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Zhao D, Li H, Mambetsariev I, Mirzapoiazova T, Chen C, Fricke J, Wheeler D, Arvanitis L, Pillai R, Afkhami M, Chen BT, Sattler M, Erhunmwunsee L, Massarelli E, Kulkarni P, Amini A, Armstrong B, Salgia R. Spatial iTME analysis of KRAS mutant NSCLC and immunotherapy outcome. NPJ Precis Oncol 2024; 8:135. [PMID: 38898200 PMCID: PMC11187132 DOI: 10.1038/s41698-024-00626-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
We conducted spatial immune tumor microenvironment (iTME) profiling using formalin-fixed paraffin-embedded (FFPE) samples of 25 KRAS-mutated non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICIs), including 12 responders and 13 non-responders. An eleven-marker panel (CD3, CD4, CD8, FOXP3, CD68, arginase-1, CD33, HLA-DR, pan-keratin (PanCK), PD-1, and PD-L1) was used to study the tumor and immune cell compositions. Spatial features at single cell level with cellular neighborhoods and fractal analysis were determined. Spatial features and different subgroups of CD68+ cells and FOXP3+ cells being associated with response or resistance to ICIs were also identified. In particular, CD68+ cells, CD33+ and FOXP3+ cells were found to be associated with resistance. Interestingly, there was also significant association between non-nuclear expression of FOXP3 being resistant to ICIs. We identified CD68dim cells in the lung cancer tissues being associated with improved responses, which should be insightful for future studies of tumor immunity.
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Affiliation(s)
- Dan Zhao
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Haiqing Li
- Integrative Genomic Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
- Department of Computational & Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Isa Mambetsariev
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Tamara Mirzapoiazova
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Chen Chen
- Department of Applied AI & Data Science, City of Hope, Duarte, CA, USA
| | - Jeremy Fricke
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Deric Wheeler
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | | | - Raju Pillai
- Department of Pathology, City of Hope, Duarte, CA, USA
| | | | - Bihong T Chen
- Department of Diagnostic Radiology, City of Hope, Duarte, CA, USA
| | - Martin Sattler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Erminia Massarelli
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Arya Amini
- Department of Radiation Oncology, City of Hope, Duarte, CA, USA
| | - Brian Armstrong
- Light Microscopy/Digital Imaging Core, City of Hope, Duarte, CA, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA.
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2
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Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria MEG, Schatz MC, Taylor J, Gottgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.02.535219. [PMID: 37066352 PMCID: PMC10103973 DOI: 10.1101/2023.04.02.535219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Knowledge of locations and activities of cis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project. The resulting catalogs of cCREs are useful resources for further studies of gene regulation in blood cells, indicated by high overlap with known functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state Regulatory Potential (esRP) scores for each cCRE in each cell type, which were used to categorize dynamic changes in cCREs. Groups of cCREs displaying similar patterns of regulatory activity in human and mouse cell types, obtained by joint clustering on esRP scores, harbored distinctive transcription factor binding motifs that were similar between species. An interspecies comparison of cCREs revealed both conserved and species-specific patterns of epigenetic evolution. Finally, we showed that comparisons of the epigenetic landscape between species can reveal elements with similar roles in regulation, even in the absence of genomic sequence alignment.
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3
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Li D, Quan Z, Ni J, Li H, Qing H. The many faces of the zinc finger protein 335 in brain development and immune system. Biomed Pharmacother 2023; 165:115257. [PMID: 37541176 DOI: 10.1016/j.biopha.2023.115257] [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: 06/02/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/06/2023] Open
Abstract
Zinc finger protein 335 (ZNF335) plays a crucial role in the methylation and, consequently, regulates the expression of a specific set of genes. Variants of the ZNF335 gene have been identified as risk factors for microcephaly in a variety of populations worldwide. Meanwhile, ZNF335 has also been identified as an essential regulator of T-cell development. However, an in-depth understanding of the role of ZNF335 in brain development and T cell maturation is still lacking. In this review, we summarize current knowledge of the molecular mechanisms underlying the involvement of ZNF335 in neuronal and T cell development across a wide range of pre-clinical, post-mortem, ex vivo, in vivo, and clinical studies. We also review the current limitations regarding the study of the pathophysiological functions of ZNF335. Finally, we hypothesize a potential role for ZNF335 in brain disorders and discuss the rationale of targeting ZNF335 as a therapeutic strategy for preventing brain disorders.
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Affiliation(s)
- Danyang Li
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Zhenzhen Quan
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Hui Li
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
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4
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Walcheck MT, Nukaya M, Ranheim EA, Matkowskyj KA, Ronnekleiv-Kelly S. Pdx1 expression in hematopoietic cells activates Kras-mutation to drive leukemia in KC ( Pdx1-Cre; LSL-KrasG12D/+) mice. Leuk Lymphoma 2023; 64:1112-1122. [PMID: 37081806 PMCID: PMC10503568 DOI: 10.1080/10428194.2023.2202788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/01/2023] [Accepted: 04/09/2023] [Indexed: 04/22/2023]
Abstract
The highly utilized KC model has a reported lethality rate of about 30%, which has been attributed to pancreas cancer. However, a competing cause of lethality in KC mice is due to the activation of mutant-Kras gene (KrasG12D/+) in the multipotent progenitor cells (MPP), and subsequent development of Kras-mutant T-cell acute lymphoblastic leukemia (T-ALL). Overall, 20% (5/25) of KC mice developed T-ALL by 9 months of age. Transplantation of pooled bone marrow from KC mice into CD45 congenic mice caused T-ALL in 100% of recipient mice, confirming that mutant-Kras expression in the hematologic compartment is driving the development of T-ALL in the KC mouse model. These results are an essential consideration for investigators using this model. Further, the lower penetrance of T-ALL in KC mice (versus existing leukemia models) suggests this model could be considered as an alternative research model to evaluate onset and factors that exacerbate the development of T-ALL.
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Affiliation(s)
- Morgan T Walcheck
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, K3/705 CSC, Madison, WI, USA
| | - Manabu Nukaya
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, K3/705 CSC, Madison, WI, USA
| | - Erik A Ranheim
- University of Wisconsin Carbone Cancer Center, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kristina A Matkowskyj
- University of Wisconsin Carbone Cancer Center, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Sean Ronnekleiv-Kelly
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, K3/705 CSC, Madison, WI, USA
- University of Wisconsin Carbone Cancer Center, Madison, WI, USA
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5
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Ratiu JJ, Barclay WE, Lin E, Wang Q, Wellford S, Mehta N, Harnois MJ, DiPalma D, Roy S, Contreras AV, Shinohara ML, Wiest D, Zhuang Y. Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-β selection thymocytes. Nat Commun 2022; 13:5901. [PMID: 36202870 PMCID: PMC9537144 DOI: 10.1038/s41467-022-33610-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023] Open
Abstract
Production of a functional peripheral T cell compartment typically involves massive expansion of the bone marrow progenitors that seed the thymus. There are two main phases of expansion during T cell development, following T lineage commitment of double-negative (DN) 2 cells and after successful rearrangement and selection for functional TCRβ chains in DN3 thymocytes, which promotes the transition of DN4 cells to the DP stage. The signals driving the expansion of DN2 thymocytes are well studied. However, factors regulating the proliferation and survival of DN4 cells remain poorly understood. Here, we uncover an unexpected link between the transcription factor Zfp335 and control of cGAS/STING-dependent cell death in post-β-selection DN4 thymocytes. Zfp335 controls survival by sustaining expression of Ankle2, which suppresses cGAS/STING-dependent cell death. Together, this study identifies Zfp335 as a key transcription factor regulating the survival of proliferating post-β-selection thymocytes and demonstrates a key role for the cGAS/STING pathway in driving apoptosis of developing T cells.
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Affiliation(s)
- Jeremy J Ratiu
- Duke University, Department of Immunology, Durham, NC, 27710, USA.
| | | | - Elliot Lin
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Qun Wang
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | | | - Naren Mehta
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | | | - Devon DiPalma
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Sumedha Roy
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Alejandra V Contreras
- Fox Chase Cancer Center, Blood Cell Development and Function Program, Philadelphia, PA, 19111, USA
| | - Mari L Shinohara
- Duke University, Department of Immunology, Durham, NC, 27710, USA
- Duke University, Department of Molecular Genetics and Microbiology, Durham, NC, 27710, USA
| | - David Wiest
- Fox Chase Cancer Center, Blood Cell Development and Function Program, Philadelphia, PA, 19111, USA
| | - Yuan Zhuang
- Duke University, Department of Immunology, Durham, NC, 27710, USA
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6
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Nathan A, Asgari S, Ishigaki K, Valencia C, Amariuta T, Luo Y, Beynor JI, Baglaenko Y, Suliman S, Price AL, Lecca L, Murray MB, Moody DB, Raychaudhuri S. Single-cell eQTL models reveal dynamic T cell state dependence of disease loci. Nature 2022; 606:120-128. [PMID: 35545678 PMCID: PMC9842455 DOI: 10.1038/s41586-022-04713-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/31/2022] [Indexed: 02/02/2023]
Abstract
Non-coding genetic variants may cause disease by modulating gene expression. However, identifying these expression quantitative trait loci (eQTLs) is complicated by differences in gene regulation across fluid functional cell states within cell types. These states-for example, neurotransmitter-driven programs in astrocytes or perivascular fibroblast differentiation-are obscured in eQTL studies that aggregate cells1,2. Here we modelled eQTLs at single-cell resolution in one complex cell type: memory T cells. Using more than 500,000 unstimulated memory T cells from 259 Peruvian individuals, we show that around one-third of 6,511 cis-eQTLs had effects that were mediated by continuous multimodally defined cell states, such as cytotoxicity and regulatory capacity. In some loci, independent eQTL variants had opposing cell-state relationships. Autoimmune variants were enriched in cell-state-dependent eQTLs, including risk variants for rheumatoid arthritis near ORMDL3 and CTLA4; this indicates that cell-state context is crucial to understanding potential eQTL pathogenicity. Moreover, continuous cell states explained more variation in eQTLs than did conventional discrete categories, such as CD4+ versus CD8+, suggesting that modelling eQTLs and cell states at single-cell resolution can expand insight into gene regulation in functionally heterogeneous cell types.
