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Li P, Pulugulla S, Das S, Oh J, Spolski R, Lin JX, Leonard WJ. A new pipeline SPICE identifies novel JUN-IKZF1 composite elements. eLife 2025; 12:RP88833. [PMID: 39786853 PMCID: PMC11717359 DOI: 10.7554/elife.88833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2025] Open
Abstract
Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. Using SPICE, we successfully identified known composite elements, such as AP1-IRF composite elements (AICEs) and STAT5 tetramers, and also uncovered several novel binding partners, including JUN-IKZF1 composite elements. One such novel interaction was identified at CNS9, an upstream conserved noncoding region in the human IL10 gene, which harbors a non-canonical IKZF1 binding site. We confirmed the cooperative binding of JUN and IKZF1 and showed that the activity of an IL10-luciferase reporter construct in primary B and T cells depended on both this site and the AP1 binding site within this composite element. Overall, our findings reveal an unappreciated global association of IKZF1 and AP1 and establish SPICE as a valuable new pipeline for predicting novel transcription binding complexes.
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Affiliation(s)
- Peng Li
- Amgen IncRockvilleUnited States
| | - Sree Pulugulla
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIHBethesdaUnited States
| | - Sonali Das
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIHBethesdaUnited States
| | - Jangsuk Oh
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIHBethesdaUnited States
| | - Rosanne Spolski
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIHBethesdaUnited States
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIHBethesdaUnited States
| | - Warren J Leonard
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIHBethesdaUnited States
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Li P, Pulugulla SH, Das S, Oh J, Spolski R, Lin JX, Leonard WJ. A new pipeline SPICE identifies novel JUN-IKZF1 composite elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.31.543110. [PMID: 39763964 PMCID: PMC11703198 DOI: 10.1101/2023.05.31.543110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
Abstract
Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. Using SPICE, we successfully identified known composite elements, such as AP1-IRF composite elements (AICEs) and STAT5 tetramers, and also uncovered several novel binding partners, including JUN-IKZF1 composite elements. One such novel interaction was identified at CNS9, an upstream conserved noncoding region in the human IL10 gene, which harbors a non-canonical IKZF1 binding site. We confirmed cooperative binding of JUN and IKZF1 and showed that the activity of an IL10 -luciferase reporter construct in primary B and T cells depended on both this site and the AP1 binding site within this composite element. Overall, our findings reveal an unappreciated global association of IKZF1 and AP1 and establish SPICE as a valuable new pipeline for predicting novel transcription binding complexes.
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Affiliation(s)
- Peng Li
- Correspondence to: P.L. () or W.J.L. ()
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Gao L, Bai Y, Zhou J, Liang C, Dong Y, Han T, Liu Y, Guo J, Wu J, Hu D. S100P facilitates LUAD progression via PKA/c-Jun-mediated tumor-associated macrophage recruitment and polarization. Cell Signal 2024; 120:111179. [PMID: 38640980 DOI: 10.1016/j.cellsig.2024.111179] [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: 01/13/2024] [Revised: 03/28/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
S100P, a member of the S100 calcium-binding protein family, is closely associated with abnormal proliferation, invasion, and metastasis of various cancers. However, its role in the lung adenocarcinoma (LUAD) tumor microenvironment (TME) remains unclear. In this study, we observed specific expression of S100P on tumor cells in LUAD patients through tissue immunofluorescence analysis. Furthermore, this expression was strongly correlated with the recruitment and polarization of tumor-associated macrophages (TAMs). Bioinformatics analysis revealed that high S100P expression is associated with poorer overall survival in LUAD patients. Subsequently, a subcutaneous mouse model demonstrated that S100P promotes recruitment and polarization of TAMs towards the M2 type. Finally, in vitro studies on LUAD cells revealed that S100P enhances the secretion of chemokines and polarizing factors by activating the PKA/c-Jun pathway, which is implicated in TAM recruitment and polarization towards the M2 phenotype. Moreover, inhibition of c-Jun expression impedes the ability of TAMs to infiltrate and polarize towards the M2 phenotype. In conclusion, our study demonstrates that S100P facilitates LUAD cells growth by recruiting M2 TAMs through PKA/c-Jun signaling, resulting in the production of various cytokines. Considering these findings, S100P holds promise as an important diagnostic marker and potential therapeutic target for LUAD.
