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Theofilatos D, Ho T, Waitt G, Äijö T, Schiapparelli LM, Soderblom EJ, Tsagaratou A. Deciphering the TET3 interactome in primary thymic developing T cells. iScience 2024; 27:109782. [PMID: 38711449 PMCID: PMC11070343 DOI: 10.1016/j.isci.2024.109782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Ten-eleven translocation (TET) proteins are DNA dioxygenases that mediate active DNA demethylation. TET3 is the most highly expressed TET protein in thymic developing T cells. TET3, either independently or in cooperation with TET1 or TET2, has been implicated in T cell lineage specification by regulating DNA demethylation. However, TET-deficient mice exhibit complex phenotypes, suggesting that TET3 exerts multifaceted roles, potentially by interacting with other proteins. We performed liquid chromatography with tandem mass spectrometry in primary developing T cells to identify TET3 interacting partners in endogenous, in vivo conditions. We discover TET3 interacting partners. Our data establish that TET3 participates in a plethora of fundamental biological processes, such as transcriptional regulation, RNA polymerase elongation, splicing, DNA repair, and DNA replication. This resource brings in the spotlight emerging functions of TET3 and sets the stage for systematic studies to dissect the precise mechanistic contributions of TET3 in shaping T cell biology.
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Affiliation(s)
- Dimitris Theofilatos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tricia Ho
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Greg Waitt
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Tarmo Äijö
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Erik J. Soderblom
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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2
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Hughes K, Conaway E, Blackwell E, Rout E, Yoshimoto J, Burnett R, Avery A. Canine T zone lymphoma is a tumor of mature, previously activated αβ T cells. Vet Immunol Immunopathol 2024; 269:110725. [PMID: 38359755 DOI: 10.1016/j.vetimm.2024.110725] [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: 10/23/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 02/17/2024]
Abstract
T cell lymphomas are a diverse group of tumors found in both dogs and humans, originating from various normal T cell types. Identifying the origin of neoplastic lymphocytes can offer valuable insights into the pathogenesis and clinical behavior of these tumors. T zone lymphoma (TZL) in dogs is characterized by the absence of CD45 expression, a strong breed predilection, and its association with adult-onset demodicosis-a condition believed to be linked to immunosuppression. In this study, our aim was to employ transcriptomic and functional data to determine the normal counterpart of TZL. Identifying the normal counterpart may help us understand both how these tumors arise and explain their clinical behavior. Gene expression profiling using NanoString and RNA seq was used to compare the transcriptome between neoplastic T zone cells, normal canine T cells and publicly available gene sets using Gene Set Enrichment Analysis. Mitogen, anti-CD3 stimulation and PMA/ionomycin stimulation were used to assess T cell proliferation in vitro, and intracellular cytokine production was measured by flow cytometry. Gene expression profiling revealed that TZL is most likely derived from an activated or memory alpha-beta T cell but the cells do not fall cleanly into an effector subtype. TZL cells express CD4-specific transcription factors GATA3 and THPOK, even though TZL cells more commonly express CD8, or neither CD4 nor CD8. TZL cells produce high levels of interferon gamma and tumor necrosis factor alpha when stimulated, further supporting the hypothesis that they are derived from an antigen experienced T cell. TZL cells do not proliferate when stimulated through the T cell receptor but will divide when the T cell receptor is bypassed with PMA and ionomycin. The observation that these cells are derived from a mature, previously activated T cell is the first step in understanding the genesis of this unique T cell tumor.
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Affiliation(s)
- Kelly Hughes
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Evan Conaway
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Emily Blackwell
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Emily Rout
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Janna Yoshimoto
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Robert Burnett
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Anne Avery
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States.
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Bakhtiyaridovvombaygi M, Yazdanparast S, Mikanik F, Izadpanah A, Parkhideh S, Shahbaz Ghasabeh A, Roshandel E, Hajifathali A, Gharehbaghian A. Cytokine-Induced Memory-Like NK Cells: Emerging strategy for AML immunotherapy. Biomed Pharmacother 2023; 168:115718. [PMID: 37857247 DOI: 10.1016/j.biopha.2023.115718] [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: 08/18/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease developed from the malignant expansion of myeloid precursor cells in the bone marrow and peripheral blood. The implementation of intensive chemotherapy and hematopoietic stem cell transplantation (HSCT) has improved outcomes associated with AML, but relapse, along with suboptimal outcomes, is still a common scenario. In the past few years, exploring new therapeutic strategies to optimize treatment outcomes has occurred rapidly. In this regard, natural killer (NK) cell-based immunotherapy has attracted clinical interest due to its critical role in immunosurveillance and their capabilities to target AML blasts. NK cells are cytotoxic innate lymphoid cells that mediate anti-viral and anti-tumor responses by producing pro-inflammatory cytokines and directly inducing cytotoxicity. Although NK cells are well known as short-lived innate immune cells with non-specific responses that have limited their clinical applications, the discovery of cytokine-induced memory-like (CIML) NK cells could overcome these challenges. NK cells pre-activated with the cytokine combination IL-12/15/18 achieved a long-term life span with adaptive immunity characteristics, termed CIML-NK cells. Previous studies documented that using CIML-NK cells in cancer treatment is safe and results in promising outcomes. This review highlights the current application, challenges, and opportunities of CIML-NK cell-based therapy in AML.
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Affiliation(s)
- Mehdi Bakhtiyaridovvombaygi
- Student Research Committee, Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Yazdanparast
- Student Research Committee, Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Mikanik
- Student Research Committee, Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirhossein Izadpanah
- Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sahar Parkhideh
- Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amin Shahbaz Ghasabeh
- Department of Hematology and Blood Bank, School of Allied Medical Science, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Elham Roshandel
- Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Abbas Hajifathali
- Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ahmad Gharehbaghian
- Department of Hematology and Blood Bank, School of Allied Medical Science, Shahid Beheshti University of Medical Science, Tehran, Iran; Pediatric Congenital Hematologic Disorders Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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4
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Ozturk K, Panwala R, Sheen J, Ford K, Payne N, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551876. [PMID: 37577681 PMCID: PMC10418284 DOI: 10.1101/2023.08.03.551876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Understanding the consequences of single amino acid substitutions in cancer driver genes remains an unmet need. Perturb-seq provides a tool to investigate the effects of individual mutations on cellular programs. Here we deploy SEUSS, a Perturb-seq like approach, to generate and assay mutations at physical interfaces of the RUNX1 Runt domain. We measured the impact of 115 mutations on RNA profiles in single myelogenous leukemia cells and used the profiles to categorize mutations into three functionally distinct groups: wild-type (WT)-like, loss-of-function (LOF)-like and hypomorphic. Notably, the largest concentration of functional mutations (non-WT-like) clustered at the DNA binding site and contained many of the more frequently observed mutations in human cancers. Hypomorphic variants shared characteristics with loss of function variants but had gene expression profiles indicative of response to neural growth factor and cytokine recruitment of neutrophils. Additionally, DNA accessibility changes upon perturbations were enriched for RUNX1 binding motifs, particularly near differentially expressed genes. Overall, our work demonstrates the potential of targeting protein interaction interfaces to better define the landscape of prospective phenotypes reachable by amino acid substitutions.
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Ober-Reynolds B, Wang C, Ko JM, Rios EJ, Aasi SZ, Davis MM, Oro AE, Greenleaf WJ. Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases. Nat Genet 2023; 55:1288-1300. [PMID: 37500727 DOI: 10.1038/s41588-023-01445-4] [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: 09/01/2022] [Accepted: 06/17/2023] [Indexed: 07/29/2023]
Abstract
Genome-wide association studies have identified many loci associated with hair and skin disease, but identification of causal variants requires deciphering of gene-regulatory networks in relevant cell types. We generated matched single-cell chromatin profiles and transcriptomes from scalp tissue from healthy controls and patients with alopecia areata, identifying diverse cell types of the hair follicle niche. By interrogating these datasets at multiple levels of cellular resolution, we infer 50-100% more enhancer-gene links than previous approaches and show that aggregate enhancer accessibility for highly regulated genes predicts expression. We use these gene-regulatory maps to prioritize cell types, genes and causal variants implicated in the pathobiology of androgenetic alopecia (AGA), eczema and other complex traits. AGA genome-wide association studies signals are enriched in dermal papilla regulatory regions, supporting the role of these cells as drivers of AGA pathogenesis. Finally, we train machine learning models to nominate single-nucleotide polymorphisms that affect gene expression through disruption of transcription factor binding, predicting candidate functional single-nucleotide polymorphism for AGA and eczema.
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Affiliation(s)
| | - Chen Wang
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Dermatology, Department of Medicine, Santa Clara Valley Medical Center, San Jose, CA, USA
- Institute of Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Justin M Ko
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Eon J Rios
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Dermatology, Department of Medicine, Santa Clara Valley Medical Center, San Jose, CA, USA
| | - Sumaira Z Aasi
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Mark M Davis
- Institute of Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Anthony E Oro
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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6
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Hussain S, Sadouni N, van Essen D, Dao LTM, Ferré Q, Charbonnier G, Torres M, Gallardo F, Lecellier CH, Sexton T, Saccani S, Spicuglia S. Short tandem repeats are important contributors to silencer elements in T cells. Nucleic Acids Res 2023; 51:4845-4866. [PMID: 36929452 PMCID: PMC10250210 DOI: 10.1093/nar/gkad187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 02/26/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
The action of cis-regulatory elements with either activation or repression functions underpins the precise regulation of gene expression during normal development and cell differentiation. Gene activation by the combined activities of promoters and distal enhancers has been extensively studied in normal and pathological contexts. In sharp contrast, gene repression by cis-acting silencers, defined as genetic elements that negatively regulate gene transcription in a position-independent fashion, is less well understood. Here, we repurpose the STARR-seq approach as a novel high-throughput reporter strategy to quantitatively assess silencer activity in mammals. We assessed silencer activity from DNase hypersensitive I sites in a mouse T cell line. Identified silencers were associated with either repressive or active chromatin marks and enriched for binding motifs of known transcriptional repressors. CRISPR-mediated genomic deletions validated the repressive function of distinct silencers involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Finally, we unravel an association of silencer activity with short tandem repeats, highlighting the role of repetitive elements in silencer activity. Our results provide a general strategy for genome-wide identification and characterization of silencer elements.