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Affiliation(s)
- Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Samira Asgari
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Cristian Valencia
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tiffany Amariuta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jessica I Beynor
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yuriy Baglaenko
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sara Suliman
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alkes L Price
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Leonid Lecca
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
- Socios En Salud Sucursal Peru, Lima, Peru
| | - Megan B Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
- Division of Global Health Equity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - D Branch Moody
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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7
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Ecovoiu AA, Ratiu AC, Micheu MM, Chifiriuc MC. Inter-Species Rescue of Mutant Phenotype—The Standard for Genetic Analysis of Human Genetic Disorders in Drosophila melanogaster Model. Int J Mol Sci 2022; 23:ijms23052613. [PMID: 35269756 PMCID: PMC8909942 DOI: 10.3390/ijms23052613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 11/16/2022] Open
Abstract
Drosophila melanogaster (the fruit fly) is arguably a superstar of genetics, an astonishing versatile experimental model which fueled no less than six Nobel prizes in medicine. Nowadays, an evolving research endeavor is to simulate and investigate human genetic diseases in the powerful D. melanogaster platform. Such a translational experimental strategy is expected to allow scientists not only to understand the molecular mechanisms of the respective disorders but also to alleviate or even cure them. In this regard, functional gene orthology should be initially confirmed in vivo by transferring human or vertebrate orthologous transgenes in specific mutant backgrounds of D. melanogaster. If such a transgene rescues, at least partially, the mutant phenotype, then it qualifies as a strong candidate for modeling the respective genetic disorder in the fruit fly. Herein, we review various examples of inter-species rescue of relevant mutant phenotypes of the fruit fly and discuss how these results recommend several human genes as candidates to study and validate genetic variants associated with human diseases. We also consider that a wider implementation of this evolutionist exploratory approach as a standard for the medicine of genetic disorders would allow this particular field of human health to advance at a faster pace.
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Affiliation(s)
- Alexandru Al. Ecovoiu
- Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania;
| | - Attila Cristian Ratiu
- Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania;
- Correspondence: ; Tel.: +40-722250366
| | - Miruna Mihaela Micheu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, 014461 Bucharest, Romania;
| | - Mariana Carmen Chifiriuc
- The Research Institute of the University of Bucharest and Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania;
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8
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Inokuchi JI, Nagafuku M. Gangliosides in T cell development and function of mice. Glycoconj J 2022; 39:229-238. [DOI: 10.1007/s10719-021-10037-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/19/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
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9
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Differential Analysis and Putative Roles of Genes, Cytokines and Apoptotic Proteins in Blood Samples of Patients with Respiratory Viral Infections: A Single Center Study. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Insights into the molecular pathogenesis of respiratory viral infections were investigated using serum and peripheral blood from patients with clinical syndromes. Signatures of expression of cytokines, genes and apoptotic proteins that discriminate symptomatic individuals from healthy individuals were determined among 21 patients. In symptomatic patients, significant upregulation of IL-1β, IL-2, IL-4, IL-6, IL-8, IL-12, IL-15, TNF-a and IFN-g (P<0.05) was noted, while IL-10 was significantly downregulated (P<0.05). This is accompanied by either up or down-regulation of various pro-apoptotic and anti-apoptotic markers, suggesting a protective role of immune responses against viral infection and the capacity of viruses to subvert host cell apoptosis. Gene expression analysis for both T and B cells were categorized according to their functional status of activation, proliferation, and differentiation. Of note, genes SH2D1A and TCL1A were upregulated only in rhinovirus samples, while PSMB7, CD4, CD8A, HLA-DMA, HLA-DRA and CD69 were upregulated in samples of Flu A and RSV but were not significant in samples of rhinovirus as compared to healthy individuals. These results demonstrated Flu A and RSV elicit different alterations in human peripheral blood gene expression as compared to rhinovirus. Overall, despite the small number of study subjects, the current study for the first time has recognized signature genes, cytokines and proteins that are used by some respiratory viruses that may serve as candidates for rapid diagnosis as well as targets for therapeutic interventions.
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10
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Salt inducible kinases 2 and 3 are required for thymic T cell development. Sci Rep 2021; 11:21550. [PMID: 34732767 PMCID: PMC8566462 DOI: 10.1038/s41598-021-00986-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 10/15/2021] [Indexed: 12/22/2022] Open
Abstract
Salt Inducible Kinases (SIKs), of which there are 3 isoforms, are established to play roles in innate immunity, metabolic control and neuronal function, but their role in adaptive immunity is unknown. To address this gap, we used a combination of SIK knockout and kinase-inactive knock-in mice. The combined loss of SIK1 and SIK2 activity did not block T cell development. Conditional knockout of SIK3 in haemopoietic cells, driven by a Vav-iCre transgene, resulted in a moderate reduction in the numbers of peripheral T cells, but normal B cell numbers. Constitutive knockout of SIK2 combined with conditional knockout of SIK3 in the haemopoietic cells resulted in a severe reduction in peripheral T cells without reducing B cell number. A similar effect was seen when SIK3 deletion was driven via CD4-Cre transgene to delete at the DP stage of T cell development. Analysis of the SIK2/3 Vav-iCre mice showed that thymocyte number was greatly reduced, but development was not blocked completely as indicated by the presence of low numbers CD4 and CD8 single positive cells. SIK2 and SIK3 were not required for rearrangement of the TCRβ locus, or for low level cell surface expression of the TCR complex on the surface of CD4/CD8 double positive thymocytes. In the absence of both SIK2 and SIK3, progression to mature single positive cells was greatly reduced, suggesting a defect in negative and/or positive selection in the thymus. In agreement with an effect on negative selection, increased apoptosis was seen in thymic TCRbeta high/CD5 positive cells from SIK2/3 knockout mice. Together, these results show an important role for SIK2 and SIK3 in thymic T cell development.
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11
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Chen ELY, Brauer PM, Martinez EC, Huang X, Yu N, Anderson MK, Li Y, Zúñiga-Pflücker JC. Cutting Edge: TCR-β Selection Is Required at the CD4 +CD8 + Stage of Human T Cell Development. THE JOURNAL OF IMMUNOLOGY 2021; 206:2271-2276. [PMID: 33941655 DOI: 10.4049/jimmunol.2100141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/18/2021] [Indexed: 12/25/2022]
Abstract
T cell development is predicated on the successful rearrangement of the TCR gene loci, which encode for Ag-specific receptors. Recombination-activating gene (RAG) 2 is required for TCR gene rearrangements, which occur during specific stages of T cell development. In this study, we differentiated human pluripotent stem cells with a CRISPR/Cas9-directed deletion of the RAG2 gene (RAG2-KO) to elucidate the requirement for the TCR β-chain in mediating β-selection during human T cell development. In stark contrast to mice, human RAG2-KO T lineage progenitors progressed to the CD4+CD8+ double-positive (DP) stage in the absence of TCRβ rearrangements. Nonetheless, RAG2-KO DPs retrovirally transduced to express a rearranged TCR β-chain showed increased survival and proliferation as compared with control-transduced RAG2-KO DPs. Furthermore, transcriptomic analysis showed that TCRβ- and control-transduced RAG2-KO DPs differed in gene pathways related to survival and proliferation. Our results provide important insights as to the distinct requirement for the TCR β-chain during human T cell development.
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Affiliation(s)
- Edward L Y Chen
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Sunnybrook Research Institute, Toronto, Ontario, Canada
| | | | | | - Xiaotian Huang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing, China
| | - Ning Yu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing, China
| | - Michele K Anderson
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Yang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing, China
| | - Juan Carlos Zúñiga-Pflücker
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada .,Sunnybrook Research Institute, Toronto, Ontario, Canada
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12
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Loss of Mef2D function enhances TLR induced IL-10 production in macrophages. Biosci Rep 2021; 40:225925. [PMID: 32725155 PMCID: PMC7442974 DOI: 10.1042/bsr20201859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/24/2022] Open
Abstract
Mef2 transcription factors comprise a family of four different isoforms that regulate a number of processes including neuronal and muscle development. While roles for Mef2C and Mef2D have been described in B-cell development their role in immunity has not been extensively studied. In innate immune cells such as macrophages, TLRs drive the production of both pro- and anti-inflammatory cytokines. IL-10 is an important anti-inflammatory cytokine produced by macrophages and it establishes an autocrine feedback loop to inhibit pro-inflammatory cytokine production. We show here that macrophages from Mef2D knockout mice have elevated levels of IL-10 mRNA induction compared with wild-type cells following LPS stimulation. The secretion of IL-10 was also higher from Mef2D knockout macrophages and this correlated to a reduction in the secretion of TNF, IL-6 and IL-12p40. The use of an IL-10 neutralising antibody showed that this reduction in pro-inflammatory cytokine production in the Mef2D knockouts was IL-10 dependent. As the IL-10 promoter has previously been reported to contain a potential binding site for Mef2D, it is possible that the binding of other Mef2 isoforms in the absence of Mef2D may result in a higher activation of the IL-10 gene. Further studies with compound Mef2 isoforms would be required to address this. We also show that Mef2D is highly expressed in the thymus, but that loss of Mef2D does not affect thymic T-cell development or the production of IFNγ from CD8 T cells.
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13
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Barraza F, Montero R, Wong-Benito V, Valenzuela H, Godoy-Guzmán C, Guzmán F, Köllner B, Wang T, Secombes CJ, Maisey K, Imarai M. Revisiting the Teleost Thymus: Current Knowledge and Future Perspectives. BIOLOGY 2020; 10:biology10010008. [PMID: 33375568 PMCID: PMC7824517 DOI: 10.3390/biology10010008] [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: 11/02/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022]
Abstract
Simple Summary The thymus is the immune organ producing T lymphocytes that are essential to create immunity after encountering pathogens or vaccination. This review summarizes the thymus localization and histological studies, cell composition, and function in teleost fishes. We also describe how seasonal changes, photoperiod, water temperature fluctuations, and hormones can affect thymus development in fish species. Overall, the information helps identify future studies needed to understand thymus function in fish species and the immune system’s evolutionary origins. Since fish are exposed to pathogens, especially under aquaculture conditions, knowledge about the fish thymus and T lymphocyte can also help improve fish farming protocols, considering intrinsic and environmental conditions that can contribute to achieving the best vaccine responsiveness for disease resistance. Abstract The thymus in vertebrates plays a critical role in producing functionally competent T-lymphocytes. Phylogenetically, the thymus emerges early during evolution in jawed cartilaginous fish, and it is usually a bilateral organ placed subcutaneously at the dorsal commissure of the operculum. In this review, we summarize the current understanding of the thymus localization, histology studies, cell composition, and function in teleost fishes. Furthermore, we consider environmental factors that affect thymus development, such as seasonal changes, photoperiod, water temperature fluctuations and hormones. Further analysis of the thymus cell distribution and function will help us understand how key stages for developing functional T cells occur in fish, and how thymus dynamics can be modulated by external factors like photoperiod. Overall, the information presented here helps identify the knowledge gaps and future steps needed for a better understanding of the immunobiology of fish thymus.
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Affiliation(s)
- Felipe Barraza
- Laboratory of Immunology, Center of Aquatic Biotechnology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Av. Bernardo O’Higgins, Estación Central, Santiago 3363, Chile; (F.B.); (V.W.-B.); (H.V.)
| | - Ruth Montero
- Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, 17493 Greifswald, Insel Riems, Germany; (R.M.); (B.K.)
| | - Valentina Wong-Benito
- Laboratory of Immunology, Center of Aquatic Biotechnology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Av. Bernardo O’Higgins, Estación Central, Santiago 3363, Chile; (F.B.); (V.W.-B.); (H.V.)
| | - Héctor Valenzuela
- Laboratory of Immunology, Center of Aquatic Biotechnology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Av. Bernardo O’Higgins, Estación Central, Santiago 3363, Chile; (F.B.); (V.W.-B.); (H.V.)
| | - Carlos Godoy-Guzmán
- Center for Biomedical and Applied Research (CIBAP), School of Medicine, Faculty of Medical Sciences, Av. Bernardo O’Higgins, Estación Central, Santiago 3363, Chile;
| | - Fanny Guzmán
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile;
| | - Bernd Köllner
- Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, 17493 Greifswald, Insel Riems, Germany; (R.M.); (B.K.)
| | - Tiehui Wang
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK; (T.W.); (C.J.S.)
| | - Christopher J. Secombes
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK; (T.W.); (C.J.S.)
| | - Kevin Maisey
- Laboratory of Comparative Immunology, Center of Aquatic Biotechnology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Av. Bernardo O’Higgins, Estación Central, Santiago 3363, Chile;
| | - Mónica Imarai
- Laboratory of Immunology, Center of Aquatic Biotechnology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Av. Bernardo O’Higgins, Estación Central, Santiago 3363, Chile; (F.B.); (V.W.-B.); (H.V.)