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Affiliation(s)
- Lu Gao
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China; Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Ying Bai
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China; Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China.
| | - Jiawei Zhou
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China; Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Chao Liang
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China; Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Yunjia Dong
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China; Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Tao Han
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China; Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Yafeng Liu
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China; Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Jianqiang Guo
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China; Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China
| | - Jing Wu
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China; Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China; Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institute, Huainan, Anhui, China; Key Laboratory of Industrial Dust Prevention and Control & Occupational Safety and Health of the Ministry of Education, Anhui University of Science and Technology, Huainan, Anhui, China.
| | - Dong Hu
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, China; Anhui Occupational Health and Safety Engineering Laboratory, Huainan, Anhui, China; Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institute, Huainan, Anhui, China; Key Laboratory of Industrial Dust Prevention and Control & Occupational Safety and Health of the Ministry of Education, Anhui University of Science and Technology, Huainan, Anhui, China.
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Qi Y, Zhang Y, Guan S, Liu L, Wang H, Chen Y, Zhou Q, Xu F, Zhang Y. Common ground on immune infiltration landscape and diagnostic biomarkers in diabetes-complicated atherosclerosis: an integrated bioinformatics analysis. Front Endocrinol (Lausanne) 2024; 15:1381229. [PMID: 39145311 PMCID: PMC11323117 DOI: 10.3389/fendo.2024.1381229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/25/2024] [Indexed: 08/16/2024] Open
Abstract
Introduction Type 2 diabetes mellitus (T2DM) is a major cause of atherosclerosis (AS). However, definitive evidence regarding the common molecular mechanisms underlying these two diseases are lacking. This study aimed to investigate the mechanisms underlying the association between T2DM and AS. Methods The gene expression profiles of T2DM (GSE159984) and AS (GSE100927) were obtained from the Gene Expression Omnibus, after which overlapping differentially expressed gene identification, bioinformatics enrichment analyses, protein-protein interaction network construction, and core genes identification were performed. We confirmed the discriminatory capacity of core genes using receiver operating curve analysis. We further identified transcription factors using TRRUST database to build a transcription factor-mRNA regulatory network. Finally, the immune infiltration and the correlation between core genes and differential infiltrating immune cells were analyzed. Results A total of 27 overlapping differentially expressed genes were identified under the two-stress conditions. Functional analyses revealed that immune responses and transcriptional regulation may be involved in the potential pathogenesis. After protein-protein interaction network deconstruction, external datasets, and qRT-PCR experimental validation, four core genes (IL1B, C1QA, CCR5, and MSR1) were identified. ROC analysis further showed the reliable value of these core genes. Four common differential infiltrating immune cells (B cells, CD4+ T cells, regulatory T cells, and M2 macrophages) between T2DM and AS datasets were selected based on immune cell infiltration. A significant correlation between core genes and common differential immune cells. Additionally, five transcription factors (RELA, NFκB1, JUN, YY1, and SPI1) regulating the transcription of core genes were mined using upstream gene regulator analysis. Discussion In this study, common target genes and co-immune infiltration landscapes were identified between T2DM and AS. The relationship among five transcription factors, four core genes, and four immune cells profiles may be crucial to understanding T2DM complicated with AS pathogenesis and therapeutic direction.
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Affiliation(s)
- Yifei Qi
- Department of General Medicine, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yan Zhang
- Department of General Medicine, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shuang Guan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Liu
- Department of General Medicine, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hongqin Wang
- Innovation Research Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yao Chen
- Department of General Medicine, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qingbing Zhou
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fengqin Xu
- Department of General Medicine, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ying Zhang
- Department of General Medicine, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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Goh W, Sudholz H, Foroutan M, Scheer S, Pfefferle A, Delconte RB, Meng X, Shen Z, Hennessey R, Kong IY, Schuster IS, Andoniou CE, Davis MJ, Hediyeh-Zadeh S, Souza-Fonseca-Guimaraes F, Parish IA, Beavis P, Thiele D, Chopin M, Degli-Esposti MA, Cursons J, Kallies A, Rautela J, Nutt SL, Huntington ND. IKAROS and AIOLOS directly regulate AP-1 transcriptional complexes and are essential for NK cell development. Nat Immunol 2024; 25:240-255. [PMID: 38182668 DOI: 10.1038/s41590-023-01718-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/22/2023] [Indexed: 01/07/2024]
Abstract
Ikaros transcription factors are essential for adaptive lymphocyte function, yet their role in innate lymphopoiesis is unknown. Using conditional genetic inactivation, we show that Ikzf1/Ikaros is essential for normal natural killer (NK) cell lymphopoiesis and IKZF1 directly represses Cish, a negative regulator of interleukin-15 receptor resulting in impaired interleukin-15 receptor signaling. Both Bcl2l11 and BIM levels, and intrinsic apoptosis were increased in Ikzf1-null NK cells, which in part accounts for NK lymphopenia as both were restored to normal levels when Ikzf1 and Bcl2l11 were co-deleted. Ikzf1-null NK cells presented extensive transcriptional alterations with reduced AP-1 transcriptional complex expression and increased expression of Ikzf2/Helios and Ikzf3/Aiolos. IKZF1 and IKZF3 directly bound AP-1 family members and deletion of both Ikzf1 and Ikzf3 in NK cells resulted in further reductions in Jun/Fos expression and complete loss of peripheral NK cells. Collectively, we show that Ikaros family members are important regulators of apoptosis, cytokine responsiveness and AP-1 transcriptional activity.