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Affiliation(s)
- Saadat Hussain
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Nori Sadouni
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Dominic van Essen
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Lan T M Dao
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Quentin Ferré
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Magali Torres
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Frederic Gallardo
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Charles-Henri Lecellier
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- LIRMM, University of Montpellier, CNRS, Montpellier, France
| | - Tom Sexton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire – IGBMC (CNRS UMR 7104, INSERM U1258, Université de Strasbourg), 67404 Illkirch, France
| | - Simona Saccani
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
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RUNX3 Meets the Ubiquitin-Proteasome System in Cancer. Cells 2023; 12:cells12050717. [PMID: 36899853 PMCID: PMC10001085 DOI: 10.3390/cells12050717] [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: 01/17/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
RUNX3 is a transcription factor with regulatory roles in cell proliferation and development. While largely characterized as a tumor suppressor, RUNX3 can also be oncogenic in certain cancers. Many factors account for the tumor suppressor function of RUNX3, which is reflected by its ability to suppress cancer cell proliferation after expression-restoration, and its inactivation in cancer cells. Ubiquitination and proteasomal degradation represent a major mechanism for the inactivation of RUNX3 and the suppression of cancer cell proliferation. On the one hand, RUNX3 has been shown to facilitate the ubiquitination and proteasomal degradation of oncogenic proteins. On the other hand, RUNX3 can be inactivated through the ubiquitin-proteasome system. This review encapsulates two facets of RUNX3 in cancer: how RUNX3 suppresses cell proliferation by facilitating the ubiquitination and proteasomal degradation of oncogenic proteins, and how RUNX3 is degraded itself through interacting RNA-, protein-, and pathogen-mediated ubiquitination and proteasomal degradation.
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TRANSPARENT: a Python tool for designing transcription factor regulatory networks. Soft comput 2023. [DOI: 10.1007/s00500-023-07888-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
AbstractTranscription factors are proteins able to selectively bind DNA short traits, namely transcription factors binding sites, in order to regulate gene expression in terms of both repression and activation. Despite plenty of studies focusing on transcription factors and on the role they play in specific biological tasks or diseases, is available in the literature, to our knowledge there is no tool able to automatically provide a list of transcription factors involved in this task and the associated interaction network through a solid computational analysis. TRANScriPtion fActor REgulatory NeTwork (TRANSPARENT) is a user-friendly Python tool designed to help researchers in studying given biological tasks or given diseases in human, by identifying transcription factors controlling and regulating the expression of genes associated with that task or disease. The tool takes in input a list of gene IDs and provides (1) a set of transcription factors that are significantly associated with the input genes, (2) the correspondent P values (i.e., the probability that this observed association was driven by chance) and (3) a transcription factor network that can be directly visualized through STRING database. The effectiveness and reliability of the tool were assessed by applying it to two different test cases: schizophrenia and autism disorders. The obtained results clearly show that identified TFs, for both datasets, are significantly associated with those disorders, in terms of both gene enrichment and coherence with the literature. The proposed tool TRANSPARENT can be a useful instrument to investigate transcription factor networks and unveil the role that TFs play in given biological tasks and diseases.
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Äijö T, Theofilatos D, Cheng M, Smith MD, Xiong Y, Baldwin AS, Tsagaratou A. TET proteins regulate T cell and iNKT cell lineage specification in a TET2 catalytic dependent manner. Front Immunol 2022; 13:940995. [PMID: 35990681 PMCID: PMC9389146 DOI: 10.3389/fimmu.2022.940995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/07/2022] [Indexed: 12/13/2022] Open
Abstract
TET proteins mediate DNA demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) and other oxidative derivatives. We have previously demonstrated a dynamic enrichment of 5hmC during T and invariant natural killer T cell lineage specification. Here, we investigate shared signatures in gene expression of Tet2/3 DKO CD4 single positive (SP) and iNKT cells in the thymus. We discover that TET proteins exert a fundamental role in regulating the expression of the lineage specifying factor Th-POK, which is encoded by Zbtb7b. We demonstrate that TET proteins mediate DNA demethylation - surrounding a proximal enhancer, critical for the intensity of Th-POK expression. In addition, TET proteins drive the DNA demethylation of site A at the Zbtb7b locus to facilitate GATA3 binding. GATA3 induces Th-POK expression in CD4 SP cells. Finally, by introducing a novel mouse model that lacks TET3 and expresses full length, catalytically inactive TET2, we establish a causal link between TET2 catalytic activity and lineage specification of both conventional and unconventional T cells.
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Affiliation(s)
- Tarmo Äijö
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Dimitris Theofilatos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Meng Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Matthew D. Smith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Albert S. Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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10
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Gong Z, Jia H, Xue L, Li D, Zeng X, Wei M, Liu Z, Tong MCF, Chen GG. The emerging role of transcription factor FOXP3 in thyroid cancer. Rev Endocr Metab Disord 2022; 23:421-429. [PMID: 34463908 DOI: 10.1007/s11154-021-09684-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Transcription factor FOXP3 is a crucial regulator in the development and function of regulatory T cells (Treg) that are essential for immunological tolerance and homeostasis. Numerous studies have indicated the correlation of tumor infiltrating FOXP3+ Treg upregulation with poor prognostic parameters in thyroid cancer, including lymph node metastases, extrathyroidal extension, and multifocality. Most immune-checkpoint molecules are expressed in Treg. The blockage of such signals with checkpoint inhibitors has been approved for several solid tumors, but not yet for thyroid cancer. Thyroid abnormalities may be induced by checkpoint inhibitors. For example, hypothyroidism, thyrotoxicosis, painless thyroiditis, or even thyroid storm are more frequently associated with anti-PD-1 antibodies (pembrolizumab and nivolumab). Therefore, Targeting FOXP3+ Treg may have impacts on checkpoint molecules and the growth of thyroid cancer. Several factors may impact the role and stability of FOXP3, such as alternative RNA splicing, mutations, and post-translational modification. In addition, the role of FOXP3+ Treg in the tumor microenvironment is also affected by the complex regulatory network formed by FOXP3 and its transcriptional partners. Here we discussed how the expression and function of FOXP3 were regulated and how FOXP3 interacted with its targets in Treg, aiming to help the development of FOXP3 as a potential therapeutic target for thyroid cancer.
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Affiliation(s)
- Zhongqin Gong
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Hao Jia
- Department of Thyroid and Breast Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Lingbin Xue
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Dongcai Li
- Shenzhen Key Laboratory of ENT, Institute of ENT & Longgang, ENT Hospital, Shenzhen, China
| | - Xianhai Zeng
- Shenzhen Key Laboratory of ENT, Institute of ENT & Longgang, ENT Hospital, Shenzhen, China
| | - Minghui Wei
- Department of Head & Neck Surgery, Cancer Hospital Chinese Academy of Medical Sciences, Shenzhen Center, Shenzhen, Guangdong, China
| | - Zhimin Liu
- Department of Biochemistry and Molecular Biology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Michael C F Tong
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.
| | - George G Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.
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11
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Date Y, Taniuchi I, Ito K. Oncogenic Runx1-Myc axis in p53-deficient thymic lymphoma. Gene 2022; 819:146234. [PMID: 35114276 DOI: 10.1016/j.gene.2022.146234] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/23/2021] [Accepted: 01/18/2022] [Indexed: 11/04/2022]
Abstract
p53 deficiency and Myc dysregulation are frequently associated with cancer. However, the molecular mechanisms linking these two major oncogenic events are poorly understood. Using an osteosarcoma model caused by p53 loss, we have recently shown that Runx3 aberrantly upregulates Myc via mR1, a Runx consensus site in the Myc promoter. Here, we focus on thymic lymphoma, a major tumour type caused by germline p53 deletion in mice, and examine whether the oncogenic Runx-Myc axis plays a notable role in the development of p53-deficient lymphoma. Mice lacking p53 specifically in thymocytes (LP mice) mostly succumbed to thymic lymphoma. Runx1 and Myc were upregulated in LP mouse lymphoma compared with the normal thymus. Depletion of Runx1 or Myc prolonged the lifespan of LP mice and suppressed lymphoma development. In lymphoma cells isolated from LP mice, knockdown of Runx1 led to Myc suppression, weakening their tumour forming ability in immunocompromised mice. The mR1 locus was enriched by both Runx1 and H3K27ac, an active chromatin marker. LP mice with mutated mR1 had a longer lifespan and a lower incidence of lymphoma. Treatment with AI-10-104, a Runx inhibitor, improved the survival of LP mice. These results suggest that Myc upregulation by Runx1 is a key event in p53-deficient thymic lymphoma development and provide a clinical rationale for targeting the Runx family in p53-deficient malignancies.
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Affiliation(s)
- Yuki Date
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kosei Ito
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan.
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12
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Hu Y, Pan Q, Zhou K, Ling Y, Wang H, Li Y. RUNX1 inhibits the antiviral immune response against influenza A virus through attenuating type I interferon signaling. Virol J 2022; 19:39. [PMID: 35248104 PMCID: PMC8897766 DOI: 10.1186/s12985-022-01764-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/14/2022] [Indexed: 11/10/2022] Open
Abstract
Background Influenza A viruses (IAVs) are zoonotic, segmented negative-stranded RNA viruses. The rapid mutation of IAVs results in host immune response escape and antiviral drug and vaccine resistance. RUNX1 is a transcription factor that not only plays essential roles in hematopoiesis, but also functions as a regulator in inflammation. However, its role in the innate immunity to IAV infection has not been well studied. Methods To investigate the effects of RUNX1 on IAV infection and explore the mechanisms that RUNX1 uses during IAV infection. We infected the human alveolar epithelial cell line (A549) with influenza virus A/Puerto Rico/8/34 (H1N1) (PR8) and examined RUNX1 expression by Western blot and qRT-PCR. We also knocked down or overexpressed RUNX1 in A549 cells, then evaluated viral replication by Western blot, qRT-PCR, and viral titration. Results We found RUNX1 expression is induced by IAV H1N1 PR8 infection, but not by poly(I:C) treatment, in the human alveolar epithelial cell line A549. Knockdown of RUNX1 significantly inhibited IAV infection. Conversely, overexpression of RUNX1 efficiently promoted production of progeny viruses. Additionally, RUNX1 knockdown increased IFN-β and ISGs production while RUNX1 overexpression compromised IFN-β and ISGs production upon PR8 infection in A549 cells. We further showed that RUNX1 may attenuate the interferon signaling transduction by hampering the expression of IRF3 and STAT1 during IAV infection. Conclusions Taken together, we found RUNX1 attenuates type I interferon signaling to facilitate IAV infection in A549 cells.
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13
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Tang H, Jiang X, Zhang J, Pei C, Zhao X, Li L, Kong X. Teleost CD4 + helper T cells: Molecular characteristics and functions and comparison with mammalian counterparts. Vet Immunol Immunopathol 2021; 240:110316. [PMID: 34474261 DOI: 10.1016/j.vetimm.2021.110316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 06/21/2021] [Accepted: 08/24/2021] [Indexed: 12/24/2022]
Abstract
CD4+ helper T cells play key and diverse roles in inducing adaptive immune responses in vertebrates. The CD4 molecule, which is found on the surfaces of CD4+ helper T cells, can be used to distinguish subsets of helper T cells. Teleosts are the oldest living species with bona-fide CD4 coreceptors. Although some components of immune systems of teleosts and mammals appear to be similar, many physiological differences are represented between them. Previous studies have shown that two CD4 paralogs are present in teleosts, whereas only one is present in mammals. Therefore, in this review, the CD4 molecular structure, expression profiles, subpopulations, and biological functions of teleost CD4+ helper T cells were summarized and compared with those of their mammalian counterparts to understand the differences in CD4 molecules between teleosts and mammals. This review provides suggestions for further studies on the CD4 molecular function and regulatory mechanism of CD4+ helper T cells in teleost fish and will help establish therapeutic strategies to control fish diseases in the future.