- Correspondence:
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14
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Papadopoulou AA, Fluhrer R. Signaling Functions of Intramembrane Aspartyl-Proteases. Front Cardiovasc Med 2020; 7:591787. [PMID: 33381526 PMCID: PMC7768045 DOI: 10.3389/fcvm.2020.591787] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/16/2020] [Indexed: 01/18/2023] Open
Abstract
Intramembrane proteolysis is more than a mechanism to “clean” the membranes from proteins no longer needed. By non-reversibly modifying transmembrane proteins, intramembrane cleaving proteases hold key roles in multiple signaling pathways and often distinguish physiological from pathological conditions. Signal peptide peptidase (SPP) and signal peptide peptidase-like proteases (SPPLs) recently have been associated with multiple functions in the field of signal transduction. SPP/SPPLs together with presenilins (PSs) are the only two families of intramembrane cleaving aspartyl proteases known in mammals. PS1 or PS2 comprise the catalytic center of the γ-secretase complex, which is well-studied in the context of Alzheimer's disease. The mammalian SPP/SPPL family of intramembrane cleaving proteases consists of five members: SPP and its homologous proteins SPPL2a, SPPL2b, SPPL2c, and SPPL3. Although these proteases were discovered due to their homology to PSs, it became evident in the past two decades that no physiological functions are shared between these two families. Based on studies in cell culture models various substrates of SPP/SPPL proteases have been identified in the past years and recently-developed mouse lines lacking individual members of this protease family, will help to further clarify the physiological functions of these proteases. In this review we concentrate on signaling roles of mammalian intramembrane cleaving aspartyl proteases. In particular, we will highlight the signaling roles of PS via its substrates NOTCH, VEGF, and others, mainly focusing on its involvement in vasculature. Delineating also signaling pathways that are affected and/or controlled by SPP/SPPL proteases. From SPP's participation in tumor progression and survival, to SPPL3's regulation of protein glycosylation and SPPL2c's control over cellular calcium stores, various crossovers between proteolytic activity of intramembrane proteases and cell signaling will be described.
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Affiliation(s)
- Alkmini A Papadopoulou
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
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15
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Maslova A, Ramirez RN, Ma K, Schmutz H, Wang C, Fox C, Ng B, Benoist C, Mostafavi S. Deep learning of immune cell differentiation. Proc Natl Acad Sci U S A 2020; 117:25655-25666. [PMID: 32978299 PMCID: PMC7568267 DOI: 10.1073/pnas.2011795117] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although we know many sequence-specific transcription factors (TFs), how the DNA sequence of cis-regulatory elements is decoded and orchestrated on the genome scale to determine immune cell differentiation is beyond our grasp. Leveraging a granular atlas of chromatin accessibility across 81 immune cell types, we asked if a convolutional neural network (CNN) could learn to infer cell type-specific chromatin accessibility solely from regulatory DNA sequences. With a tailored architecture and an ensemble approach to CNN parameter interpretation, we show that our trained network ("AI-TAC") does so by rediscovering ab initio the binding motifs for known regulators and some unknown ones. Motifs whose importance is learned virtually as functionally important overlap strikingly well with positions determined by chromatin immunoprecipitation for several TFs. AI-TAC establishes a hierarchy of TFs and their interactions that drives lineage specification and also identifies stage-specific interactions, like Pax5/Ebf1 vs. Pax5/Prdm1, or the role of different NF-κB dimers in different cell types. AI-TAC assigns Spi1/Cebp and Pax5/Ebf1 as the drivers necessary for myeloid and B lineage fates, respectively, but no factors seemed as dominantly required for T cell differentiation, which may represent a fall-back pathway. Mouse-trained AI-TAC can parse human DNA, revealing a strikingly similar ranking of influential TFs and providing additional support that AI-TAC is a generalizable regulatory sequence decoder. Thus, deep learning can reveal the regulatory syntax predictive of the full differentiative complexity of the immune system.
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Affiliation(s)
- Alexandra Maslova
- Department of Statistics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | - Ke Ma
- Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Hugo Schmutz
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Chendi Wang
- Department of Statistics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Curtis Fox
- Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Bernard Ng
- Department of Statistics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | - Sara Mostafavi
- Department of Statistics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Canadian Institute for Advanced Research, CIFAR AI, Toronto, ON M5G 1M1, Canada
- Vector Institute, Toronto, ON M5G 1M1, Canada
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16
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Hwang S, Lee C, Park K, Oh S, Jeon S, Kang B, Kim Y, Oh J, Jeon SH, Satake M, Taniuchi I, Lee H, Seong RH. Twist2 promotes CD8 + T-cell differentiation by repressing ThPOK expression. Cell Death Differ 2020; 27:3053-3064. [PMID: 32424141 DOI: 10.1038/s41418-020-0560-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
CD4/CD8 T-cell lineage differentiation is a key process in immune system development; however, a defined regulator(s) that converts the signal from T-cell receptor and co-receptor complexes into lineage differentiation remains unclear. Here, we show that Twist2 is a critical factor in CD4/CD8 thymocyte differentiation. Twist2 expression is differentially regulated by T-cell receptor signaling, leading to differentiation into the CD4 or CD8 lineage. Forced Twist2 expression perturbed CD4+ thymocyte differentiation while enhancing CD8+ thymocyte differentiation. Furthermore, Twist2 expression produced mature CD8+ thymocytes in B2m-/- mice, while its deficiency significantly impaired CD8+ cells in MHC class-II-/- and TCR transgenic mice, favoring CD8 T-cell differentiation. During CD8 lineage differentiation, Twist2 interacted with Runx3 to bind to the silencer region of the ThPOK locus, thereby blocking ThPOK expression. These findings indicate that Twist2 is a part of the transcription factor network controlling CD8 lineage differentiation.
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Affiliation(s)
- Sunsook Hwang
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Changjin Lee
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea.,Hugel, Inc., Chuncheon-si, Korea
| | - Kyungsoo Park
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Sangwook Oh
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Shin Jeon
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Byeonggeun Kang
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Yehyun Kim
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Jaehak Oh
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Sung Ho Jeon
- Department of Life Science, Hallym University, Chuncheon, Korea
| | - Masanobu Satake
- Department of Molecular Immunology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RCAI, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ho Lee
- Cancer Experimental Resources Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Rho Hyun Seong
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea.
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17
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RNA editing enzyme ADAR1 is required for early T cell development. BLOOD SCIENCE 2020; 2:27-32. [PMID: 35399867 PMCID: PMC8974940 DOI: 10.1097/bs9.0000000000000039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/10/2019] [Indexed: 11/25/2022] Open
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18
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Thymic precursor cells generate acute myeloid leukemia in NUP98-PHF23/NUP98-HOXD13 double transgenic mice. Sci Rep 2019; 9:17213. [PMID: 31748606 PMCID: PMC6868234 DOI: 10.1038/s41598-019-53610-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/02/2019] [Indexed: 11/23/2022] Open
Abstract
Transgenic mice that express either a NUP98–PHF23 (NP23) or NUP98-HOXD13 (NHD13) fusion in the hematopoietic compartment develop a wide spectrum of leukemias, including myeloid, erythroid, megakaryocytic and lymphoid, at age 9–14 months. NP23-NHD13 double transgenic mice were generated by interbreeding NP23 and NHD13 mice. Remarkably, 100% of the NP23-NHD13 double transgenic mice developed acute myeloid leukemia (AML) within three months, characterized by replacement of the thymus with leukemic myeloblasts. The marked infiltration of thymus led to the intriguing hypothesis that AML generated in NP23-NHD13 mice arose in the thymus, as opposed to the bone marrow (BM). Transplantation of CD4-CD8- double negative (DN) thymocytes (which were also negative for Mac1 and Gr1) from leukemic NHD13/NP23 mice demonstrated that DN thymocytes could transmit AML, and limiting dilution studies showed that leukemia initiating cells were increased 14-fold in the thymus compared to BM. Further thymocyte fractionation demonstrated that DN1 and DN2, but not DN3 or DN4 fractions transmitted AML, and a marked expansion (100-fold) of Lineage-Sca1 + Kit + (LSK) cells in the thymus of the NP23-NHD13 mice. Taken together, these results show that the thymus of NP23-NHD13 mice acts as a reservoir for AML initiating cells and that thymic progenitors can transmit AML.
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19
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Harris LJ, Hughes KL, Ehrhart EJ, Labadie JD, Yoshimoto J, Avery AC. Canine CD4+ T-cell lymphoma identified by flow cytometry exhibits a consistent histomorphology and gene expression profile. Vet Comp Oncol 2019; 17:253-264. [PMID: 30684308 DOI: 10.1111/vco.12460] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 12/16/2022]
Abstract
T-cell lymphomas (TCL) are a diverse group of neoplasms with variable diagnostic features, pathophysiologies, therapeutic responses and clinical outcomes. In dogs, TCL includes indolent and aggressive tumours such as T-zone lymphoma (TZL) and peripheral T-cell lymphoma (PTCL), respectively. Delineation of molecular subtypes and investigation into underlying pathophysiologies of aggressive TCLs remains inadequate. We investigate the correlations between flow cytometry and histopathology of 73 cases of nodal TCL. The majority of cases (82.2%) were characterized as CD4+ TCL by flow cytometry. Fewer cases were classified as CD8+ TCL (6.8%) or CD4- CD8- TCL (11.0%). All cases, regardless of immunophenotype, exhibited conserved histologic features consistent with the WHO classification of PTCL. Histologic subsets of PTCL corresponding to immunophenotypic features were not identified. Neoplastic cell size determined by flow cytometry correlated significantly with mitotic rate. RNA-seq was performed on a subset of CD4+ PTCL cases (n = 6) and compared with sorted control CD4+ T-cells. The gene expression pattern of CD4+ PTCL was similar between all cases regardless of breed. PTCL was enriched in pathways representing G-coupled protein receptor signalling, extracellular matrix remodelling and vascular development, immune signalling and mitotic activity. Furthermore, global gene expression changes were consistent with downregulation of PTEN signalling and upregulation of the MTOR-PI3K-ATK axis. In this study, we evaluated the correlations between flow cytometry, histopathology and gene expression within a large cohort of nodal TCLs. We further demonstrate the ability of flow cytometry to identify a subtype of T-cell lymphoma, CD4+ PTCL, with a uniform histomorphology and gene expression profile.