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Affiliation(s)
- Wilford Goh
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Harrison Sudholz
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Momeneh Foroutan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Sebastian Scheer
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Aline Pfefferle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Rebecca B Delconte
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiangpeng Meng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Zihan Shen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Robert Hennessey
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Isabella Y Kong
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Iona S Schuster
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Christopher E Andoniou
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
- The South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Soroor Hediyeh-Zadeh
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Thiele
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Michael Chopin
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Mariapia A Degli-Esposti
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Joe Cursons
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Axel Kallies
- Department of Microbiology & Immunology, Faculty of Medicine, Dentistry and Health Sciences & Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jai Rautela
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nicholas D Huntington
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia.
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Zhao J, Ding C, Li HB. N 6 - Methyladenosine defines a new checkpoint in γδ T cell development. Bioessays 2023; 45:e2300002. [PMID: 36942692 DOI: 10.1002/bies.202300002] [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: 01/05/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
T cells, which are derived from hematopoietic stem cells (HSCs), are the most important components of adaptive immune system. Based on the expression of αβ and γδ receptors, T cells are mainly divided into αβ and γδ T cells. In the thymus, they share common progenitor cells, while undergoing a series of well-characterized and different developmental processes. N6 -Methyladenosine (m6 A), one of the most abundant modifications in mRNAs, plays critical roles in cell development and maintenance of function. Recently, we have demonstrated that the depletion of m6 A demethylase ALKBH5 in lymphocytes specifically induces an expansion of γδ T cells through the regulation of Jag1/Notch2 signaling, but not αβ T cells, indicating a checkpoint role of ALKBH5 and m6 A modification in the early development of γδ T cells. Based on previous studies, many key pathway molecules, which exert dominant roles in γδ T cell fate determination, have been identified as the targets regulated by m6 A modification. In this review, we mainly summarize the potential regulation between m6 A modification and these key signaling molecules in the γδ T cell lineage commitment, to provide new perspectives in the checkpoint of γδ T cell development.
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Affiliation(s)
- Jiachen Zhao
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenbo Ding
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Inflammatory Cytokines That Enhance Antigen Responsiveness of Naïve CD8 + T Lymphocytes Modulate Chromatin Accessibility of Genes Impacted by Antigen Stimulation. Int J Mol Sci 2022; 23:ijms232214122. [PMID: 36430600 PMCID: PMC9698886 DOI: 10.3390/ijms232214122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
Naïve CD8+ T lymphocytes exposed to certain inflammatory cytokines undergo proliferation and display increased sensitivity to antigens. Such 'cytokine priming' can promote the activation of potentially autoreactive and antitumor CD8+ T cells by weak tissue antigens and tumor antigens. To elucidate the molecular mechanisms of cytokine priming, naïve PMEL-1 TCR transgenic CD8+ T lymphocytes were stimulated with IL-15 and IL-21, and chromatin accessibility was assessed using the assay for transposase-accessible chromatin (ATAC) sequencing. PMEL-1 cells stimulated by the cognate antigenic peptide mgp10025-33 served as controls. Cytokine-primed cells showed a limited number of opening and closing chromatin accessibility peaks compared to antigen-stimulated cells. However, the ATACseq peaks in cytokine-primed cells substantially overlapped with those of antigen-stimulated cells and mapped to several genes implicated in T cell signaling, activation, effector differentiation, negative regulation and exhaustion. Nonetheless, the expression of most of these genes was remarkably different between cytokine-primed and antigen-stimulated cells. In addition, cytokine priming impacted the expression of several genes following antigen stimulation in a synergistic or antagonistic manner. Our findings indicate that chromatin accessibility changes in cytokine-primed naïve CD8+ T cells not only underlie their increased antigen responsiveness but may also enhance their functional fitness by reducing exhaustion without compromising regulatory controls.