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Affiliation(s)
- Hairong Tang
- College of Life Science, Henan Normal University, Henan Province, PR China; Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Xinyu Jiang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Jie Zhang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Chao Pei
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Xianliang Zhao
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Li Li
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Xianghui Kong
- College of Life Science, Henan Normal University, Henan Province, PR China; Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China.
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14
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Kubota H, Masuda T, Noura M, Furuichi K, Matsuo H, Hirata M, Kataoka TR, Hiramatsu H, Yasumi T, Nakahata T, Imai Y, Takita J, Adachi S, Sugiyama H, Kamikubo Y. RUNX inhibitor suppresses graft‐versus‐host disease through targeting
RUNX‐NFATC2
axis. EJHAEM 2021; 2:449-458. [PMID: 35844683 PMCID: PMC9175814 DOI: 10.1002/jha2.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 11/13/2022]
Abstract
Patients with refractory graft‐versus‐host disease (GVHD) have a dismal prognosis. Therefore, novel therapeutic targets are still needed to be identified. Runt‐related transcriptional factor (RUNX) family transcription factors are essential transcription factors that mediate the essential roles in effector T cells. However, whether RUNX targeting can suppress, and GVHD is yet unknown. Here, we showed that RUNX family members have a redundant role in directly transactivating NFATC2 expression in T cells. We also found that our novel RUNX inhibitor, Chb‐M’, which is the inhibitor that switches off the entire RUNX family by alkylating agent–conjugated pyrrole‐imidazole (PI) polyamides, inhibited T‐cell receptor mediated T cell proliferation and allogenic T cell response. These were designed to specifically bind to consensus RUNX‐binding sequences (TGTGGT). Chb‐M’ also suppressed the expression of NFATC2 and pro‐inflammatory cytokine genes in vitro. Using xenogeneic GVHD model, mice injected by Chb‐M’ showed almost no sign of GVHD. Especially, the CD4 T cell was decreased and GVHD‐associated cytokines including tissue necrosis factor‐α and granulocyte‐macrophage colony‐stimulating factor were reduced in the peripheral blood of Chb‐M’ injected mice. Taken together, our data demonstrates that RUNX family transcriptionally upregulates NFATC2 in T cells, and RUNX‐NFATC2 axis can be a novel therapeutic target against GVHD.
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Affiliation(s)
- Hirohito Kubota
- Department of Pediatrics Graduate School of Medicine Kyoto University Sakyo‐ku Kyoto Japan
| | - Tatsuya Masuda
- Department of Human Health Sciences Graduate School of Medicine Kyoto, University, Sakyo‐ku Kyoto Japan
| | - Mina Noura
- Department of Human Health Sciences Graduate School of Medicine Kyoto, University, Sakyo‐ku Kyoto Japan
| | - Kana Furuichi
- Department of Human Health Sciences Graduate School of Medicine Kyoto, University, Sakyo‐ku Kyoto Japan
| | - Hidemasa Matsuo
- Department of Human Health Sciences Graduate School of Medicine Kyoto, University, Sakyo‐ku Kyoto Japan
| | - Masahiro Hirata
- Department of Diagnostic Pathology Kyoto University Hospital Sakyo‐ku Kyoto Japan
| | - Tatsuki R. Kataoka
- Department of Diagnostic Pathology Kyoto University Hospital Sakyo‐ku Kyoto Japan
| | - Hidefumi Hiramatsu
- Department of Pediatrics Graduate School of Medicine Kyoto University Sakyo‐ku Kyoto Japan
| | - Takahiro Yasumi
- Department of Pediatrics Graduate School of Medicine Kyoto University Sakyo‐ku Kyoto Japan
| | - Tatsutoshi Nakahata
- Drug Discovery Technology Development Office Center for iPS cell research and application (CiRA) Kyoto University Sakyo‐ku Kyoto Japan
| | - Yoichi Imai
- Department of Hematology/Oncology IMSUT Hospital The Institute of Medical Science The University of Tokyo Tokyo Japan
| | - Junko Takita
- Department of Pediatrics Graduate School of Medicine Kyoto University Sakyo‐ku Kyoto Japan
| | - Souichi Adachi
- Department of Human Health Sciences Graduate School of Medicine Kyoto, University, Sakyo‐ku Kyoto Japan
| | - Hiroshi Sugiyama
- Department of Chemistry Graduate School of Science Kyoto University Sakyo‐ku Kyoto Japan
| | - Yasuhiko Kamikubo
- Department of Human Health Sciences Graduate School of Medicine Kyoto, University, Sakyo‐ku Kyoto Japan
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15
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Hu Y, Knecht KM, Shen Q, Xiong Y. Multifaceted HIV-1 Vif interactions with human E3 ubiquitin ligase and APOBEC3s. FEBS J 2021; 288:3407-3417. [PMID: 32893454 PMCID: PMC8172064 DOI: 10.1111/febs.15550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/01/2020] [Indexed: 12/31/2022]
Abstract
APOBEC3 (A3) proteins are a family of host antiviral restriction factors that potently inhibit various retroviral infections, including human immunodeficiency virus (HIV)-1. To overcome this restriction, HIV-1 virion infectivity factor (Vif) recruits the cellular cofactor CBFβ to assist in targeting A3 proteins to a host E3 ligase complex for polyubiquitination and subsequent proteasomal degradation. Intervention of the Vif-A3 interactions could be a promising therapeutic strategy to facilitate A3-mediated suppression of HIV-1 in patients. In this structural snapshot, we review the structural features of the recently determined structure of human A3F in complex with HIV-1 Vif and its cofactor CBFβ, discuss insights into the molecular principles of Vif-A3 interplay during the arms race between the virus and host, and highlight the therapeutic implications.
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Affiliation(s)
- Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kirsten M. Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Qi Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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16
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Dybska E, Adams AT, Duclaux-Loras R, Walkowiak J, Nowak JK. Waiting in the wings: RUNX3 reveals hidden depths of immune regulation with potential implications for inflammatory bowel disease. Scand J Immunol 2021; 93:e13025. [PMID: 33528856 DOI: 10.1111/sji.13025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/11/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Complex interactions between the environment and the mucosal immune system underlie inflammatory bowel disease (IBD). The involved cytokine signalling pathways are modulated by a number of transcription factors, one of which is runt-related transcription factor 3 (RUNX3). OBJECTIVE To systematically review the immune roles of RUNX3 in immune regulation, with a focus on the context of IBD. METHODS Relevant articles and reviews were identified through a Scopus search in April 2020. Information was categorized by immune cell types, analysed and synthesized. IBD transcriptome data sets and FANTOM5 regulatory networks were processed in order to complement the literature review. RESULTS The available evidence on the immune roles of RUNX3 allowed for its description in twelve cell types: intraepithelial lymphocyte, Th1, Th2, Th17, Treg, double-positive T, cytotoxic T, B, dendritic, innate lymphoid, natural killer and macrophages. In the gut, the activity of RUNX3 is multifaceted and context-dependent: it may promote homeostasis or exacerbated reactions via cytokine signalling and regulation of receptor expression. RUNX3 is mostly engaged in pathways involving ThPOK, T-bet, IFN-γ, TGF-β/IL-2Rβ, GATA/CBF-β, SMAD/p300 and a number of miRNAs. RUNX3 targets relevant to IBD may include RAG1, OSM and IL-17B. Moreover, in IBD RUNX3 expression correlates positively with GZMM, and negatively with IFNAR1, whereas in controls, it strongly associates with TGFBR3. CONCLUSIONS Dysregulation of RUNX3, mostly in the form of deficiency, likely contributes to IBD pathogenesis. More clinical research is needed to examine RUNX3 in IBD.
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Affiliation(s)
- Emilia Dybska
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Alex T Adams
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Rémi Duclaux-Loras
- INSERM U1111, Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Lyon, France
| | - Jarosław Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Jan K Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
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17
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Knecht KM, Hu Y, Rubene D, Cook M, Ziegler SJ, Jónsson SR, Xiong Y. Maedi-visna virus Vif protein uses motifs distinct from HIV-1 Vif to bind zinc and the cofactor required for A3 degradation. J Biol Chem 2021; 296:100045. [PMID: 33465707 PMCID: PMC7949081 DOI: 10.1074/jbc.ra120.015828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/23/2020] [Accepted: 11/09/2020] [Indexed: 11/06/2022] Open
Abstract
The mammalian apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3 or A3) family of cytidine deaminases restrict viral infections by mutating viral DNA and impeding reverse transcription. To overcome this antiviral activity, most lentiviruses express a viral accessory protein called the virion infectivity factor (Vif), which recruits A3 proteins to cullin-RING E3 ubiquitin ligases such as cullin-5 (Cul5) for ubiquitylation and subsequent proteasomal degradation. Although Vif proteins from primate lentiviruses such as HIV-1 utilize the transcription factor core-binding factor subunit beta as a noncanonical cofactor to stabilize the complex, the maedi-visna virus (MVV) Vif hijacks cyclophilin A (CypA) instead. Because core-binding factor subunit beta and CypA are both highly conserved among mammals, the requirement for two different cellular cofactors suggests that these two A3-targeting Vif proteins have different biochemical and structural properties. To investigate this topic, we used a combination of in vitro biochemical assays and in vivo A3 degradation assays to study motifs required for the MVV Vif to bind zinc ion, Cul5, and the cofactor CypA. Our results demonstrate that although some common motifs between the HIV-1 Vif and MVV Vif are involved in recruiting Cul5, different determinants in the MVV Vif are required for cofactor binding and stabilization of the E3 ligase complex, such as the zinc-binding motif and N- and C-terminal regions of the protein. Results from this study advance our understanding of the mechanism of MVV Vif recruitment of cellular factors and the evolution of lentiviral Vif proteins.
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Affiliation(s)
- Kirsten M Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Diana Rubene
- Institute for Experimental Pathology, University of Iceland, Keldur, Iceland
| | - Matthew Cook
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Samantha J Ziegler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Stefán R Jónsson
- Institute for Experimental Pathology, University of Iceland, Keldur, Iceland
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
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18
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Li K, Wu Y, Li Y, Yu Q, Tian Z, Wei H, Qu K. Landscape and Dynamics of the Transcriptional Regulatory Network During Natural Killer Cell Differentiation. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:501-515. [PMID: 33385611 PMCID: PMC8377244 DOI: 10.1016/j.gpb.2020.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/10/2018] [Accepted: 03/04/2019] [Indexed: 12/24/2022]
Abstract
Natural killer (NK) cells are essential in controlling cancer and infection. However, little is known about the dynamics of the transcriptional regulatory machinery during NK cell differentiation. In this study, we applied the assay of transposase accessible chromatin with sequencing (ATAC-seq) technique in a home-developed in vitro NK cell differentiation system. Analysis of ATAC-seq data illustrated two distinct transcription factor (TF) clusters that dynamically regulate NK cell differentiation. Moreover, two TFs from the second cluster, FOS-like 2 (FOSL2) and early growth response 2 (EGR2), were identified as novel essential TFs that control NK cell maturation and function. Knocking down either of these two TFs significantly impacted NK cell differentiation. Finally, we constructed a genome-wide transcriptional regulatory network that provides a better understanding of the regulatory dynamics during NK cell differentiation.