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Affiliation(s)
- Lauren J Harris
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado
| | - Kelly L Hughes
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado
| | - E J Ehrhart
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado.,Ethos Diagnostic Science Division, Ethos Veterinary Health, San Diego, California
| | - Julia D Labadie
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado
| | - Janna Yoshimoto
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado
| | - Anne C Avery
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado
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20
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Nakayama H, Nagafuku M, Suzuki A, Iwabuchi K, Inokuchi JI. The regulatory roles of glycosphingolipid-enriched lipid rafts in immune systems. FEBS Lett 2018; 592:3921-3942. [PMID: 30320884 DOI: 10.1002/1873-3468.13275] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 01/04/2023]
Abstract
Lipid rafts formed by glycosphingolipids (GSLs) on cellular membranes play important roles in innate and adaptive immunity. Lactosylceramide (LacCer) forms lipid rafts on plasma and granular membranes of human neutrophils. These LacCer-enriched lipid rafts bind directly to pathogenic components, such as pathogenic fungi-derived β-glucan and Mycobacteria-derived lipoarabinomannan via carbohydrate-carbohydrate interactions, and mediate innate immune responses to these pathogens. In contrast, a-series and o-series gangliosides form distinct rafts on CD4+ and CD8+ T cell subsets, respectively, contributing to the respective functions of these cells and stimulating adaptive immune responses through T cell receptors. These findings suggest that gangliosides play indispensable roles in T cell selection and activation. This Review introduces the involvement of GSL-enriched lipid rafts in innate and adaptive immunity.
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Affiliation(s)
- Hitoshi Nakayama
- Laboratory of Biochemistry, Juntendo University Faculty of Health Care and Nursing, Urayasu, Japan.,Institute for Environmental and Gender-specific Medicine, Juntendo University Graduate School of Medicine, Urayasu, Japan
| | - Masakazu Nagafuku
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Akemi Suzuki
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Kazuhisa Iwabuchi
- Laboratory of Biochemistry, Juntendo University Faculty of Health Care and Nursing, Urayasu, Japan.,Institute for Environmental and Gender-specific Medicine, Juntendo University Graduate School of Medicine, Urayasu, Japan.,Infection Control Nursing, Juntendo University Graduate School of Health Care and Nursing, Urayasu, Japan
| | - Jin-Ichi Inokuchi
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
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21
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Smith-Raska MR, Arenzana TL, D'Cruz LM, Khodadadi-Jamayran A, Tsirigos A, Goldrath AW, Reizis B. The Transcription Factor Zfx Regulates Peripheral T Cell Self-Renewal and Proliferation. Front Immunol 2018; 9:1482. [PMID: 30022979 PMCID: PMC6039547 DOI: 10.3389/fimmu.2018.01482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/14/2018] [Indexed: 12/02/2022] Open
Abstract
Peripheral T lymphocytes share many functional properties with hematopoietic stem cells (HSCs), including long-term maintenance, quiescence, and latent proliferative potential. In addition, peripheral T cells retain the capacity for further differentiation into a variety of subsets, much like HSCs. While the similarities between T cells and HSC have long been hypothesized, the potential common genetic regulation of HSCs and T cells has not been widely explored. We have studied the T cell-intrinsic role of Zfx, a transcription factor specifically required for HSC maintenance. We report that T cell-specific deletion of Zfx caused age-dependent depletion of naïve peripheral T cells. Zfx-deficient T cells also failed to undergo homeostatic proliferation in a lymphopenic environment, and showed impaired antigen-specific expansion and memory response. In addition, the invariant natural killer T cell compartment was severely reduced. RNA-Seq analysis revealed that the most dysregulated genes in Zfx-deficient T cells were similar to those observed in Zfx-deficient HSC and B cells. These studies identify Zfx as an important regulator of peripheral T cell maintenance and expansion and highlight the common molecular basis of HSC and lymphocyte homeostasis.
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Affiliation(s)
- Matthew R Smith-Raska
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, United States
| | - Teresita L Arenzana
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, United States
| | - Louise M D'Cruz
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, United States.,Department of Pathology, NYU School of Medicine, New York, NY, United States
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, United States.,Department of Pathology, NYU School of Medicine, New York, NY, United States
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States
| | - Boris Reizis
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, United States.,Department of Pathology, NYU School of Medicine, New York, NY, United States
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22
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Navarro J, Gozalbo-López B, Méndez AC, Dantzer F, Schreiber V, Martínez C, Arana DM, Farrés J, Revilla-Nuin B, Bueno MF, Ampurdanés C, Galindo-Campos MA, Knobel PA, Segura-Bayona S, Martin-Caballero J, Stracker TH, Aparicio P, Del Val M, Yélamos J. PARP-1/PARP-2 double deficiency in mouse T cells results in faulty immune responses and T lymphomas. Sci Rep 2017; 7:41962. [PMID: 28181505 PMCID: PMC5299517 DOI: 10.1038/srep41962] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022] Open
Abstract
The maintenance of T-cell homeostasis must be tightly regulated. Here, we have identified a coordinated role of Poly(ADP-ribose) polymerase-1 (PARP-1) and PARP-2 in maintaining T-lymphocyte number and function. Mice bearing a T-cell specific deficiency of PARP-2 in a PARP-1-deficient background showed defective thymocyte maturation and diminished numbers of peripheral CD4+ and CD8+ T-cells. Meanwhile, peripheral T-cell number was not affected in single PARP-1 or PARP-2-deficient mice. T-cell lymphopenia was associated with dampened in vivo immune responses to synthetic T-dependent antigens and virus, increased DNA damage and T-cell death. Moreover, double-deficiency in PARP-1/PARP-2 in T-cells led to highly aggressive T-cell lymphomas with long latency. Our findings establish a coordinated role of PARP-1 and PARP-2 in T-cell homeostasis that might impact on the development of PARP-centred therapies.
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Affiliation(s)
- Judith Navarro
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Beatriz Gozalbo-López
- Inmunología Viral, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Andrea C Méndez
- Inmunología Viral, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Françoise Dantzer
- Biotechnology and Cell Signaling, UMR7242-CNRS, Laboratory of Excellence Medalis, ESBS, Illkirch, France
| | - Valérie Schreiber
- Biotechnology and Cell Signaling, UMR7242-CNRS, Laboratory of Excellence Medalis, ESBS, Illkirch, France
| | - Carlos Martínez
- Experimental Pathology Unit, IMIB-LAIB-Arrixaca, Murcia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - David M Arana
- Inmunología Viral, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Jordi Farrés
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Beatriz Revilla-Nuin
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain.,Genomic Unit. IMIB-LAIB-Arrixaca, Murcia, Spain
| | - María F Bueno
- Inmunología Viral, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Coral Ampurdanés
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Miguel A Galindo-Campos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Philip A Knobel
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sandra Segura-Bayona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Pedro Aparicio
- Department of Biochemistry, Molecular Biology and Immunology, University of Murcia, Murcia, Spain
| | - Margarita Del Val
- Inmunología Viral, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain.,Department of Immunology, Hospital del Mar, Barcelona, Spain
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Constitutive Kit activity triggers B-cell acute lymphoblastic leukemia-like disease in mice. Exp Hematol 2016; 45:45-55.e6. [PMID: 27664314 DOI: 10.1016/j.exphem.2016.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 08/17/2016] [Accepted: 09/14/2016] [Indexed: 11/21/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy and, in most cases, is of pro- or pre-B cell origin (B-ALL). The receptor tyrosine kinase KIT is expressed by hematopoietic stem and precursor cells. Gain-of-function mutations of KIT cause systemic mastocytosis, which is characterized by abnormal accumulations of mast cells. We previously reported a mouse model of mastocytosis based on conditional expression of a constitutively active Kit protein. Half of these animals developed leukemic disease of B-lineage origin. Herein, we report that this condition bears striking similarities to human B-ALL. The immuno-phenotype of the leukemic cells was compatible with a pro-B-cell origin, as was the finding of immunoglobulin heavy-chain gene rearrangements in all cases, whereas light-chain loci were mostly not rearranged. Leukemogenesis was independent of pre-B-cell receptor expression. Primary leukemic cells and permanent cell lines derived from these were serially transplantable and rapidly killed the recipients. In a few animals, the leukemia was of T-cell origin with abnormal CD4/8 double-positive T-cell precursors dominating in the circulation. In summary, we report a novel ALL mouse model that may prove useful for in vivo drug testing and identification of novel oncogenic mutations and principles.
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24
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Sahni H, Ross S, Barbarulo A, Solanki A, Lau CI, Furmanski A, Saldaña JI, Ono M, Hubank M, Barenco M, Crompton T. A genome wide transcriptional model of the complex response to pre-TCR signalling during thymocyte differentiation. Oncotarget 2016; 6:28646-60. [PMID: 26415229 PMCID: PMC4745683 DOI: 10.18632/oncotarget.5796] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/08/2015] [Indexed: 01/19/2023] Open
Abstract
Developing thymocytes require pre-TCR signalling to differentiate from CD4-CD8- double negative to CD4+CD8+ double positive cell. Here we followed the transcriptional response to pre-TCR signalling in a synchronised population of differentiating double negative thymocytes. This time series analysis revealed a complex transcriptional response, in which thousands of genes were up and down-regulated before changes in cell surface phenotype were detected. Genome-wide measurement of RNA degradation of individual genes showed great heterogeneity in the rate of degradation between different genes. We therefore used time course expression and degradation data and a genome wide transcriptional modelling (GWTM) strategy to model the transcriptional response of genes up-regulated on pre-TCR signal transduction. This analysis revealed five major temporally distinct transcriptional activities that up regulate transcription through time, whereas down-regulation of expression occurred in three waves. Our model thus placed known regulators in a temporal perspective, and in addition identified novel candidate regulators of thymocyte differentiation.
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Affiliation(s)
- Hemant Sahni
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Susan Ross
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | | | - Anisha Solanki
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Ching-In Lau
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Anna Furmanski
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | | | - Masahiro Ono
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Mike Hubank
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Martino Barenco
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Tessa Crompton
- Institute of Child Health, University College London, London WC1N 1EH, UK
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25
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Tang H, Zhang J, Sun X, Qian X, Zhang Y, Jin R. Thymic DCs derived IL-27 regulates the final maturation of CD4(+) SP thymocytes. Sci Rep 2016; 6:30448. [PMID: 27469302 PMCID: PMC5387111 DOI: 10.1038/srep30448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/05/2016] [Indexed: 12/17/2022] Open
Abstract
IL-27, as a pleiotropic cytokine, promotes the differentiation of naïve T cells to Th1, while suppressing Th2 and Th17 differentiation in the periphery. However, the role of IL-27 in the thymocyte development remains unknown. Here we showed that IL-27 was highly expressed in thymic plasmacytoid dendritic cells (pDCs) while its receptor expression was mainly detected in CD4+ single-positive (SP) thymocytes. Deletion of the p28 subunit in DCs resulted in a reduction of the most mature Qa-2+ subsets of CD4+ SP T cells. This defect was rescued by intrathymic administration of exogenous IL-27. In vitro differentiation assay further demonstrated that IL-27 alone was able to drive the maturation of the newly generated 6C10+CD69+CD4+ SP cells into Qa-2+ cells. Collectively, this study has revealed an important role of thymic DCs-derived IL-27 in the regulation of the phenotypic maturation of CD4+ SP thymocytes.
