knowledge in the future to effectively manipulate IFN-γ expression for the treatment of infections, cancer, inflammation, and autoimmune diseases.
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47
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Sungnak W, Wang C, Kuchroo VK. Multilayer regulation of CD4 T cell subset differentiation in the era of single cell genomics. Adv Immunol 2019; 141:1-31. [PMID: 30904130 DOI: 10.1016/bs.ai.2018.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CD4 T cells are major immune cell types that mediate effector responses appropriate for diverse incoming threats. These cells have been categorized into different subsets based on how they are induced, expression of specific master transcription factors, and the resulting effector cell phenotypes as defined by expression of signature cytokines. However, recent studies assessing the expression of gene modules in single CD4 T cells, rather than expression of one or a few signature genes, have provided a more complex picture in which the canonical model does not fit as cleanly as proposed. Here, we review the concepts of lineage commitment, plasticity and functional heterogeneity in the context of this greater complexity. We then apply our current understanding of CD4 T cell subsets to discuss outstanding questions regarding follicular helper T cells and follicular regulatory T cells with respect to their shared features with other known CD4 T cell subsets.
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Affiliation(s)
- Waradon Sungnak
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, United States
| | - Chao Wang
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, United States
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, United States; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, United States.
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Hirata H, Yukawa T, Tanaka A, Miyao T, Fukuda T, Fukushima Y, Kurasawa K, Arima M. Th2 cell differentiation from naive CD4 + T cells is enhanced by autocrine CC chemokines in atopic diseases. Clin Exp Allergy 2018; 49:474-483. [PMID: 30431203 DOI: 10.1111/cea.13313] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/22/2018] [Accepted: 09/28/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Chemokines are involved not only in regulating leucocyte recruitment, but also in other activities. However, functions other than cell recruitment remain poorly understood. We have already shown that the production of CC chemokine ligand (CCL)17 and CCL22 by antigen-stimulated naïve CD4+ T cells was higher in asthmatic patients than in healthy controls. However, the role of these chemokines in stimulated naïve CD4+ T cells remains unclear. OBJECTIVE To clarify the biological function of CCL17 and CCL22 on naïve CD4+ T, we examined effects of these two chemokines on naïve CD4+ T cells expressing CC chemokine receptor (CCR)4 (a receptor for CCL17 and CCL22) during differentiation of Th2 cells in asthmatic patients as allergic subjects. METHODS Naïve CD4+ T cells were prepared from healthy controls and patients with asthma. We analysed effect of CCL17 and CCL22, and blocking their receptor on differentiation of Th2 cells. RESULTS Production of CCL17 and CCL22 by activated naive CD4+ T cells under Th2 condition was much more in asthmatic patients than in healthy controls. Proliferation and survival of the Th2 differentiating cells and restimulation-induced IL-4 production were much greater in asthmatic patients than in healthy controls. These cell biological phenomena were inhibited by blockade of CCR4. The biological effects of exogenous CCL17 and CCL22 were apparently observed in both healthy controls and asthmatic patients. The effectiveness of these chemokines on naïve CD4+ T cells from healthy controls was stronger than those from asthmatic patients. We found that thymic stromal lymphopoietin (TSLP), a Th2 promoting chemokine, is involved in the activation of CD4+ naïve T cells via production of CCL17 and CCL22. CONCLUSIONS AND CLINICAL RELEVANCE These data suggest that CCL17 and CCL22 produced by TSLP-primed naïve CD4+ T cells in asthma might contribute to an increase in Th2 cells via autocrine loops.