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Affiliation(s)
- Kun Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
| | - Yang Wu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
| | - Young Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
| | - Qiaoni Yu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
| | - Zhigang Tian
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China; CAS Center for Excellence in Molecular Cell Sciences, The CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei 230027, China
| | - Haiming Wei
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China; CAS Center for Excellence in Molecular Cell Sciences, The CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei 230027, China.
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China; CAS Center for Excellence in Molecular Cell Sciences, The CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei 230027, China; School of Data Science, University of Science and Technology of China, Hefei 230026, China.
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19
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Chopp LB, Gopalan V, Ciucci T, Ruchinskas A, Rae Z, Lagarde M, Gao Y, Li C, Bosticardo M, Pala F, Livak F, Kelly MC, Hannenhalli S, Bosselut R. An Integrated Epigenomic and Transcriptomic Map of Mouse and Human αβ T Cell Development. Immunity 2020; 53:1182-1201.e8. [PMID: 33242395 PMCID: PMC8641659 DOI: 10.1016/j.immuni.2020.10.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/25/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022]
Abstract
αβ lineage T cells, most of which are CD4+ or CD8+ and recognize MHC I- or MHC II-presented antigens, are essential for immune responses and develop from CD4+CD8+ thymocytes. The absence of in vitro models and the heterogeneity of αβ thymocytes have hampered analyses of their intrathymic differentiation. Here, combining single-cell RNA and ATAC (chromatin accessibility) sequencing, we identified mouse and human αβ thymocyte developmental trajectories. We demonstrated asymmetric emergence of CD4+ and CD8+ lineages, matched differentiation programs of agonist-signaled cells to their MHC specificity, and identified correspondences between mouse and human transcriptomic and epigenomic patterns. Through computational analysis of single-cell data and binding sites for the CD4+-lineage transcription factor Thpok, we inferred transcriptional networks associated with CD4+- or CD8+-lineage differentiation, and with expression of Thpok or of the CD8+-lineage factor Runx3. Our findings provide insight into the mechanisms of CD4+ and CD8+ T cell differentiation and a foundation for mechanistic investigations of αβ T cell development.
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Affiliation(s)
- Laura B Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Immunology Graduate Group, University of Pennsylvania Medical School, Philadelphia, PA, USA
| | - Vishaka Gopalan
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Ciucci
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison Ruchinskas
- Cancer Research Technology Program, Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Zachary Rae
- Cancer Research Technology Program, Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Manon Lagarde
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yayi Gao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Caiyi Li
- Laboratory of Genomic Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ferenc Livak
- Laboratory of Genomic Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael C Kelly
- Cancer Research Technology Program, Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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20
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Spinner CA, Lazarevic V. Transcriptional regulation of adaptive and innate lymphoid lineage specification. Immunol Rev 2020; 300:65-81. [PMID: 33615514 DOI: 10.1111/imr.12935] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/26/2020] [Accepted: 11/16/2020] [Indexed: 12/28/2022]
Abstract
Once alerted to the presence of a pathogen, activated CD4+ T cells initiate distinct gene expression programs that produce multiple functionally specialized T helper (Th) subsets. The cytokine milieu present at the time of antigen encounter instructs CD4+ T cells to differentiate into interferon-(IFN)-γ-producing Th1 cells, interleukin-(IL)-4-producing Th2 cells, IL-17-producing Th17 cells, follicular T helper (Tfh) cells, or regulatory T (Treg) cells. In each of these Th cell subsets, a single transcription factor has been identified as a critical regulator of its specialized differentiation program. In this context, the expression of the "master regulator" is necessary and sufficient to activate lineage-specific genes while restricting the gene expression program of alternative Th fates. Thus, the transcription factor T-bet controls Th1 differentiation program, while the development of Th2, Th17, Tfh, and Treg cells is dependent on transcription factors GATA3, RORγt, Bcl6, and Foxp3, respectively. Nevertheless, master regulators or, more precisely, lineage-defining transcription factors do not function in isolation. In fact, they interact with a complex network of transcription factors, orchestrating cell lineage specification programs. In this review, we discuss the concept of the combinatorial interactions of key transcription factors in determining helper T cell identity. Additionally, lineage-defining transcription factors have well-established functions beyond their role in CD4+ Th subsets. They play critically important functions at distinct stages during T cell development in the thymus and they control the development of innate lymphoid cells (ILCs) in the bone marrow. In tracking the journey of T cells traversing from the thymus to the periphery and during the immune response, we discuss in broad terms developmental stage and context-dependent functions of lineage-defining transcription factors in regulating specification programs of innate and adaptive lymphocytes.
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Affiliation(s)
- Camille A Spinner
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vanja Lazarevic
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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21
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Liu Q, Zaba LC, Satpathy AT, Longmire M, Zhang W, Li K, Granja J, Guo C, Lin J, Li R, Tolentino K, Kania G, Distler O, Fiorentino D, Chung L, Qu K, Chang HY. Chromatin accessibility landscapes of skin cells in systemic sclerosis nominate dendritic cells in disease pathogenesis. Nat Commun 2020; 11:5843. [PMID: 33203843 PMCID: PMC7672105 DOI: 10.1038/s41467-020-19702-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022] Open
Abstract
Systemic sclerosis (SSc) is a disease at the intersection of autoimmunity and fibrosis. However, the epigenetic regulation and the contributions of diverse cell types to SSc remain unclear. Here we survey, using ATAC-seq, the active DNA regulatory elements of eight types of primary cells in normal skin from healthy controls, as well as clinically affected and unaffected skin from SSc patients. We find that accessible DNA elements in skin-resident dendritic cells (DCs) exhibit the highest enrichment of SSc-associated single-nucleotide polymorphisms (SNPs) and predict the degrees of skin fibrosis in patients. DCs also have the greatest disease-associated changes in chromatin accessibility and the strongest alteration of cell-cell interactions in SSc lesions. Lastly, data from an independent cohort of patients with SSc confirm a significant increase of DCs in lesioned skin. Thus, the DCs epigenome links inherited susceptibility and clinically apparent fibrosis in SSc skin, and can be an important driver of SSc pathogenesis.
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Affiliation(s)
- Qian Liu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Lisa C Zaba
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Michelle Longmire
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Wen Zhang
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Kun Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Jeffrey Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chuang Guo
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Jun Lin
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Karen Tolentino
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gabriela Kania
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Oliver Distler
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - David Fiorentino
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lorinda Chung
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China.
- CAS Center for Excellence in Molecular Cell Sciences, University of Science and Technology of China, Hefei, 230027, China.
- School of Data Sciences, University of Science and Technology of China, Hefei, 230027, China.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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22
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Daams R, Sime W, Leandersson K, Sitnicka E, Massoumi R. Deletion of Nemo-like Kinase in T Cells Reduces Single-Positive CD8 + Thymocyte Population. THE JOURNAL OF IMMUNOLOGY 2020; 205:1830-1841. [PMID: 32839237 DOI: 10.4049/jimmunol.2000109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/23/2020] [Indexed: 12/18/2022]
Abstract
The β-catenin/Wnt signaling pathway plays an important role in all stages of T cell development. Nemo-like kinase (NLK) is an evolutionary conserved serine/threonine kinase and a negative regulator of the Wnt signaling pathway. NLK can directly phosphorylate histone deacetylase 1 (HDAC1), as well as T cell factor/lymphoid enhancer-binding factor (TCF/LEF), causing subsequent repression of target gene transcription. By engineering mice lacking NLK in early stages of T cell development, we set out to characterize the role NLK plays in T cell development and found that deletion of NLK does not affect mouse health or lymphoid tissue development. Instead, these mice harbored a reduced number of single-positive (SP) CD8+ thymocytes without any defects in the SP CD4+ thymocyte population. The decrease in SP CD8+ thymocytes was not caused by a block in differentiation from double-positive CD4+CD8+ cells. Neither TCR signaling nor activation was altered in the absence of NLK. Instead, we observed a significant increase in cell death and reduced phosphorylation of LEF1 as well as HDAC1 among NLK-deleted SP CD8+ cells. Thus, NLK seems to play an important role in the survival of CD8+ thymocytes. Our data provide evidence for a new function for NLK with regard to its involvement in T cell development and supporting survival of SP CD8+ thymocytes.
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Affiliation(s)
- Renée Daams
- Molecular Tumor Pathology, Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Wondossen Sime
- Molecular Tumor Pathology, Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Karin Leandersson
- Cancer Immunology, Department of Translational Medicine, Lund University, 214 28 Malmö, Sweden; and
| | - Ewa Sitnicka
- Lymphoid Development and Regulation, Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, 221 84 Lund, Sweden
| | - Ramin Massoumi
- Molecular Tumor Pathology, Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden;
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23
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Transcriptional Regulation of Natural Killer Cell Development and Functions. Cancers (Basel) 2020; 12:cancers12061591. [PMID: 32560225 PMCID: PMC7352776 DOI: 10.3390/cancers12061591] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 02/08/2023] Open
Abstract
Natural killer (NK) cells are the major lymphocyte subset of the innate immune system. Their ability to mediate anti-tumor cytotoxicity and produce cytokines is well-established. However, the molecular mechanisms associated with the development of human or murine NK cells are not fully understood. Knowledge is being gained about the environmental cues, the receptors that sense the cues, signaling pathways, and the transcriptional programs responsible for the development of NK cells. Specifically, a complex network of transcription factors (TFs) following microenvironmental stimuli coordinate the development and maturation of NK cells. Multiple TFs are involved in the development of NK cells in a stage-specific manner. In this review, we summarize the recent advances in the understandings of TFs involved in the regulation of NK cell development, maturation, and effector function, in the aspects of their mechanisms, potential targets, and functions.
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24
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Delviks-Frankenberry KA, Desimmie BA, Pathak VK. Structural Insights into APOBEC3-Mediated Lentiviral Restriction. Viruses 2020; 12:E587. [PMID: 32471198 PMCID: PMC7354603 DOI: 10.3390/v12060587] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 01/18/2023] Open
Abstract
Mammals have developed clever adaptive and innate immune defense mechanisms to protect against invading bacterial and viral pathogens. Human innate immunity is continuously evolving to expand the repertoire of restriction factors and one such family of intrinsic restriction factors is the APOBEC3 (A3) family of cytidine deaminases. The coordinated expression of seven members of the A3 family of cytidine deaminases provides intrinsic immunity against numerous foreign infectious agents and protects the host from exogenous retroviruses and endogenous retroelements. Four members of the A3 proteins-A3G, A3F, A3H, and A3D-restrict HIV-1 in the absence of virion infectivity factor (Vif); their incorporation into progeny virions is a prerequisite for cytidine deaminase-dependent and -independent activities that inhibit viral replication in the host target cell. HIV-1 encodes Vif, an accessory protein that antagonizes A3 proteins by targeting them for polyubiquitination and subsequent proteasomal degradation in the virus producing cells. In this review, we summarize our current understanding of the role of human A3 proteins as barriers against HIV-1 infection, how Vif overcomes their antiviral activity, and highlight recent structural and functional insights into A3-mediated restriction of lentiviruses.