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Affiliation(s)
- Hui Tang
- Key Laboratory of Medical Immunology, Department of Immunology, Ministry of Health, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xue Yuan Road, Beijing, China
| | - Jie Zhang
- Key Laboratory of Medical Immunology, Department of Immunology, Ministry of Health, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xue Yuan Road, Beijing, China
| | - Xiuyuan Sun
- Key Laboratory of Medical Immunology, Department of Immunology, Ministry of Health, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xue Yuan Road, Beijing, China
| | - Xiaoping Qian
- Key Laboratory of Medical Immunology, Department of Immunology, Ministry of Health, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xue Yuan Road, Beijing, China
| | - Yu Zhang
- Key Laboratory of Medical Immunology, Department of Immunology, Ministry of Health, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xue Yuan Road, Beijing, China
| | - Rong Jin
- Key Laboratory of Medical Immunology, Department of Immunology, Ministry of Health, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xue Yuan Road, Beijing, China
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26
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Golec DP, Henao Caviedes LM, Baldwin TA. RasGRP1 and RasGRP3 Are Required for Efficient Generation of Early Thymic Progenitors. THE JOURNAL OF IMMUNOLOGY 2016; 197:1743-53. [PMID: 27465532 DOI: 10.4049/jimmunol.1502107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 06/28/2016] [Indexed: 11/19/2022]
Abstract
T cell development is dependent on the migration of progenitor cells from the bone marrow to the thymus. Upon reaching the thymus, progenitors undergo a complex developmental program that requires inputs from various highly conserved signaling pathways including the Notch and Wnt pathways. To date, Ras signaling has not been implicated in the very earliest stages of T cell differentiation, but members of a family of Ras activators called RasGRPs have been shown to be involved at multiple stages of T cell development. We examined early T cell development in mice lacking RasGRP1, RasGRP3, and RasGRPs 1 and 3. We report that RasGRP1- and RasGRP3-deficient thymi show significantly reduced numbers of early thymic progenitors (ETPs) relative to wild type thymi. Furthermore, RasGRP1/3 double-deficient thymi show significant reductions in ETP numbers compared with either RasGRP1 or RasGRP3 single-deficient thymi, suggesting that both RasGRP1 and RasGRP3 regulate the generation of ETPs. In addition, competitive bone marrow chimera experiments reveal that RasGRP1/3 double-deficient progenitors intrinsically generate ETPs less efficiently than wild type progenitors. Finally, RasGRP1/3-deficient progenitors show impaired migration toward the CCR9 ligand, CCL25, suggesting that RasGRP1 and RasGRP3 may regulate progenitor entry into the thymus through a CCR9-dependent mechanism. These data demonstrate that, in addition to Notch and Wnt, the highly conserved Ras pathway is critical for the earliest stages of T cell development and further highlight the importance of Ras signaling during thymocyte maturation.
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Affiliation(s)
- Dominic P Golec
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Laura M Henao Caviedes
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Troy A Baldwin
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
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27
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TNF-alpha and Notch signaling regulates the expression of HOXB4 and GATA3 during early T lymphopoiesis. In Vitro Cell Dev Biol Anim 2016; 52:920-934. [PMID: 27251160 DOI: 10.1007/s11626-016-0055-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
During the early thymus colonization, Notch signaling activation on hematopoietic progenitor cells (HPCs) drives proliferation and T cell commitment. Although these processes are driven by transcription factors such as HOXB4 and GATA3, there is no evidence that Notch directly regulates their transcription. To evaluate the role of NOTCH and TNF signaling in this process, human CD34+ HPCs were cocultured with OP9-DL1 cells, in the presence or absence of TNF. The use of a Notch signaling inhibitor and a protein synthesis inhibitor allowed us to distinguish primary effects, mediated by direct signaling downstream Notch and TNF, from secondary effects, mediated by de novo synthesized proteins. A low and physiologically relevant concentration of TNF promoted T lymphopoiesis in OP9-DL1 cocultures. TNF positively modulated the expression of both transcripts in a Notch-dependent manner; however, GATA3 induction was mediated by a direct mechanism, while HOXB4 induction was indirect. Induction of both transcripts was repressed by a GSK3β inhibitor, indicating that activation of canonical Wnt signaling inhibits rather than induces their expression. Our study provides novel evidences of the mechanisms integrating Notch and TNF-alpha signaling in the transcriptional induction of GATA3 and HOXB4. This mechanism has direct implications in the control of self-renewal, proliferation, commitment, and T cell differentiation.
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28
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Khaziri N, Mohammadi M, Aliyari Z, Soleimani Rad J, Tayefi Nasrabadi H, Nozad Charoudeh H. Cord Blood Mononuclear Cells Have a Potential to Produce NK Cells Using IL2Rg Cytokines. Adv Pharm Bull 2016; 6:5-8. [PMID: 27123412 DOI: 10.15171/apb.2016.01] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 08/30/2015] [Accepted: 08/31/2015] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Although bone marrow represents the main site for NK cell development and also distinct thymic-dependentNK cell pathway was identified, the cytokines effect on the NK cell generation from cord blood is unclear. Studies were identified the role of cytokines in the regulation of bone marrow and thymic NK cells. Previous studies reported that IL15 are critical for bone marrow dependent and IL7 is important for thymic NK cells. It is remain unclear the cytokines influence on the expantion of NK cells in cord blood mononuclear cells. METHODS We evaluated cultured cord blood mononuclear cells suplememnted with combinations of cytokines using FACS in distinct time points. In this study, we presented the role of IL2, IL7 and IL15 as members of the common gamma receptor -chain (Il2rg) on the expansion NK cells from cord blood cells. RESULTS By investigating cord blood mononuclear cells in vitro , we demonstrated that IL2 and IL15 are important for expansion of NK cells. IL2 in comparision with IL15 has more influences in NK cell expansion. In contrast IL-7 is dispensable for NK cell generation in cord blood. CONCLUSION Thus,IL-2Rg cytokines play complementary roles and are indispensable for homeostasis of NK cell development in cord blood. Probably these cytokines could help to use NK beneficials in engrafment of transplanted cells and Anti tumor activity of NK cells.
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Affiliation(s)
- Nahid Khaziri
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Momeneh Mohammadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zeinab Aliyari
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Soleimani Rad
- Tissue Engineering Group, Novin School of Advanced Research Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Tayefi Nasrabadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.; Tissue Engineering Group, Novin School of Advanced Research Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hojjatollah Nozad Charoudeh
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.; Tissue Engineering Group, Novin School of Advanced Research Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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29
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Äijö T, Huang Y, Mannerström H, Chavez L, Tsagaratou A, Rao A, Lähdesmäki H. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways. Genome Biol 2016; 17:49. [PMID: 26975309 PMCID: PMC4792102 DOI: 10.1186/s13059-016-0911-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/24/2016] [Indexed: 01/07/2023] Open
Abstract
We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylase-assisted bisulfite sequencing data. Lux models all cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC) simultaneously together with experimental parameters, including bisulfite conversion and oxidation efficiencies, as well as various chemical labeling and protection steps. We show that Lux improves the quantification and comparison of cytosine modification levels and that Lux can process any oxidized methylcytosine sequencing data sets to quantify all cytosine modifications. Analysis of targeted data from Tet2-knockdown embryonic stem cells and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathways and reveals 5hmC localization in putative regulatory regions.
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Affiliation(s)
- Tarmo Äijö
- />Department of Computer Science, Aalto University School of Science, Aalto, FI-00076 Finland
- />Present address: Simons Center for Data Analysis, Simons Foundation, New York, NY 10010 USA
| | - Yun Huang
- />La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
- />Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA
- />Present address: Institute of Biosciences & Technology, Texas A&M University Health Science Center, 2121 W. Holcombe Blvd, Houston, TX 77030 USA
| | - Henrik Mannerström
- />Department of Computer Science, Aalto University School of Science, Aalto, FI-00076 Finland
| | - Lukas Chavez
- />La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
- />Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA
- />Present address: Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, 69120 Germany
| | | | - Anjana Rao
- />La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
- />Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA
- />Department of Pharmacology and Moores Cancer Center, University of California, La Jolla, CA 92037 USA
- />Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, San Diego, CA 92037 USA
| | - Harri Lähdesmäki
- />Department of Computer Science, Aalto University School of Science, Aalto, FI-00076 Finland
- />Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, FI-20520 Finland
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30
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Khaziri N, Mohammadi M, Aliyari Z, Soleimani Rad J, Tayefi Nasrabadi H, Nozad Charoudeh H. Cord Blood Mononuclear Cells Have a Potential to Produce NK Cells Using IL2Rg Cytokines. Adv Pharm Bull 2016; 6:5-8. [PMID: 27123412 PMCID: PMC4845556 DOI: 10.15171/apb.2016.02] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 08/30/2015] [Accepted: 08/31/2015] [Indexed: 08/05/2023] Open
Abstract
PURPOSE Although bone marrow represents the main site for NK cell development and also distinct thymic-dependentNK cell pathway was identified, the cytokines effect on the NK cell generation from cord blood is unclear. Studies were identified the role of cytokines in the regulation of bone marrow and thymic NK cells. Previous studies reported that IL15 are critical for bone marrow dependent and IL7 is important for thymic NK cells. It is remain unclear the cytokines influence on the expantion of NK cells in cord blood mononuclear cells. METHODS We evaluated cultured cord blood mononuclear cells suplememnted with combinations of cytokines using FACS in distinct time points. In this study, we presented the role of IL2, IL7 and IL15 as members of the common gamma receptor -chain (Il2rg) on the expansion NK cells from cord blood cells. RESULTS By investigating cord blood mononuclear cells in vitro , we demonstrated that IL2 and IL15 are important for expansion of NK cells. IL2 in comparision with IL15 has more influences in NK cell expansion. In contrast IL-7 is dispensable for NK cell generation in cord blood. CONCLUSION Thus,IL-2Rg cytokines play complementary roles and are indispensable for homeostasis of NK cell development in cord blood. Probably these cytokines could help to use NK beneficials in engrafment of transplanted cells and Anti tumor activity of NK cells.