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Affiliation(s)
- Hirokuni Hirata
- Department of Respiratory Medicine and Clinical Immunology, Dokkyo Medical University Koshigaya Hospital, Koshigaya, Japan
| | - Tatsuo Yukawa
- Department of Pulmonary Medicine and Clinical Immunology, School of Medicine, Dokkyo Medical University, Mibu, Japan
| | - Ayae Tanaka
- Department of Rheumatology, School of Medicine, Dokkyo Medical University, Mibu, Japan
| | - Tomoyuki Miyao
- Department of Rheumatology, School of Medicine, Dokkyo Medical University, Mibu, Japan
| | - Takeshi Fukuda
- Department of Pulmonary Medicine and Clinical Immunology, School of Medicine, Dokkyo Medical University, Mibu, Japan
| | - Yasutsugu Fukushima
- Department of Respiratory Medicine and Clinical Immunology, Dokkyo Medical University Koshigaya Hospital, Koshigaya, Japan
| | - Kazuhiro Kurasawa
- Department of Rheumatology, School of Medicine, Dokkyo Medical University, Mibu, Japan
| | - Masafumi Arima
- Department of Rheumatology, School of Medicine, Dokkyo Medical University, Mibu, Japan
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49
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Previte DM, Piganelli JD. Reactive Oxygen Species and Their Implications on CD4 + T Cells in Type 1 Diabetes. Antioxid Redox Signal 2018; 29:1399-1414. [PMID: 28990401 DOI: 10.1089/ars.2017.7357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Previous work has indicated that type 1 diabetes (T1D) pathology is highly driven by reactive oxygen species (ROS). One way in which ROS shape the autoimmune response demonstrated in T1D is by promoting CD4+ T cell activation and differentiation. As CD4+ T cells are a significant contributor to pancreatic β cell destruction in T1D, understanding how ROS impact their development, activation, and differentiation is critical. Recent Advances: CD4+ T cells themselves generate ROS via nicotinamide adenine dinucleotide phosphate (NADPH) oxidase expression and electron transport chain activity. Moreover, T cells can also be exposed to exogenous ROS generated by other immune cells (e.g., macrophages and dendritic cells) and β cells. Genetically modified animals and ROS inhibitors have demonstrated that ROS blockade during activation results in CD4+ T cell hyporesponsiveness and reduced diabetes incidence. Critical Issues and Future Directions: Although the majority of studies with regard to T1D and CD4+ T cells have been done to examine the influence of redox on CD4+ T cell activation, this is not the only circumstance in which a T cell can be impacted by redox. ROS and redox have also been shown to play roles in CD4+ T cell-related tolerogenic mechanisms, including thymic selection and regulatory T cell-mediated suppression. However, the effect of these mechanisms with respect to T1D pathogenesis remains elusive. Therefore, pursuing these avenues may provide valuable insight into the global role of ROS and redox in autoreactive CD4+ T cell formation and function.
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Affiliation(s)
- Dana M Previte
- Department of Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center , Pittsburgh, Pennsylvania
| | - Jon D Piganelli
- Department of Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center , Pittsburgh, Pennsylvania
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50
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Pramanik J, Chen X, Kar G, Henriksson J, Gomes T, Park JE, Natarajan K, Meyer KB, Miao Z, McKenzie ANJ, Mahata B, Teichmann SA. Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation. Genome Med 2018; 10:76. [PMID: 30355343 PMCID: PMC6199730 DOI: 10.1186/s13073-018-0589-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/12/2018] [Indexed: 12/24/2022] Open
Abstract
Background The IRE1a-XBP1 pathway is a conserved adaptive mediator of the unfolded protein response. The pathway is indispensable for the development of secretory cells by facilitating protein folding and enhancing secretory capacity. In the immune system, it is known to function in dendritic cells, plasma cells, and eosinophil development and differentiation, while its role in T helper cell is unexplored. Here, we investigated the role of the IRE1a-XBP1 pathway in regulating activation and differentiation of type-2 T helper cell (Th2), a major T helper cell type involved in allergy, asthma, helminth infection, pregnancy, and tumor immunosuppression. Methods We perturbed the IRE1a-XBP1 pathway and interrogated its role in Th2 cell differentiation. We performed genome-wide transcriptomic analysis of differential gene expression to reveal IRE1a-XBP1 pathway-regulated genes and predict their biological role. To identify direct target genes of XBP1 and define XBP1’s regulatory network, we performed XBP1 ChIPmentation (ChIP-seq). We validated our predictions by flow cytometry, ELISA, and qPCR. We also used a fluorescent ubiquitin cell cycle indicator mouse to demonstrate the role of XBP1 in the cell cycle. Results We show that Th2 lymphocytes induce the IRE1a-XBP1 pathway during in vitro and in vivo activation. Genome-wide transcriptomic analysis of differential gene expression by perturbing the IRE1a-XBP1 pathway reveals XBP1-controlled genes and biological pathways. Performing XBP1 ChIPmentation (ChIP-seq) and integrating with transcriptomic data, we identify XBP1-controlled direct target genes and its transcriptional regulatory network. We observed that the IRE1a-XBP1 pathway controls cytokine secretion and the expression of two Th2 signature cytokines, IL13 and IL5. We also discovered that the IRE1a-XBP1 pathway facilitates activation-dependent Th2 cell proliferation by facilitating cell cycle progression through S and G2/M phase. Conclusions We confirm and detail the critical role of the IRE1a-XBP1 pathway during Th2 lymphocyte activation in regulating cytokine expression, secretion, and cell proliferation. Our high-quality genome-wide XBP1 ChIP and gene expression data provide a rich resource for investigating XBP1-regulated genes. We provide a browsable online database available at http://data.teichlab.org. Electronic supplementary material The online version of this article (10.1186/s13073-018-0589-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Gozde Kar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Johan Henriksson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kedar Natarajan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Zhichao Miao
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Andrew N J McKenzie
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Bidesh Mahata
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. .,Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge, CB3 0HE, UK.
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