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Affiliation(s)
| | | | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; (K.A.D.-F.); (B.A.D.)
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25
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Chu F, Li HS, Liu X, Cao J, Ma W, Ma Y, Weng J, Zhu Z, Cheng X, Wang Z, Liu J, Jiang ZY, Luong AU, Peng W, Wang J, Balakrishnan K, Yee C, Dong C, Davis RE, Watowich SS, Neelapu SS. CXCR5 +CD8 + T cells are a distinct functional subset with an antitumor activity. Leukemia 2019; 33:2640-2653. [PMID: 31028278 PMCID: PMC6814517 DOI: 10.1038/s41375-019-0464-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 01/09/2023]
Abstract
CXCR5 mediates homing of both B and follicular helper T (TFH) cells into follicles of secondary lymphoid organs. We found that CXCR5+CD8+ T cells are present in human tonsils and follicular lymphoma, inhibit TFH-mediated B cell differentiation, and exhibit strong cytotoxic activity. Consistent with these findings, adoptive transfer of CXCR5+CD8+ T cells into an animal model of lymphoma resulted in significantly greater antitumor activity than CXCR5-CD8+ T cells. Furthermore, RNA-Seq-based transcriptional profiling revealed 77 differentially expressed genes unique to CXCR5+CD8+ T cells. Among these, a signature comprised of 33 upregulated genes correlated with improved survival in follicular lymphoma patients. We also showed that CXCR5+CD8+ T cells could be induced and expanded ex vivo using IL-23 plus TGF-β, suggesting a possible strategy to generate these cells for clinical application. In summary, our study identified CXCR5+CD8+ T cells as a distinct T cell subset with ability to suppress TFH-mediated B cell differentiation, exert strong antitumor activity, and confer favorable prognosis in follicular lymphoma patients.
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Affiliation(s)
- Fuliang Chu
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Haiyan S Li
- Department of Immunology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Xindong Liu
- Department of Immunology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, 400038, Chongqing, China
| | - Jingjing Cao
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Wencai Ma
- Department of Biostatistics, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Ying Ma
- Department of Melanoma Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Jinsheng Weng
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Zheng Zhu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, 400038, Chongqing, China
| | - Xiaoyun Cheng
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Zhiqiang Wang
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Jingwei Liu
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Zi Yang Jiang
- Department of Otorhinolaryngology-Head and Neck Surgery, The University of Texas Health Science Center of Houston, Houston, TX, USA
| | - Amber U Luong
- Department of Otorhinolaryngology-Head and Neck Surgery, The University of Texas Health Science Center of Houston, Houston, TX, USA
| | - Weiyi Peng
- Department of Melanoma Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Jing Wang
- Department of Biostatistics, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Kumudha Balakrishnan
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Chen Dong
- Department of Immunology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
- Tsinghua University Institute for Immunology and School of Medicine, 100084, Beijing, China
| | - Richard Eric Davis
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Stephanie S Watowich
- Department of Immunology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Sattva S Neelapu
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA.
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26
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Men S, Yu Y, Zhang Y, Wang Y, Qian Q, Li W, Yin C. Methylation Landscape of RUNX3 Promoter Region as a Predictive Marker for Th1/Th2 Imbalance in Bronchiolitis. Med Sci Monit 2019; 25:7795-7807. [PMID: 31622282 PMCID: PMC6820333 DOI: 10.12659/msm.917196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background The methylation status of RUNX3 promoter region, its impact on RUNX3 gene expression, and Th1/Th2 imbalance are unknown in bronchiolitis. This study aimed to explore the predictors of bronchiolitis developing into asthma. Material/Methods The methylation status of RUNX3 promoter was assessed using Illumina HiSeq platform method. The relative RUNX3 mRNA levels in PBMCs were measured by qRT-PCR. Serum IL-4 and IFN-γ concentrations were measured by ELISA. Results A series of sites with significantly higher levels of methylation as compared to their corresponding controls were identified, including 24 sites in group Ba vs. group Cn, 13 sites in group Ba vs. group Ca, 7 sites in group Ba vs. group Bn, 16 sites in group Bn vs. group Cn, 11 sites in group Ca vs. group Cn, and 23 sites in group B vs. group C; P<0.05. The relative mRNA levels in group Ba were significantly lower than those in groups Cn, Ca, Bn; P<0.05. The serum IL-4 concentrations in group Ba were significantly higher than those in group Cn; P<0.05. The serum IFN-γ concentrations in group Ba were significantly lower than those in groups Cn, Ca, Bn; P<0.05. Correlation analysis showed that differentially methylated RUNX3 promoter region sites were significantly negatively correlated with levels of relative RUNX3 mRNA and IFN-γ, and were significantly positively correlated with IL-4 levels. Conclusions The methylation status of RUNX3 promoter region plays a role in Th1/Th2 imbalance by silencing RUNX3 gene expression, which can serve as predictive marker for the development of bronchiolitis into asthma.
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Affiliation(s)
- Shuai Men
- Pediatric Asthma Department, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China (mainland)
| | - Yanyan Yu
- Pediatric Asthma Department, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China (mainland)
| | - Yuhong Zhang
- Pediatric Asthma Department, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China (mainland)
| | - Yifen Wang
- Pediatric Asthma Department, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China (mainland)
| | - Qian Qian
- Pediatric Asthma Department, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China (mainland)
| | - Wei Li
- Pediatric Asthma Department, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China (mainland)
| | - Chuang Yin
- Pediatric Asthma Department, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China (mainland)
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27
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Insights into Thymus Development and Viral Thymic Infections. Viruses 2019; 11:v11090836. [PMID: 31505755 PMCID: PMC6784209 DOI: 10.3390/v11090836] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/16/2022] Open
Abstract
T-cell development in the thymus is a complex and highly regulated process, involving a wide variety of cells and molecules which orchestrate thymocyte maturation into either CD4+ or CD8+ single-positive (SP) T cells. Here, we briefly review the process regulating T-cell differentiation, which includes the latest advances in this field. In particular, we highlight how, starting from a pool of hematopoietic stem cells in the bone marrow, the sequential action of transcriptional factors and cytokines dictates the proliferation, restriction of lineage potential, T-cell antigen receptors (TCR) gene rearrangements, and selection events on the T-cell progenitors, ultimately leading to the generation of mature T cells. Moreover, this review discusses paradigmatic examples of viral infections affecting the thymus that, by inducing functional changes within this lymphoid gland, consequently influence the behavior of peripheral mature T-lymphocytes.
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28
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Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system. Nat Immunol 2019; 20:1372-1380. [PMID: 31451789 PMCID: PMC6754753 DOI: 10.1038/s41590-019-0471-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/16/2019] [Indexed: 12/12/2022]
Abstract
In multicellular organisms, duplicated genes can diverge through tissue-specific gene expression patterns, as exemplified by highly regulated expression of Runx transcription factor paralogs with apparent functional redundancy. Here we asked what cell type-specific biologies might be supported by the selective expression of Runx paralogs during Langerhans cell and inducible regulatory T cell differentiation. We uncovered functional non-equivalence between Runx paralogs. Selective expression of native paralogs allowed integration of transcription factor activity with extrinsic signals, while non-native paralogs enforced differentiation even in the absence of exogenous inducers. DNA-binding affinity was controlled by divergent amino acids within the otherwise highly conserved RUNT domain, and evolutionary reconstruction suggested convergence of RUNT domain residues towards sub-maximal strength. Hence, the selective expression of gene duplicates in specialized cell types can synergize with the acquisition of functional differences to enable appropriate gene expression, lineage choice and differentiation in the mammalian immune system.
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29
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Di Vito C, Mikulak J, Mavilio D. On the Way to Become a Natural Killer Cell. Front Immunol 2019; 10:1812. [PMID: 31428098 PMCID: PMC6688484 DOI: 10.3389/fimmu.2019.01812] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
Natural Killer (NK) cells are innate lymphocytes playing pivotal roles in host defense and immune-surveillance. The homeostatic modulation of germ-line encoded/non-rearranged activating and inhibitory NK cell receptors (NKRs) determines the capability of these innate lymphocytes to either spare "self" cells or to kill viral-infected, tumor-transformed and heterologous cell targets. However, despite being discovered more than 40 years ago, several aspects of NK cell biology remain unknown or are still being debated. In particular, our knowledge of human NK cell ontogenesis and differentiation is still in its infancy as the majority of our experimental evidence on this topic mainly comes from findings obtained in vitro or with animal models in vivo. Although both the generation and the maintenance of human NK cells are sustained by hematopoietic stem cells (HSCs), the precise site(s) of NK cell development are still poorly defined. Indeed, HSCs and hematopoietic precursors are localized in different anatomical compartments that also change their ontogenic commitments before and after birth as well as in aging. Currently, the main site of NK cell generation and maturation in adulthood is considered the bone marrow, where their interactions with stromal cells, cytokines, growth factors, and other soluble molecules support and drive maturation. Different sequential stages of NK cell development have been identified on the basis of the differential expression of specific markers and NKRs as well as on the acquisition of specific effector-functions. All these phenotypic and functional features are key in inducing and regulating homing, activation and tissue-residency of NK cells in different human anatomic sites, where different homeostatic mechanisms ensure a perfect balance between immune tolerance and immune-surveillance. The present review summarizes our current knowledge on human NK cell ontogenesis and on the related pathways orchestrating a proper maturation, functions, and distributions.
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Affiliation(s)
- Clara Di Vito
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center, Milan, Italy
| | - Joanna Mikulak
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center, Milan, Italy.,Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, Milan, Italy
| | - Domenico Mavilio
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center, Milan, Italy.,Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, Milan, Italy
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30
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Abstract
Tissue-resident memory T (TRM) cells have emerged as a major component of T cell biology. Recent investigations have greatly advanced our understanding of TRMs. Common features have been discovered to distinguish memory T cells residing in various mucosal and non-mucosal tissues from their circulating counterparts. Given that most organs and tissues contain a unique microenvironment, local signal-induced tissue-specific features are tightly associated with the differentiation, homeostasis, and protective functions of TRMs. Here, we discuss recent advances in the TRM field with a special emphasis on the interaction between local signals and TRMs in the context of individual tissue environment.