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Affiliation(s)
- Nahid Khaziri
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Momeneh Mohammadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zeinab Aliyari
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Soleimani Rad
- Tissue Engineering Group, Novin School of Advanced Research Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Tayefi Nasrabadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Tissue Engineering Group, Novin School of Advanced Research Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hojjatollah Nozad Charoudeh
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Tissue Engineering Group, Novin School of Advanced Research Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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31
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Uddin S, Bhat AA, Krishnankutty R, Mir F, Kulinski M, Mohammad RM. Involvement of F-BOX proteins in progression and development of human malignancies. Semin Cancer Biol 2016; 36:18-32. [PMID: 26410033 DOI: 10.1016/j.semcancer.2015.09.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 12/13/2022]
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32
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Ohmura S, Mizuno S, Oishi H, Ku CJ, Hermann M, Hosoya T, Takahashi S, Engel JD. Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs. J Clin Invest 2016; 126:865-78. [PMID: 26808502 DOI: 10.1172/jci83894] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/10/2015] [Indexed: 01/09/2023] Open
Abstract
The transcription factor GATA3 is essential for the genesis and maturation of the T cell lineage, and GATA3 dysregulation has pathological consequences. Previous studies have shown that GATA3 function in T cell development is regulated by multiple signaling pathways and that the Notch nuclear effector, RBP-J, binds specifically to the Gata3 promoter. We previously identified a T cell-specific Gata3 enhancer (Tce1) lying 280 kb downstream from the structural gene and demonstrated in transgenic mice that Tce1 promoted T lymphocyte-specific transcription of reporter genes throughout T cell development; however, it was not clear if Tce1 is required for Gata3 transcription in vivo. Here, we determined that the canonical Gata3 promoter is insufficient for Gata3 transcriptional activation in T cells in vivo, precluding the possibility that promoter binding by a host of previously implicated transcription factors alone is responsible for Gata3 expression in T cells. Instead, we demonstrated that multiple lineage-affiliated transcription factors bind to Tce1 and that this enhancer confers T lymphocyte-specific Gata3 activation in vivo, as targeted deletion of Tce1 in a mouse model abrogated critical functions of this T cell-regulatory element. Together, our data show that Tce1 is both necessary and sufficient for critical aspects of Gata3 T cell-specific transcriptional activity.
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33
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Staal FJT, Wiekmeijer AS, Brugman MH, Pike-Overzet K. The functional relationship between hematopoietic stem cells and developing T lymphocytes. Ann N Y Acad Sci 2016; 1370:36-44. [PMID: 26773328 DOI: 10.1111/nyas.12995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In contrast to all other blood and immune cells, T lymphocytes do not develop in the bone marrow (BM), but in the specialized microenvironment provided by the thymus. Similar to the other lineages, however, all T cells arise from multipotent hematopoietic stem cells (HSCs) that reside in the BM. Not all HSCs give rise to T cells; but how many and what kind of developmental checkpoints are located along this intricate differentiation path is the subject of intense research. Traditionally, this process has been studied almost exclusively using mouse cells, but recent advances in immunodeficient mouse models, high-speed cell sorting, lentiviral transduction protocols, and deep sequencing techniques have allowed these questions to be addressed using human cells. Here we review the process of thymic seeding by BM-derived cells and T cell commitment in humans, discussing recent insights into the clonal composition of the thymus and the definition of developmental checkpoints, on the basis of insights from human severe combined immunodeficiency patients.
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Affiliation(s)
- Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Anna-Sophia Wiekmeijer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Martijn H Brugman
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Karin Pike-Overzet
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
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34
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Drusenheimer N, Migdal B, Jäckel S, Tveriakhina L, Scheider K, Schulz K, Gröper J, Köhrer K, Klein T. The Mammalian Orthologs of Drosophila Lgd, CC2D1A and CC2D1B, Function in the Endocytic Pathway, but Their Individual Loss of Function Does Not Affect Notch Signalling. PLoS Genet 2015; 11:e1005749. [PMID: 26720614 PMCID: PMC4697852 DOI: 10.1371/journal.pgen.1005749] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/24/2015] [Indexed: 12/14/2022] Open
Abstract
CC2D1A and CC2D1B belong to the evolutionary conserved Lgd protein family with members in all multi-cellular animals. Several functions such as centrosomal cleavage, involvement in signalling pathways, immune response and synapse maturation have been described for CC2D1A. Moreover, the Drosophila melanogaster ortholog Lgd was shown to be involved in the endosomal trafficking of the Notch receptor and other transmembrane receptors and physically interacts with the ESCRT-III component Shrub/CHMP4. To determine if this function is conserved in mammals we generated and characterized Cc2d1a and Cc2d1b conditional knockout mice. While Cc2d1b deficient mice displayed no obvious phenotype, we found that Cc2d1a deficient mice as well as conditional mutants that lack CC2D1A only in the nervous system die shortly after birth due to respiratory distress. This finding confirms the suspicion that the breathing defect is caused by the central nervous system. However, an involvement in centrosomal function could not be confirmed in Cc2d1a deficient MEF cells. To analyse an influence on Notch signalling, we generated intestine specific Cc2d1a mutant mice. These mice did not display any alterations in goblet cell number, proliferating cell number or expression of the Notch reporter Hes1-emGFP, suggesting that CC2D1A is not required for Notch signalling. However, our EM analysis revealed that the average size of endosomes of Cc2d1a mutant cells, but not Cc2d1b mutant cells, is increased, indicating a defect in endosomal morphogenesis. We could show that CC2D1A and its interaction partner CHMP4B are localised on endosomes in MEF cells, when the activity of the endosomal protein VPS4 is reduced. This indicates that CC2D1A cycles between the cytosol and the endosomal membrane. Additionally, in rescue experiments in D. melanogaster, CC2D1A and CC2D1B were able to functionally replace Lgd. Altogether our data suggest a functional conservation of the Lgd protein family in the ESCRT-III mediated process in metazoans. The proteins of the Lgd/CC2D1 family are conserved in all multicellular animals. The Drosophila melanogaster ortholog Lgd is involved in the regulation of signalling receptor degradation via the endosomal pathway. Loss of lgd function causes ectopic ligand-independent activation of the Notch signalling pathway due to a defect in the endosomal pathway. For the mammalian proteins no endosomal function has been defined so far. Here, we asked whether the function of Lgd is conserved in mammals with the focus on the question whether its orthologs are also involved in the endosomal pathway and regulation of Notch pathway activity. Therefore, we generated and characterised Cc2d1a and Cc2d1b conditional knockout mice. We found that the loss of Cc2d1b does not lead to an obvious phenotype, while the known lethality of Cc2d1a deficient newborns is nervous system dependent. In experiments with MEFs isolated from knockout animals we provide evidence that both CC2D1 proteins are involved in the function of the ESCRT-III complex in a similar manner as Lgd in D. melanogaster. Moreover, we found that the loss of one CC2D1 protein is not sufficient to cause ectopic activation of Notch signalling.
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Affiliation(s)
- Nadja Drusenheimer
- Institut für Genetik, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- * E-mail: (ND); (TK)
| | - Bernhard Migdal
- Institut für Genetik, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Sandra Jäckel
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Lena Tveriakhina
- Institut für Molekularbiologie OE5250, Medizinische Hochschule Hannover, Hannover, Germany
| | - Kristina Scheider
- Institut für Genetik, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Katharina Schulz
- Institut für Genetik, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jieny Gröper
- Institut für Genetik, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Karl Köhrer
- Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory (GTL), Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Thomas Klein
- Institut für Genetik, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- * E-mail: (ND); (TK)
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Cauchy P, Maqbool MA, Zacarias-Cabeza J, Vanhille L, Koch F, Fenouil R, Gut M, Gut I, Santana MA, Griffon A, Imbert J, Moraes-Cabé C, Bories JC, Ferrier P, Spicuglia S, Andrau JC. Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation. Nucleic Acids Res 2015; 44:3567-85. [PMID: 26673693 PMCID: PMC4856961 DOI: 10.1093/nar/gkv1475] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/03/2015] [Indexed: 12/20/2022] Open
Abstract
Ets1 is a sequence-specific transcription factor that plays an important role during hematopoiesis, and is essential for the transition of CD4−/CD8− double negative (DN) to CD4+/CD8+ double positive (DP) thymocytes. Using genome-wide and functional approaches, we investigated the binding properties, transcriptional role and chromatin environment of Ets1 during this transition. We found that while Ets1 binding at distal sites was associated with active genes at both DN and DP stages, its enhancer activity was attained at the DP stage, as reflected by levels of the core transcriptional hallmarks H3K4me1/3, RNA Polymerase II and eRNA. This dual, stage-specific ability reflected a switch from non-T hematopoietic toward T-cell specific gene expression programs during the DN-to-DP transition, as indicated by transcriptome analyses of Ets1−/− thymic cells. Coincidentally, Ets1 associates more specifically with Runx1 in DN and with TCF1 in DP cells. We also provide evidence that Ets1 predominantly binds distal nucleosome-occupied regions in DN and nucleosome-depleted regions in DP. Finally and importantly, we demonstrate that Ets1 induces chromatin remodeling by displacing H3K4me1-marked nucleosomes. Our results thus provide an original model whereby the ability of a transcription factor to bind nucleosomal DNA changes during differentiation with consequences on its cognate enhancer activity.
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Affiliation(s)
- Pierre Cauchy
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Muhammad A Maqbool
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919 Route de Mende, Montpellier F-34293, France
| | - Joaquin Zacarias-Cabeza
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Laurent Vanhille
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Frederic Koch
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Romain Fenouil
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Marta Gut
- Centre Nacional D'Anàlisi Genòmica, Parc Científic de Barcelona, Baldiri i Reixac 4, Barcelona ES-08028, Spain
| | - Ivo Gut
- Centre Nacional D'Anàlisi Genòmica, Parc Científic de Barcelona, Baldiri i Reixac 4, Barcelona ES-08028, Spain
| | - Maria A Santana
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Aurélien Griffon
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Jean Imbert
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Carolina Moraes-Cabé
- INSERM UMR 1126 Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris F-75475, France
| | - Jean-Christophe Bories
- INSERM UMR 1126 Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris F-75475, France
| | - Pierre Ferrier
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Salvatore Spicuglia
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919 Route de Mende, Montpellier F-34293, France
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Ezeh PC, Xu H, Lauer FT, Liu KJ, Hudson LG, Burchiel SW. Monomethylarsonous acid (MMA+3) Inhibits IL-7 Signaling in Mouse Pre-B Cells. Toxicol Sci 2015; 149:289-99. [PMID: 26518055 DOI: 10.1093/toxsci/kfv233] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Our previously published data show that As(+3) in vivo and in vitro, at very low concentrations, inhibits lymphoid, but not myeloid stem cell development in mouse bone marrow. We also showed that the As(+3) metabolite, monomethylarsonous acid (MMA(+3)), was responsible for the observed pre-B cell toxicity caused by As(+3). Interleukin-7 (IL-7) is the primary growth factor responsible for pre-lymphoid development in mouse and human bone marrow, and Signal Transducer and Activator of Transcription 5 (STAT5) is a transcriptional factor in the IL-7 signaling pathway. We found that MMA(+3) inhibited STAT5 phosphorylation at a concentration as low as 50 nM in mouse bone marrow pre-B cells. Inhibition of STAT5 phosphorylation by As(+3) occurred only at a concentration of 500 nM. In the IL-7 dependent mouse pre-B 2E8 cell line, we also found selective inhibition of STAT5 phosphorylation by MMA(+3), and this inhibition was dependent on effects on JAK3 phosphorylation. IL-7 receptor expression on 2E8 cell surface was also suppressed by 50 nM MMA(+3) at 18 h. As further evidence for the inhibition of STAT5, we found that the induction of several genes required in B cell development, cyclin D1, E2A, EBF1, and PAX5, were selectively inhibited by MMA(+3). Since 2E8 cells lack the enzymes responsible for the conversion of As(+3) to MMA(+3) in vitro, the results of these studies suggest that As(+3) induced inhibition of pre-B cell formation in vivo is likely dependent on the formation of MMA(+3) which in turn inhibits IL-7 signaling at several steps in mouse pre-B cells.