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Affiliation(s)
- Yong Liu
- Department of Microbiology, Immunology and Molecular Genetics, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229; Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South Univeristy, Changsha, Hunan 410008, China
| | - Chaoyu Ma
- Department of Microbiology, Immunology and Molecular Genetics, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Nu Zhang
- Department of Microbiology, Immunology and Molecular Genetics, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229; The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
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31
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Sekimata M, Yoshida D, Araki A, Asao H, Iseki K, Murakami-Sekimata A. Runx1 and RORγt Cooperate to Upregulate IL-22 Expression in Th Cells through Its Distal Enhancer. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 202:3198-3210. [PMID: 31028121 DOI: 10.4049/jimmunol.1800672] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 04/01/2019] [Indexed: 12/29/2022]
Abstract
IL-22 is a cytokine that plays a pivotal role in regulating tissue homeostasis at barrier surfaces and is produced by activated CD4+ Th cells. Currently, the molecular mechanisms regulating Il22 gene expression are still unclear. In this study, we have identified a crucial cis-regulatory element located 32 kb upstream of the mouse Il22 promoter, termed conserved noncoding sequence (CNS)-32. We demonstrated that CNS-32 acts as an enhancer in reporter assays and contains binding motifs for Runt-related transcription factor (Runx)1 and retinoic acid-related orphan receptor γt (RORγt). Mutation of these motifs significantly abrogated the reporter activity, suggesting a role for both factors in the control of enhancer-mediated Il22 expression. Runx1 and RORγt occupancy and elevated histone H4 acetylation at CNS-32 were evident, as naive T cells differentiated into IL-22-producing Th22 cells. Overexpression of Runx1 promoted IL-22 production by inducing RORγt and IL-23 receptor, all critical to Th22 cell induction. Although Runx1 alone enhanced IL-22 production in Th22 cells, it was further enhanced in the presence of RORγt. Conversely, short hairpin RNA-mediated knockdown of core-binding factor β, a cofactor essential for Runx1 activity, was effective in limiting IL-22 production. Collectively, our results suggest that IL-22 production is controlled by a regulatory circuit in which Runx1 induces RORγt and then partners with RORγt to direct Il22 expression through their targeting of the Il22 enhancer.
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MESH Headings
- Amino Acid Motifs/genetics
- Animals
- Cell Differentiation
- Cells, Cultured
- Conserved Sequence/genetics
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Enhancer Elements, Genetic/genetics
- Interleukins/genetics
- Interleukins/metabolism
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mutation/genetics
- Nuclear Receptor Subfamily 1, Group F, Member 3/genetics
- Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism
- Protein Binding
- RNA, Small Interfering/genetics
- Receptors, Interleukin/genetics
- Receptors, Interleukin/metabolism
- T-Lymphocytes, Helper-Inducer/immunology
- Up-Regulation
- Interleukin-22
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Affiliation(s)
- Masayuki Sekimata
- Radioisotope Research Center, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan;
- Division of Theoretical Nursing and Genetics, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan
| | - Daiki Yoshida
- Radioisotope Research Center, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
- Division of Theoretical Nursing and Genetics, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan
| | - Akemi Araki
- Department of Immunology, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan; and
| | - Hironobu Asao
- Department of Immunology, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan; and
| | - Ken Iseki
- Department of Emergency and Critical Care Medicine, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Akiko Murakami-Sekimata
- Division of Theoretical Nursing and Genetics, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan
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32
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Dysregulation of the TOX-RUNX3 pathway in cutaneous T-cell lymphoma. Oncotarget 2019; 10:3104-3113. [PMID: 31139323 PMCID: PMC6517103 DOI: 10.18632/oncotarget.5742] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/18/2015] [Indexed: 12/31/2022] Open
Abstract
Studies have examined gene expression changes in Sézary syndrome (SS), but disease pathogenesis remains largely unknown, and diagnosis and treatment are difficult. TOX is a transcription factor involved in CD4+ T-cell development with downstream effects on RUNX3, a known tumor suppressor gene. We sought to identify genes involved in SS disease pathogenesis with the potential to enable diagnosis and treatment. We utilized previously reported transcriptome sequencing data to construct a list of candidate genes, which was narrowed using pathway analysis. qRT-PCR confirmed TOX upregulation (>7 fold increase) in SS (n = 5), as well as two established markers, PLS3 and KIRD3DL2. We also evaluated expression of members of the TOX-RUNX3 pathway and confirmed downregulation of RUNX3 (0.59 fold decrease) and upregulation of GATA3 (2 fold increase). Moreover, TOX and RUNX3 expression were significantly inversely proportional. Using siRNA to suppress TOX, we demonstrated that TOX knockdown rescues RUNX3 expression and reduces cell viability. We evaluated TOX protein expression in paraffin-embedded skin biopsies with immunohistochemistry, showing nuclear staining of CTCL infiltrates, suggesting it is a candidate diagnostic biomarker. Further studies validating our findings and evaluating the TOX-RUNX3 pathway and the role of TOX as a disease marker and therapeutic target are warranted.
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33
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Zeidan N, Damen H, Roy DC, Dave VP. Critical Role for TCR Signal Strength and MHC Specificity in ThPOK-Induced CD4 Helper Lineage Choice. THE JOURNAL OF IMMUNOLOGY 2019; 202:3211-3225. [PMID: 31036767 DOI: 10.4049/jimmunol.1801464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/26/2019] [Indexed: 01/08/2023]
Abstract
Sustained TCR signaling is critical for ThPOK induction in MHC class II (MHCII)-signaled thymocytes leading to the CD4 helper lineage commitment. ThPOK suppresses the cytotoxic program in the signaled thymocytes and is shown to be necessary and sufficient for the CD4 helper lineage choice. Accordingly, loss and gain of ThPOK function redirects MHCII- and MHC class I (MHCI)-signaled thymocytes into the CD8 cytotoxic and CD4 helper lineage, respectively. However, the impact of a defined ThPOK level on the CD4 helper lineage choice of MHCII- and MHCI-specific thymocytes and the role of TCR signaling in this process is not evaluated. Equally, it is not clear if suppression of the cytotoxic program by ThPOK is sufficient in redirecting MHCI-restricted thymocytes into the CD4 helper lineage. In this study, we have investigated CD8 to CD4 helper lineage redirection in three independent ThPOK overexpressing transgenic mouse lines. Our analysis shows that one of the transgenic lines, despite overexpressing ThPOK compared with wild-type CD4 mature T cells and compromising cytotoxic program, failed to redirect all MHCI-signaled thymocytes into the CD4 helper lineage, resulting in the continued presence of CD8+ mature T cells and the generation of a large number of double negative mature T cells. Critically, the same ThPOK transgene completely restored the CD4 helper lineage commitment of MHCII-specific Thpok -/- thymocytes. Importantly, augmenting TCR signaling significantly enhanced the ThPOK-mediated CD4 helper lineage choice of MHCI-specific thymocytes but was still substantially less efficient than that of MHCII-specific thymocytes expressing the same amount of ThPOK. Together, these data suggest that the ThPOK-induced CD4 helper lineage commitment is strongly influenced by TCR signal strength and MHC specificity of developing thymocytes.
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Affiliation(s)
- Nabil Zeidan
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada.,Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada; and
| | - Hassan Damen
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada
| | - Denis-Claude Roy
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Vibhuti P Dave
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada; .,Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada; and
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34
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Ebihara T, Taniuchi I. Transcription Factors in the Development and Function of Group 2 Innate Lymphoid Cells. Int J Mol Sci 2019; 20:ijms20061377. [PMID: 30893794 PMCID: PMC6470746 DOI: 10.3390/ijms20061377] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Group 2 innate lymphoid cells (ILC2s) are tissue-resident cells and are a major source of innate TH2 cytokine secretion upon allergen exposure or parasitic-worm infection. Accumulating studies have revealed that transcription factors, including GATA-3, Bcl11b, Gfi1, RORα, and Ets-1, play a role in ILC2 differentiation. Recent reports have further revealed that the characteristics and functions of ILC2 are influenced by the physiological state of the tissues. Specifically, the type of inflammation strongly affects the ILC2 phenotype in tissues. Inhibitory ILC2s, memory-like ILC2s, and ex-ILC2s with ILC1 features acquire their characteristic properties following exposure to their specific inflammatory environment. We have recently reported a new ILC2 population, designated as exhausted-like ILC2s, which emerges after a severe allergic inflammation. Exhausted-like ILC2s are featured with low reactivity and high expression of inhibitory receptors. Therefore, for a more comprehensive understanding of ILC2 function and differentiation, we review the recent knowledge of transcriptional regulation of ILC2 differentiation and discuss the roles of the Runx transcription factor in controlling the emergence of exhausted-like ILC2s. The concept of exhausted-like ILC2s sheds a light on a new aspect of ILC2 biology in allergic diseases.
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Affiliation(s)
- Takashi Ebihara
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
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35
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Miyamoto C, Kojo S, Yamashita M, Moro K, Lacaud G, Shiroguchi K, Taniuchi I, Ebihara T. Runx/Cbfβ complexes protect group 2 innate lymphoid cells from exhausted-like hyporesponsiveness during allergic airway inflammation. Nat Commun 2019; 10:447. [PMID: 30683858 PMCID: PMC6347616 DOI: 10.1038/s41467-019-08365-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/08/2019] [Indexed: 01/01/2023] Open
Abstract
Group 2 innate lymphoid cells (ILC2s) have tissue-resident competence and contribute to the pathogenesis of allergic diseases. However, the mechanisms regulating prolonged ILC2-mediated TH2 cytokine production under chronic inflammatory conditions are unclear. Here we show that, at homeostasis, Runx deficiency induces excessive ILC2 activation due to overly active GATA-3 functions. By contrast, during allergic inflammation, the absence of Runx impairs the ability of ILC2s to proliferate and produce effector TH2 cytokines and chemokines. Instead, functional deletion of Runx induces the expression of exhaustion markers, such as IL-10 and TIGIT, on ILC2s. Finally, these 'exhausted-like' ILC2s are unable to induce type 2 immune responses to repeated allergen exposures. Thus, Runx confers competence for sustained ILC2 activity at the mucosa, and contributes to allergic pathogenesis.
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Affiliation(s)
- Chizuko Miyamoto
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoshi Kojo
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Motoi Yamashita
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kazuyo Moro
- Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Georges Lacaud
- Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
| | - Katsuyuki Shiroguchi
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Laboratory for Prediction of Cell Systems Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, 565-0874, Japan
- JST PRESTO, Kawaguchi, 332-0012, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takashi Ebihara
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
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36
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Collins PL, Cella M, Porter SI, Li S, Gurewitz GL, Hong HS, Johnson RP, Oltz EM, Colonna M. Gene Regulatory Programs Conferring Phenotypic Identities to Human NK Cells. Cell 2018; 176:348-360.e12. [PMID: 30595449 DOI: 10.1016/j.cell.2018.11.045] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/09/2018] [Accepted: 11/28/2018] [Indexed: 01/03/2023]
Abstract
Natural killer (NK) cells develop from common progenitors but diverge into distinct subsets, which differ in cytokine production, cytotoxicity, homing, and memory traits. Given their promise in adoptive cell therapies for cancer, a deeper understanding of regulatory modules controlling clinically beneficial NK phenotypes is of high priority. We report integrated "-omics" analysis of human NK subsets, which revealed super-enhancers associated with gene cohorts that may coordinate NK functions and localization. A transcription factor-based regulatory scheme also emerged, which is evolutionarily conserved and shared by innate and adaptive lymphocytes. For both NK and T lineages, a TCF1-LEF1-MYC axis dominated the regulatory landscape of long-lived, proliferative subsets that traffic to lymph nodes. In contrast, effector populations circulating between blood and peripheral tissues shared a PRDM1-dominant landscape. This resource defines transcriptional modules, regulated by feedback loops, which may be leveraged to enhance phenotypes for NK cell-based therapies.
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Affiliation(s)
- Patrick L Collins
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sofia I Porter
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shasha Li
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Greer L Gurewitz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | | | - R Paul Johnson
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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37
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Abstract
The molecular basis for T cell memory differentiation remains elusive. Wang et al. (2018) identify Runx3 as an initiating transcription factor that specifies regulatory regions required for cytotoxic T cell (CTL) memory differentiation early after TCR signaling and constrains the ability of T-bet to drive terminal effector generation.
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Affiliation(s)
- Yohei Mikami
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuka Kanno
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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38
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Rytkönen KT, Erkenbrack EM, Poutanen M, Elo LL, Pavlicev M, Wagner GP. Decidualization of Human Endometrial Stromal Fibroblasts is a Multiphasic Process Involving Distinct Transcriptional Programs. Reprod Sci 2018; 26:323-336. [PMID: 30309298 DOI: 10.1177/1933719118802056] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Decidual stromal cells differentiate from endometrial stromal fibroblasts (ESFs) under the influence of progesterone and cyclic adenosine monophosphate (cAMP) and are essential for implantation and the maintenance of pregnancy. They evolved in the stem lineage of placental (eutherian) mammals coincidental with the evolution of implantation. Here we use the well-established in vitro decidualization protocol to compare early (3 days) and late (8 days) gene transcription patterns in immortalized human ESF. We document extensive, dynamic changes in the early and late decidual cell transcriptomes. The data suggest the existence of an early signal transducer and activator of transcription (STAT) pathway dominated state and a later nuclear factor κB (NFKB) pathway regulated state. Transcription factor expression in both phases is characterized by putative or known progesterone receptor ( PGR) target genes, suggesting that both phases are under progesterone control. Decidualization leads to proliferative quiescence, which is reversible by progesterone withdrawal after 3 days but to a lesser extent after 8 days of decidualization. In contrast, progesterone withdrawal induces cell death at comparable levels after short or long exposure to progestins and cAMP. We conclude that decidualization is characterized by a biphasic gene expression dynamic that likely corresponds to different phases in the establishment of the fetal-maternal interface.
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Affiliation(s)
- Kalle T Rytkönen
- 1 Yale Systems Biology Institute, West Haven, CT, USA.,2 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,3 Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu, Finland.,4 Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Eric M Erkenbrack
- 1 Yale Systems Biology Institute, West Haven, CT, USA.,2 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Matti Poutanen
- 3 Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Kiinamyllynkatu, Finland
| | - Laura L Elo
- 4 Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Mihaela Pavlicev
- 5 Cincinnati Children's Hospital and Medical Center, Cincinnati, OH, USA
| | - Günter P Wagner
- 1 Yale Systems Biology Institute, West Haven, CT, USA.,2 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,6 Department of Obstetrics, Yale Medical School, New Haven, CT, USA.,7 Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
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39
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Behr FM, Chuwonpad A, Stark R, van Gisbergen KPJM. Armed and Ready: Transcriptional Regulation of Tissue-Resident Memory CD8 T Cells. Front Immunol 2018; 9:1770. [PMID: 30131803 PMCID: PMC6090154 DOI: 10.3389/fimmu.2018.01770] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/17/2018] [Indexed: 11/13/2022] Open
Abstract
A fundamental benefit of immunological memory is the ability to respond in an enhanced manner upon secondary encounter with the same pathogen. Tissue-resident memory CD8 T (TRM) cells contribute to improved protection against reinfection through the generation of immediate effector responses at the site of pathogen entry. Key to the potential of TRM cells to develop rapid recall responses is their location within the epithelia of the skin, lungs, and intestines at prime entry sites of pathogens. TRM cells are among the first immune cells to respond to pathogens that have been previously encountered in an antigen-specific manner. Upon recognition of invading pathogens, TRM cells release IFN-γ and other pro-inflammatory cytokines and chemokines. These effector molecules activate the surrounding epithelial tissue and recruit other immune cells including natural killer (NK) cells, B cells, and circulating memory CD8 T cells to the site of infection. The repertoire of TRM effector functions also includes the direct lysis of infected cells through the release of cytotoxic molecules such as perforin and granzymes. The mechanisms enabling TRM cells to respond in such a rapid manner are gradually being uncovered. In this review, we will address the signals that instruct TRM generation and maintenance as well as the underlying transcriptional network that keeps TRM cells in a deployment-ready modus. Furthermore, we will discuss how TRM cells respond to reinfection of the tissue and how transcription factors may control immediate and proliferative TRM responses.
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Affiliation(s)
- Felix M Behr
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory AMC/UvA, Amsterdam, Netherlands.,Department of Experimental Immunology, Academic Medical Center, Amsterdam, Netherlands
| | - Ammarina Chuwonpad
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory AMC/UvA, Amsterdam, Netherlands
| | - Regina Stark
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory AMC/UvA, Amsterdam, Netherlands.,Department of Experimental Immunology, Academic Medical Center, Amsterdam, Netherlands
| | - Klaas P J M van Gisbergen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory AMC/UvA, Amsterdam, Netherlands.,Department of Experimental Immunology, Academic Medical Center, Amsterdam, Netherlands
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40
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Rapp M, Lau CM, Adams NM, Weizman OE, O'Sullivan TE, Geary CD, Sun JC. Core-binding factor β and Runx transcription factors promote adaptive natural killer cell responses. Sci Immunol 2018; 2:2/18/eaan3796. [PMID: 29222089 DOI: 10.1126/sciimmunol.aan3796] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 09/12/2017] [Accepted: 11/02/2017] [Indexed: 01/03/2023]
Abstract
Natural killer (NK) cells are innate lymphocytes that have features of adaptive immunity such as clonal expansion and generation of long-lived memory. Interleukin-12 (IL-12) signaling through its downstream transcription factor signal transducer and activator of transcription 4 (STAT4) is required for the generation of memory NK cells after expansion. We identify gene loci that are highly enriched for STAT4 binding using chromatin immunoprecipitation sequencing for STAT4 and the permissive histone mark H3K4me3 in activated NK cells. We found that promoter regions of Runx1 and Runx3 are targets of STAT4 and that STAT4 binding during NK cell activation induces epigenetic modifications of Runx gene loci resulting in increased expression. Furthermore, specific ablation of Runx1, Runx3, or their binding partner Cbfb in NK cells resulted in defective clonal expansion and memory formation during viral infection, with evidence for Runx1-mediated control of a cell cycle program. Thus, our study reveals a mechanism whereby STAT4-mediated epigenetic control of individual Runx transcription factors promotes the adaptive behavior of antiviral NK cells.
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Affiliation(s)
- Moritz Rapp
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colleen M Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Orr-El Weizman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timothy E O'Sullivan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Clair D Geary
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA
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41
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Memory responses of innate lymphocytes and parallels with T cells. Semin Immunopathol 2018; 40:343-355. [PMID: 29808388 DOI: 10.1007/s00281-018-0686-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/04/2018] [Indexed: 12/23/2022]
Abstract
Natural killer (NK) cells are classified as innate immune cells, given their ability to rapidly respond and kill transformed or virally infected cells without prior sensitization. Recently, accumulating evidence suggests that NK cells also exhibit many characteristics similar to cells of the adaptive immune system. Analogous to T cells, NK cells acquire self-tolerance during development, express antigen-specific receptors, undergo clonal-like expansion, and can become long-lived, self-renewing memory cells with potent effector function providing potent protection against reappearing pathogens. In this review, we discuss the requirements for memory NK cell generation and highlight the similarities with the formation of memory T cells.
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42
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Verbaro DJ, Sakurai N, Kim B, Shinkai Y, Egawa T. Cutting Edge: The Histone Methyltransferase G9a Is Required for Silencing of Helper T Lineage-Associated Genes in Proliferating CD8 T Cells. THE JOURNAL OF IMMUNOLOGY 2018; 200:3891-3896. [PMID: 29720423 DOI: 10.4049/jimmunol.1701700] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/11/2018] [Indexed: 11/19/2022]
Abstract
Helper versus cytotoxic T lineage decision in the thymus has been studied as a model for silencing of alternative lineage genes. Although the transcription factor RUNX3 is required for the initiation of Cd4 silencing in developing CD8 T cells, it is unknown how silencing of Cd4 and other helper T lineage genes is maintained. We show that the histone methyltransferase G9a is necessary for silencing helper T lineage genes in proliferating mouse CD8 T cells. Despite normal initial Cd4 downregulation, G9a-deficient CD8 T cells derepress Cd4 and other helper lineage genes during repeated division in lymphopenia or in response to tumor Ag. However, G9a was dispensable for continued silencing of those genes in CD8 T cells that respond to infection by Listeria monocytogenes These results demonstrate that G9a facilitates maintenance of cellular identity of CD8 T cells during cell division, which is further reinforced by inflammatory signals.
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Affiliation(s)
- Daniel J Verbaro
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; and
| | - Nagisa Sakurai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; and
| | - Byungil Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; and
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; and
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43
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Satpathy AT, Saligrama N, Buenrostro JD, Wei Y, Wu B, Rubin AJ, Granja JM, Lareau CA, Li R, Qi Y, Parker KR, Mumbach MR, Serratelli WS, Gennert DG, Schep AN, Corces MR, Khodadoust MS, Kim YH, Khavari PA, Greenleaf WJ, Davis MM, Chang HY. Transcript-indexed ATAC-seq for precision immune profiling. Nat Med 2018; 24:580-590. [PMID: 29686426 PMCID: PMC5948148 DOI: 10.1038/s41591-018-0008-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 02/07/2018] [Indexed: 02/04/2023]
Abstract
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy.
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Affiliation(s)
- Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Naresha Saligrama
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason D Buenrostro
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Beijing Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam J Rubin
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Caleb A Lareau
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - William S Serratelli
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - David G Gennert
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alicia N Schep
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael S Khodadoust
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Youn H Kim
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Applied Physics, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. .,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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44
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Lu F, Liu Q. Validation of RUNX1 as a potential target for treating circadian clock-induced obesity through preventing migration of group 3 innate lymphoid cells into intestine. Med Hypotheses 2018. [PMID: 29523306 DOI: 10.1016/j.mehy.2018.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The impact of unrhythmic circadian clock on obesity has started to be increasingly appreciated nowadays. Recently it was discovered that interaction between intestinal microbiota and unrhythmic circadian clock plays a key role in such a process. It involves relaying signals from microbiota through dendritic cells to group 3 innate lymphoid cells in the intestine and in the end impacting some of the key transcription factors of circadian clock. Breaking such a signal relay may prove to be an effective way reducing unrhythmic circadian clock-induced obesity. Here, we propose a hypothesis and design experiments to prove that suppressing one of the transcription factors, RUNX1, plays a key role in the homing of ILC3 cells to intestine. Such suppression is in response to a retinoic acid-RARα binding initiated pathway and results in the upregulation of gut-homing chemokine receptor CCR9 and downregulation of lymphoid tissue-homing receptor CCR7, which can then guide ILC3 cells to intestine. Therapies that can specifically sustain Runx1 expression in ILC3 cells may assist preventing the ever-escalating obesity problem in modern society.
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Affiliation(s)
- Fangjia Lu
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47906, USA
| | - Qingyang Liu
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47906, USA.