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Affiliation(s)
- Peace C Ezeh
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico, 87131-0001
| | - Huan Xu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico, 87131-0001
| | - Fredine T Lauer
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico, 87131-0001
| | - Ke Jian Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico, 87131-0001
| | - Laurie G Hudson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico, 87131-0001
| | - Scott W Burchiel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico, 87131-0001
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Barra MM, Richards DM, Hansson J, Hofer AC, Delacher M, Hettinger J, Krijgsveld J, Feuerer M. Transcription Factor 7 Limits Regulatory T Cell Generation in the Thymus. THE JOURNAL OF IMMUNOLOGY 2015; 195:3058-70. [DOI: 10.4049/jimmunol.1500821] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/23/2015] [Indexed: 02/06/2023]
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38
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Khan IS, Park CY, Mavropoulos A, Shariat N, Pollack JL, Barczak AJ, Erle DJ, McManus MT, Anderson MS, Jeker LT. Identification of MiR-205 As a MicroRNA That Is Highly Expressed in Medullary Thymic Epithelial Cells. PLoS One 2015; 10:e0135440. [PMID: 26270036 PMCID: PMC4535774 DOI: 10.1371/journal.pone.0135440] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/22/2015] [Indexed: 11/30/2022] Open
Abstract
Thymic epithelial cells (TECs) support T cell development in the thymus. Cortical thymic epithelial cells (cTECs) facilitate positive selection of developing thymocytes whereas medullary thymic epithelial cells (mTECs) facilitate the deletion of self-reactive thymocytes in order to prevent autoimmunity. The mTEC compartment is highly dynamic with continuous maturation and turnover, but the genetic regulation of these processes remains poorly understood. MicroRNAs (miRNAs) are important regulators of TEC genetic programs since miRNA-deficient TECs are severely defective. However, the individual miRNAs important for TEC maintenance and function and their mechanisms of action remain unknown. Here, we demonstrate that miR-205 is highly and preferentially expressed in mTECs during both thymic ontogeny and in the postnatal thymus. This distinct expression is suggestive of functional importance for TEC biology. Genetic ablation of miR-205 in TECs, however, neither revealed a role for miR-205 in TEC function during homeostatic conditions nor during recovery from thymic stress conditions. Thus, despite its distinct expression, miR-205 on its own is largely dispensable for mTEC biology.
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Affiliation(s)
- Imran S. Khan
- UCSF Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
| | - Chong Y. Park
- UCSF Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- WM Keck Center for Noncoding RNAs, University of California San Francisco, San Francisco, California, United States of America
| | - Anastasia Mavropoulos
- UCSF Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Nikki Shariat
- UCSF Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- WM Keck Center for Noncoding RNAs, University of California San Francisco, San Francisco, California, United States of America
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Joshua L. Pollack
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Andrea J. Barczak
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - David J. Erle
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Michael T. McManus
- UCSF Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- WM Keck Center for Noncoding RNAs, University of California San Francisco, San Francisco, California, United States of America
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Mark S. Anderson
- UCSF Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (MSA); (LTJ)
| | - Lukas T. Jeker
- UCSF Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (MSA); (LTJ)
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Hernández-Munain C. Recent insights into the transcriptional control of the Tcra/Tcrd locus by distant enhancers during the development of T-lymphocytes. Transcription 2015; 6:65-73. [PMID: 26230488 DOI: 10.1080/21541264.2015.1078429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Tcra/Tcrd includes 2 genes with distinct developmental programs controlled by 2 distant enhancers, Eα and Eδ. These enhancers work as a developmental switch during thymocyte development and they are essential for generation of αβ and γδ T-lymphocytes. Tcra and Tcrd transit from an unrearranged configuration to a rearranged configuration during T-cell development. Eα and Eδ are responsible for transcription of their respective unrearranged genes in thymocytes but are dispensable for such functions in the context of the rearranged genes in mature T-cells. Interestingly, Eα activates transcription of the rearranged Tcrd in γδ T-lymphocytes but it is inactive in αβ T-lymphocytes.
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Affiliation(s)
- Cristina Hernández-Munain
- a Department of Cellular Biology and Immunology ; Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC); Parque Tecnológico de Ciencias de la Salud (PTS) ; Armilla , Granada , Spain
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40
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López-Rodríguez C, Aramburu J, Berga-Bolaños R. Transcription factors and target genes of pre-TCR signaling. Cell Mol Life Sci 2015; 72:2305-21. [PMID: 25702312 PMCID: PMC11113633 DOI: 10.1007/s00018-015-1864-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/22/2015] [Accepted: 02/16/2015] [Indexed: 11/27/2022]
Abstract
Almost 30 years ago pioneering work by the laboratories of Harald von Boehmer and Susumo Tonegawa provided the first indications that developing thymocytes could assemble a functional TCRβ chain-containing receptor complex, the pre-TCR, before TCRα expression. The discovery and study of the pre-TCR complex revealed paradigms of signaling pathways in control of cell survival and proliferation, and culminated in the recognition of the multifunctional nature of this receptor. As a receptor integrated in a dynamic developmental process, the pre-TCR must be viewed not only in the light of the biological outcomes it promotes, but also in context with those molecular processes that drive its expression in thymocytes. This review article focuses on transcription factors and target genes activated by the pre-TCR to drive its different outcomes.
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Affiliation(s)
- Cristina López-Rodríguez
- Immunology Unit, Department of Experimental and Health Sciences and Barcelona Biomedical Research Park, Universitat Pompeu Fabra, C/Doctor Aiguader Nº88, 08003, Barcelona, Barcelona, Spain,
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Premature expression of Foxp3 in double-negative thymocytes. PLoS One 2015; 10:e0127038. [PMID: 25978037 PMCID: PMC4433242 DOI: 10.1371/journal.pone.0127038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/14/2015] [Indexed: 01/09/2023] Open
Abstract
Peripheral immune regulation depends on the generation of thymic-derived regulatory T (tTreg) cells to maintain self-tolerance and to counterbalance overshooting immune responses. The expression of the Treg lineage defining transcription factor Foxp3 in developing tTreg cells depends on TCR signaling during the thymic selection process of these T cells. In this study, we surprisingly identify Foxp3+ immature thymocytes at the double-negative (DN) stage in transcription factor 7 (Tcf7)-deficient mice. These Foxp3+ cells did not express a TCR (β or γδ chains), CD3 or CD5 and therefore these cells were true DN cells. Further investigation of this phenomenon in a transgenic TCR model showed that Foxp3-expressing DN cells could not respond to TCR stimulation in vivo. These data suggest that Foxp3 expression in these DN cells occurred independently of TCR signaling. Interestingly, these Foxp3+ DN cells were located in a transition state between DN1 and DN2 (CD4-CD8-CD3-TCR-CD44highCD25low). Our results indicate that Tcf7 is involved in preventing the premature expression of Foxp3 in DN thymocytes.
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42
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Abstract
The Tcra enhancer (Eα) is essential for Tcra locus germ-line transcription and primary Vα-to-Jα recombination during thymocyte development. We found that Eα is inhibited late during thymocyte differentiation and in αβ T lymphocytes, indicating that it is not required to drive transcription of rearranged Tcra genes. Eα inactivation resulted in the disruption of functional long-range enhancer-promoter interactions and was associated with loss of Eα-dependent histone modifications at promoter and enhancer regions, and reduced expression and recruitment of E2A to the Eα enhanceosome in T cells. Enhancer activity could not be recovered by T-cell activation, by forced expression of E2A or by the up-regulation of this and other transcription factors in the context of T helper differentiation. Our results argue that the major function of Eα is to coordinate the formation of a chromatin hub that drives Vα and Jα germ-line transcription and primary rearrangements in thymocytes and imply the existence of an Eα-independent mechanism to activate transcription of the rearranged Tcra locus in αβ T cells.
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43
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Muro R, Nitta T, Okada T, Ideta H, Tsubata T, Suzuki H. The Ras GTPase-activating protein Rasal3 supports survival of naive T cells. PLoS One 2015; 10:e0119898. [PMID: 25793935 PMCID: PMC4368693 DOI: 10.1371/journal.pone.0119898] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 01/16/2015] [Indexed: 11/19/2022] Open
Abstract
The Ras-mitogen-activated protein kinase (MAPK) pathway is crucial for T cell receptor (TCR) signaling in the development and function of T cells. The significance of various modulators of the Ras-MAPK pathway in T cells, however, remains to be fully understood. Ras-activating protein-like 3 (Rasal3) is an uncharacterized member of the SynGAP family that contains a conserved Ras GTPase-activating protein (GAP) domain, and is predominantly expressed in the T cell lineage. In the current study, we investigated the function and physiological roles of Rasal3. Our results showed that Rasal3 possesses RasGAP activity, but not Rap1GAP activity, and represses TCR-stimulated ERK phosphorylation in a T cell line. In systemic Rasal3-deficient mice, T cell development in the thymus including positive selection, negative selection, and β-selection was unaffected. However, the number of naive, but not effector memory CD4 and CD8 T cell in the periphery was significantly reduced in Rasal3-deficient mice, and associated with a marked increase in apoptosis of these cells. Indeed, survival of Rasal3 deficient naive CD4 T cells in vivo by adoptive transfer was significantly impaired, whereas IL-7-dependent survival of naive CD4 T cells in vitro was unaltered. Collectively, Rasal3 is required for in vivo survival of peripheral naive T cells, contributing to the maintenance of optimal T cell numbers.
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Affiliation(s)
- Ryunosuke Muro
- Department of Immunology and Pathology, Research Institute, National Center for Global Health and Medicine, Ichikawa-shi, Chiba, Japan
- Department of Immunology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Takeshi Nitta
- Department of Immunology and Pathology, Research Institute, National Center for Global Health and Medicine, Ichikawa-shi, Chiba, Japan
| | - Toshiyuki Okada
- Department of Immunology and Pathology, Research Institute, National Center for Global Health and Medicine, Ichikawa-shi, Chiba, Japan
| | - Hitoshi Ideta
- Department of Immunology and Pathology, Research Institute, National Center for Global Health and Medicine, Ichikawa-shi, Chiba, Japan
| | - Takeshi Tsubata
- Department of Immunology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Harumi Suzuki
- Department of Immunology and Pathology, Research Institute, National Center for Global Health and Medicine, Ichikawa-shi, Chiba, Japan
- * E-mail:
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ShcA regulates thymocyte proliferation through specific transcription factors and a c-Abl-dependent signaling axis. Mol Cell Biol 2015; 35:1462-76. [PMID: 25691660 DOI: 10.1128/mcb.01084-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Signaling via the pre-T-cell receptor (pre-TCR), along with associated signals from Notch and chemokine receptors, regulates the β-selection checkpoint that operates on CD4(-) CD8(-) doubly negative (DN) thymocytes. Since many hematopoietic malignancies arise at the immature developmental stages of lymphocytes, understanding the signal integration and how specific signaling molecules and distal transcription factors regulate cellular outcomes is of importance. Here, a series of molecular and genetic approaches revealed that the ShcA adapter protein critically influences proliferation and differentiation during β-selection. We found that ShcA functions downstream of the pre-TCR and p56(Lck) and show that ShcA is important for extracellular signal-regulated kinase (ERK)-dependent upregulation of transcription factors early growth factor 1 (Egr1) and Egr3 in immature thymocytes and, in turn, of the expression and function of the Id3 and E2A helix-loop-helix (HLH) proteins. ShcA also contributes to pre-TCR-mediated induction of c-Myc and additional cell cycle regulators. Moreover, using an unbiased Saccharomyces cerevisiae (yeast) screen, we identified c-Abl as a binding partner of phosphorylated ShcA and demonstrated the relevance of the ShcA-c-Abl interaction in immature thymocytes. Collectively, these data identify multiple modes by which ShcA can fine-tune the development of early thymocytes, including a previously unappreciated ShcA-c-Abl axis that regulates thymocyte proliferation.