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45
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Takada K, Amano R, Nomura Y, Tanaka Y, Sugiyama S, Nagata T, Katahira M, Nakamura Y, Kozu T, Sakamoto T. Characterisation of an aptamer against the Runt domain of AML1 (RUNX1) by NMR and mutational analyses. FEBS Open Bio 2018; 8:264-270. [PMID: 29435416 PMCID: PMC5794459 DOI: 10.1002/2211-5463.12368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/20/2017] [Accepted: 12/02/2017] [Indexed: 01/15/2023] Open
Abstract
Since the invention of systematic evolution of ligands by exponential enrichment, many short oligonucleotides (or aptamers) have been reported that can bind to a wide range of target molecules with high affinity and specificity. Previously, we reported an RNA aptamer that shows high affinity to the Runt domain (RD) of the AML1 protein, a transcription factor with roles in haematopoiesis and immune function. From kinetic and thermodynamic studies, it was suggested that the aptamer recognises a large surface area of the RD, using numerous weak interactions. In this study, we identified the secondary structure by nuclear magnetic resonance spectroscopy and performed a mutational study to reveal the residue critical for binding to the RD. It was suggested that the large contact area was formed by a DNA‐mimicking motif and a multibranched loop, which confers the high affinity and specificity of binding.
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Affiliation(s)
- Kenta Takada
- Department of Life and Environmental Sciences Faculty of Engineering Chiba Institute of Technology Narashino Japan
| | - Ryo Amano
- Department of Life and Environmental Sciences Faculty of Engineering Chiba Institute of Technology Narashino Japan
| | - Yusuke Nomura
- Division of Medical Devices National Institute of Health Sciences Tokyo Japan
| | - Yoichiro Tanaka
- Facility for RI Research and Education Instrumental Analysis Center Yokohama National University Japan
| | | | | | | | - Yoshikazu Nakamura
- RIBOMIC Inc.Tokyo Japan.,Department of Basic Medical Sciences Institute of Medical Science University of Tokyo Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology Saitama Cancer CenterIna Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences Faculty of Engineering Chiba Institute of Technology Narashino Japan
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46
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Mao AP, Ishizuka IE, Kasal DN, Mandal M, Bendelac A. A shared Runx1-bound Zbtb16 enhancer directs innate and innate-like lymphoid lineage development. Nat Commun 2017; 8:863. [PMID: 29038474 PMCID: PMC5643357 DOI: 10.1038/s41467-017-00882-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/02/2017] [Indexed: 02/07/2023] Open
Abstract
Zbtb16-encoded PLZF is a signature transcription factor (TF) that directs the acquisition of T-helper effector programs during the development of multiple innate lymphocyte lineages, including natural killer T cell, innate lymphoid cell, mucosal-associated invariant T cell and γδ lineages. PLZF is also essential in osteoblast and spermatogonial development. How Zbtb16 itself is regulated in different lineages is incompletely understood. Here, by systematic CRISPR/Cas9-assisted deletions of chromatin accessible regions within the Zbtb16 locus in mouse, we identify a critical enhancer controlling PLZF expression exclusively in innate lymphoid lineages. Multiple sites within this enhancer express canonical motifs for the TF Runx1, which is essential for the development of these lineages. Notably, some regulatory sites control the kinetic rather than the overall level of PLZF expression. Thus, our comprehensive, unbiased analysis of regulatory elements in vivo reveals critical mechanisms of Zbtb16 regulation shared between innate and innate-like lymphoid lineages. Zbtb16-encoded transcription factor PLZF directs the differentiation of multiple innate and innate-like cell lineages, but how Zbtb16 itself is regulated remains unclear. Here the authors show, using CRISPR gene editing, ATAC-seq and ChIP-seq, that specific Runx1-bound enhancer elements critically modulate lineage-dependent expressions of PLZF.
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Affiliation(s)
- Ai-Ping Mao
- Committee on Immunology, University of Chicago, Chicago, IL, 60637, USA.,Department of Pathology, University of Chicago, Chicago, IL, 60637, USA
| | - Isabel E Ishizuka
- Committee on Immunology, University of Chicago, Chicago, IL, 60637, USA.,Department of Pathology, University of Chicago, Chicago, IL, 60637, USA
| | - Darshan N Kasal
- Committee on Immunology, University of Chicago, Chicago, IL, 60637, USA.,Department of Pathology, University of Chicago, Chicago, IL, 60637, USA
| | - Malay Mandal
- Committee on Immunology, University of Chicago, Chicago, IL, 60637, USA.,Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637, USA
| | - Albert Bendelac
- Committee on Immunology, University of Chicago, Chicago, IL, 60637, USA. .,Department of Pathology, University of Chicago, Chicago, IL, 60637, USA.
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Identification of lineage-specifying cytokines that signal all CD8 +-cytotoxic-lineage-fate 'decisions' in the thymus. Nat Immunol 2017; 18:1218-1227. [PMID: 28945245 PMCID: PMC5659273 DOI: 10.1038/ni.3847] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/29/2017] [Indexed: 12/11/2022]
Abstract
T cell antigen receptor (TCR) signaling in the thymus initiates positive selection but CD8 lineage fate is thought to be induced by cytokines after TCR signaling has ceased, although this remains controversial and unproven. We now identify four non-common gamma chain (γc) receptor-signaling cytokines (IL-6, IFN-γ, TSLP, TGF-β) that, like IL-7 and IL-15, induce expression of the lineage-specifying transcription factor Runx3d and signal the generation of CD8 T cells. Remarkably, elimination of in vivo signaling by all ‘lineage-specifying cytokines’ during positive selection eliminated Runx3d expression and completely abrogated CD8 single-positive thymocyte generation. Thus, this study proves that signaling during positive selection by lineage-specifying cytokines is responsible for all CD8 lineage fate decisions in the thymus.
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48
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Vacchio MS, Bosselut R. What Happens in the Thymus Does Not Stay in the Thymus: How T Cells Recycle the CD4+-CD8+ Lineage Commitment Transcriptional Circuitry To Control Their Function. THE JOURNAL OF IMMUNOLOGY 2017; 196:4848-56. [PMID: 27260768 DOI: 10.4049/jimmunol.1600415] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/06/2016] [Indexed: 12/24/2022]
Abstract
MHC-restricted CD4(+) and CD8(+) T cells are at the core of most adaptive immune responses. Although these cells carry distinct functions, they arise from a common precursor during thymic differentiation, in a developmental sequence that matches CD4 and CD8 expression and functional potential with MHC restriction. Although the transcriptional control of CD4(+)-CD8(+) lineage choice in the thymus is now better understood, less was known about what maintains the CD4(+) and CD8(+) lineage integrity of mature T cells. In this review, we discuss the mechanisms that establish in the thymus, and maintain in postthymic cells, the separation of these lineages. We focus on recent studies that address the mechanisms of epigenetic control of Cd4 expression and emphasize how maintaining a transcriptional circuitry nucleated around Thpok and Runx proteins, the key architects of CD4(+)-CD8(+) lineage commitment in the thymus, is critical for CD4(+) T cell helper functions.
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Affiliation(s)
- Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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49
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Carpenter AC, Wohlfert E, Chopp LB, Vacchio MS, Nie J, Zhao Y, Shetty J, Xiao Q, Deng C, Tran B, Cam M, Gaida MM, Belkaid Y, Bosselut R. Control of Regulatory T Cell Differentiation by the Transcription Factors Thpok and LRF. THE JOURNAL OF IMMUNOLOGY 2017; 199:1716-1728. [PMID: 28754678 DOI: 10.4049/jimmunol.1700181] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/06/2017] [Indexed: 01/10/2023]
Abstract
The CD4+ lineage-specific transcription factor Thpok is required for intrathymic CD4+ T cell differentiation and, together with its homolog LRF, supports CD4+ T cell helper effector responses. However, it is not known whether these factors are needed for the regulatory T cell (Treg) arm of MHC class II responses. In this study, by inactivating in mice the genes encoding both factors in differentiated Tregs, we show that Thpok and LRF are redundantly required to maintain the size and functions of the postthymic Treg pool. They support IL-2-mediated gene expression and the functions of the Treg-specific factor Foxp3. Accordingly, Treg-specific disruption of Thpok and Lrf causes a lethal inflammatory syndrome similar to that resulting from Treg deficiency. Unlike in conventional T cells, Thpok and LRF functions in Tregs are not mediated by their repression of the transcription factor Runx3. Additionally, we found that Thpok is needed for the differentiation of thymic Treg precursors, an observation in line with the fact that Foxp3+ Tregs are CD4+ cells. Thus, a common Thpok-LRF node supports both helper and regulatory arms of MHC class II responses.
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Affiliation(s)
- Andrea C Carpenter
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth Wohlfert
- Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.,Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Laura B Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.,Immunology Graduate Group, University of Pennsylvania Medical School, Philadelphia, PA 19104
| | - Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jia Nie
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Yongmei Zhao
- Center for Cancer Research Sequencing Facility, Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702
| | - Jyoti Shetty
- Center for Cancer Research Sequencing Facility, Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702
| | - Qi Xiao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Callie Deng
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Bao Tran
- Center for Cancer Research Sequencing Facility, Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702
| | - Margaret Cam
- Center for Cancer Research Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Matthias M Gaida
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.,Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Yasmine Belkaid
- Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.,Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892;
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50
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Zhou X, Zhu J, Bian T, Wang R, Gao F. Mislocalization of Runt-related transcription factor 3 results in airway inflammation and airway hyper-responsiveness in a murine asthma model. Exp Ther Med 2017; 14:2695-2701. [PMID: 28962214 DOI: 10.3892/etm.2017.4812] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/18/2016] [Indexed: 02/07/2023] Open
Abstract
The Runt-related transcription factor (RUNX) gene family consists of three members, RUNX1, -2 and -3, which heterodimerize with a common protein, core-binding factor β, and contain the highly conserved Runt-homology domain. RUNX1 and -2 have essential roles in hematopoiesis and osteogenesis. Runx3 protein regulates cell lineage decisions in neurogenesis and thymopoiesis. The aim of the present study was to determine the expression features of the Runx3 protein in a murine asthma model. In vivo, Runx3 protein and mRNA were found to be almost equivalently expressed in the murine lung tissue of the control, ovalbumin (OVA) and genistein groups; however, the nuclear Runx3 protein was abated in lung tissue in OVA-immunized and challenged mice. Following treatment with genistein, which is a flavonoid previously demonstrated to decrease airway inflammation in asthma, the allergic airway inflammation and airway hyper-responsiveness were attenuated and the Runx3 protein tended to augment in the nucleus. These results were further determined in vitro. These results indicated that the mislocalization of Runx3 protein is a molecular mechanism of allergic inflammation and airway hyper-responsiveness in a murine asthma model.
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Affiliation(s)
- Xiaoyan Zhou
- Department of Respiratory Medicine, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| | - Jinxiao Zhu
- Department of Stomatology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Tao Bian
- Department of Respiratory Medicine, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Ruiqian Wang
- Department of Respiratory Medicine, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Fei Gao
- Department of Respiratory Medicine, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
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