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45
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Tindemans I, Serafini N, Di Santo JP, Hendriks RW. GATA-3 function in innate and adaptive immunity. Immunity 2014; 41:191-206. [PMID: 25148023 DOI: 10.1016/j.immuni.2014.06.006] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/19/2014] [Indexed: 02/07/2023]
Abstract
The zinc-finger transcription factor GATA-3 has received much attention as a master regulator of T helper 2 (Th2) cell differentiation, during which it controls interleukin-4 (IL-4), IL-5, and IL-13 expression. More recently, GATA-3 was shown to contribute to type 2 immunity through regulation of group 2 innate lymphoid cell (ILC2) development and function. Furthermore, during thymopoiesis, GATA-3 represses B cell potential in early T cell precursors, activates TCR signaling in pre-T cells, and promotes the CD4(+) T cell lineage after positive selection. GATA-3 also functions outside the thymus in hematopoietic stem cells, regulatory T cells, CD8(+) T cells, thymic natural killer cells, and ILC precursors. Here we discuss the varied functions of GATA-3 in innate and adaptive immune cells, with emphasis on its activity in T cells and ILCs, and examine the mechanistic basis for the dose-dependent, developmental-stage- and cell-lineage-specific activity of this transcription factor.
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Affiliation(s)
- Irma Tindemans
- Department of Pulmonary Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Nicolas Serafini
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U668, 75724 Paris, France
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U668, 75724 Paris, France
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands.
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46
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Mcph1/Brit1 deficiency promotes genomic instability and tumor formation in a mouse model. Oncogene 2014; 34:4368-78. [PMID: 25362854 PMCID: PMC4417661 DOI: 10.1038/onc.2014.367] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 09/01/2014] [Accepted: 09/27/2014] [Indexed: 12/12/2022]
Abstract
MCPH1, also known as BRIT1, has recently been identified as a novel key regulatory gene of the DNA damage response pathway. MCPH1 is located on human chromosome 8p23.1, where human cancers frequently show loss of heterozygosity. As such, MCPH1 is aberrantly expressed in many malignancies, including breast and ovarian cancers, and the function of MCPH1 has been implicated in tumor suppression. However, it remains poorly understood whether MCPH1 deficiency leads to tumorigenesis. Here we generated and studied both Mcph1(-/-) and Mcph1(-/-)p53(-/-) mice; we showed that Mcph1(-/-) mice developed tumors with long latency, and that primary lymphoma developed significantly earlier in Mcph1(-/-)p53(-/-) mice than in Mcph11(+/+)p53(-/-) and Mcph1(+/-)p53(-/-) mice. The Mcph1(-/-)p53(-/-) lymphomas and derived murine embryonic fibroblasts (MEFs) were both more sensitive to irradiation. Mcph1 deficiency resulted in remarkably increased chromosome and chromatid breaks in Mcph1(-/-)p53(-/-) lymphomas and MEFs, as determined by metaphase spread assay and spectral karyotyping analysis. In addition, Mcph1 deficiency significantly enhanced aneuploidy as well as abnormal centrosome multiplication in Mcph1(-/-)p53(-/-) cells. Meanwhile, Mcph1 deficiency impaired double strand break (DSB) repair in Mcph1(-/-)p53(-/-) MEFs as demonstrated by neutral Comet assay. Compared with Mcph1(+/+)p53(-/-) MEFs, homologous recombination and non-homologous end-joining activities were significantly decreased in Mcph1(-/-)p53(-/-) MEFs. Notably, reconstituted MCPH1 rescued the defects of DSB repair and alleviated chromosomal aberrations in Mcph1(-/-)p53(-/-) MEFs. Taken together, our data demonstrate MCPH1 deficiency promotes genomic instability and increases cancer susceptibility. Our study using knockout mouse models provides convincing genetic evidence that MCPH1 is a bona fide tumor suppressor gene. Its deficiency leading to defective DNA repair in tumors can be used to develop novel targeted cancer therapies in the future.
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47
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Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation. Proc Natl Acad Sci U S A 2014; 111:E3306-15. [PMID: 25071199 DOI: 10.1073/pnas.1412327111] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The discovery of Ten Eleven Translocation proteins, enzymes that oxidize 5-methylcytosine (5mC) in DNA, has revealed novel mechanisms for the regulation of DNA methylation. We have mapped 5-hydroxymethylcytosine (5hmC) at different stages of T-cell development in the thymus and T-cell differentiation in the periphery. We show that 5hmC is enriched in the gene body of highly expressed genes at all developmental stages and that its presence correlates positively with gene expression. Further emphasizing the connection with gene expression, we find that 5hmC is enriched in active thymus-specific enhancers and that genes encoding key transcriptional regulators display high intragenic 5hmC levels in precursor cells at those developmental stages where they exert a positive effect. Our data constitute a valuable resource that will facilitate detailed analysis of the role of 5hmC in T-cell development and differentiation.
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Robert J, Edholm ES. A prominent role for invariant T cells in the amphibian Xenopus laevis tadpoles. Immunogenetics 2014; 66:513-23. [PMID: 24898512 DOI: 10.1007/s00251-014-0781-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 05/12/2014] [Indexed: 12/20/2022]
Abstract
Invariant T (iT) cells expressing an invariant or semi-invariant T cell receptor (TCR) repertoire have gained attention in recent years because of their potential as specialized regulators of immune function. These iT cells are typically restricted by nonclassical MHC class I molecules (e.g., CD1d and MR1) and undergo differentiation pathways distinct from conventional T cells. While the benefit of a limited TCR repertoire may appear counterintuitive in regard to the advantage of the diversified repertoire of conventional T cells allowing for exquisite specificity to antigens, the full biological importance and evolutionary conservation of iT cells are just starting to emerge. It is generally considered that iT cells are specialized to recognize conserved antigens equivalent to pathogen-associated molecular pattern. Until recently, little was known about the evolution of iT cells. The identification of class Ib and class I-like genes in nonmammalian vertebrates, despite the heterogeneity and variable numbers of these genes among species, suggests that iT cells are also present in ectothermic vertebrates. Indeed, recent studies in the amphibian Xenopus have revealed a drastic overrepresentation of several invariant TCRs in tadpoles and identified a prominent nonclassical MHC class I-restricted iT cell subset critical for tadpole antiviral immunity. This suggests an important and perhaps even dominant role of multiple nonclassical MHC class I-restricted iT cell populations in tadpoles and, by extension, other aquatic vertebrates with rapid external development that are under pressure to produce a functional lymphocyte repertoire with small numbers of cells.
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Affiliation(s)
- Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA,
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Chang CW, Lai YS, Lamb LS, Townes TM. Broad T-cell receptor repertoire in T-lymphocytes derived from human induced pluripotent stem cells. PLoS One 2014; 9:e97335. [PMID: 24828440 PMCID: PMC4020825 DOI: 10.1371/journal.pone.0097335] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/16/2014] [Indexed: 12/11/2022] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) have enormous potential for the treatment of inherited and acquired disorders. Recently, antigen-specific T lymphocytes derived from hiPSCs have been reported. However, T lymphocyte populations with broad T cell receptor (TCR) diversity have not been generated. We report that hiPSCs derived from skin biopsy are capable of producing T lymphocyte populations with a broad TCR repertoire. In vitro T cell differentiation follows a similar developmental program as observed in vivo, indicated by sequential expression of CD7, intracellular CD3 and surface CD3. The γδ TCR locus is rearranged first and is followed by rearrangement of the αβ locus. Both γδ and αβ T cells display a diverse TCR repertoire. Upon activation, the cells express CD25, CD69, cytokines (TNF-α, IFN-γ, IL-2) and cytolytic proteins (Perforin and Granzyme-B). These results suggest that most, if not all, mechanisms required to generate functional T cells with a broad TCR repertoire are intact in our in vitro differentiation protocol. These data provide a foundation for production of patient-specific T cells for the treatment of acquired or inherited immune disorders and for cancer immunotherapy.
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Affiliation(s)
- Chia-Wei Chang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, Birmingham, Alabama, United States of America
- UAB Stem Cell Institute, University of Alabama at Birmingham, Schools of Medicine and Dentistry, Birmingham, Alabama, United States of America
| | - Yi-Shin Lai
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, Birmingham, Alabama, United States of America
- UAB Stem Cell Institute, University of Alabama at Birmingham, Schools of Medicine and Dentistry, Birmingham, Alabama, United States of America
| | - Lawrence S. Lamb
- Department of Medicine, University of Alabama at Birmingham, Schools of Medicine and Dentistry, Birmingham, Alabama, United States of America
- Cell Therapy Lab, University of Alabama at Birmingham, Schools of Medicine and Dentistry, Birmingham, Alabama, United States of America
| | - Tim M. Townes
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, Birmingham, Alabama, United States of America
- UAB Stem Cell Institute, University of Alabama at Birmingham, Schools of Medicine and Dentistry, Birmingham, Alabama, United States of America
- * E-mail:
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Xu X, Ge Q. Maturation and migration of murine CD4 single positive thymocytes and thymic emigrants. Comput Struct Biotechnol J 2014; 9:e201403003. [PMID: 24757506 PMCID: PMC3995209 DOI: 10.5936/csbj.201403003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/18/2014] [Accepted: 03/23/2014] [Indexed: 11/22/2022] Open
Abstract
T lymphopoiesis in the thymus was thought to be completed once they reach the single positive (SP) stage, when they are “fully mature” and wait to be exported at random or follow a “first in-first out” manner. Recently, accumulating evidence has revealed that newly generated SP thymocytes undergo further maturation in the thymic medulla before they follow a tightly regulated emigrating process to become recent thymic emigrants (RTEs). RTEs in the periphery then experience a post-thymic maturation and peripheral tolerance and eventually become licensed as mature naïve T cells. This review summarizes the recent progress in the late stage T cell development in and outside of the thymus. The regulation of this developmental process is also discussed.
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Affiliation(s)
- Xi Xu
- Key Laboratory of Medical Immunology, Ministry of Health. Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xue Yuan Road, Beijing 100191, P R China
| | - Qing Ge
- Key Laboratory of Medical Immunology, Ministry of Health. Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xue Yuan Road, Beijing 100191, P R China
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