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8
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Boehme L, Roels J, Taghon T. Development of γδ T cells in the thymus - A human perspective. Semin Immunol 2022; 61-64:101662. [PMID: 36374779 DOI: 10.1016/j.smim.2022.101662] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/05/2022] [Indexed: 12/14/2022]
Abstract
γδ T cells are increasingly emerging as crucial immune regulators that can take on innate and adaptive roles in the defence against pathogens. Although they arise within the thymus from the same hematopoietic precursors as conventional αβ T cells, the development of γδ T cells is less well understood. In this review, we focus on summarising the current state of knowledge about the cellular and molecular processes involved in the generation of γδ T cells in human.
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Affiliation(s)
- Lena Boehme
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Juliette Roels
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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9
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Corbett RJ, Luttman AM, Herrera-Uribe J, Liu H, Raney NE, Grabowski JM, Loving CL, Tuggle CK, Ernst CW. Assessment of DNA methylation in porcine immune cells reveals novel regulatory elements associated with cell-specific gene expression and immune capacity traits. BMC Genomics 2022; 23:575. [PMID: 35953767 PMCID: PMC9367135 DOI: 10.1186/s12864-022-08773-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/18/2022] [Indexed: 11/15/2022] Open
Abstract
Background Genetics studies in the porcine immune system have enhanced selection practices for disease resistance phenotypes and increased the efficacy of porcine models in biomedical research; however limited functional annotation of the porcine immunome has hindered progress on both fronts. Among epigenetic mechanisms that regulate gene expression, DNA methylation is the most ubiquitous modification made to the DNA molecule and influences transcription factor binding as well as gene and phenotype expression. Human and mouse DNA methylation studies have improved mapping of regulatory elements in these species, but comparable studies in the pig have been limited in scope. Results We performed whole-genome bisulfite sequencing to assess DNA methylation patterns in nine pig immune cell populations: CD21+ and CD21− B cells, four T cell fractions (CD4+, CD8+, CD8+CD4+, and SWC6γδ+), natural killer and myeloid cells, and neutrophils. We identified 54,391 cell differentially methylated regions (cDMRs), and clustering by cDMR methylation rate grouped samples by cell lineage. 32,737 cDMRs were classified as cell lowly methylated regions (cLMRs) in at least one cell type, and cLMRs were broadly enriched in genes and regions of intermediate CpG density. We observed strong correlations between differential methylation and expression across immune cell populations, with cell-specific low methylation disproportionately impacting genes exhibiting enriched gene expression in the same cell type. Motif analysis of cLMRs revealed cell type-specific enrichment of transcription factor binding motifs, indicating that cell-specific methylation patterns may influence accessibility by trans-acting factors. Lastly, cDMRs were enriched for immune capacity GWAS SNPs, and many such overlaps occurred within genes known to influence immune cell development and function (CD8B, NDRG1). Conclusion Our DNA methylation data improve functional annotation of the porcine genome through characterization of epigenomic regulatory patterns that contribute to immune cell identity and function, and increase the potential for identifying mechanistic links between genotype and phenotype. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08773-5.
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Affiliation(s)
- Ryan J Corbett
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, USA
| | - Andrea M Luttman
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, USA
| | | | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Nancy E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Jenna M Grabowski
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | | | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, USA.
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10
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Wu H, Dong J, Yu H, Wang K, Dai W, Zhang X, Hu N, Yin L, Tang D, Liu F, Dai Y. Single-Cell RNA and ATAC Sequencing Reveal Hemodialysis-Related Immune Dysregulation of Circulating Immune Cell Subpopulations. Front Immunol 2022; 13:878226. [PMID: 35720370 PMCID: PMC9205630 DOI: 10.3389/fimmu.2022.878226] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Background An increased risk of infection, malignancy, and cardiovascular diseases in maintenance hemodialysis patients is associated with hemodialysis-related immunity disturbances. Although defects in T-lymphocyte-dependent immune responses and preactivation of antigen-presenting cells have been documented in hemodialysis patients, the effects of long-term hemodialysis on the transcriptional program and chromosomal accessibility of circulating immune cell subpopulations remain poorly defined. Methods We integrated single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to characterize the transcriptome profiles of peripheral mononuclear cells (PBMCs) from healthy controls and maintenance hemodialysis patients. Validation of differentially expressed genes in CD4+ T cells and monocytes were performed by magnetic bead separation and quantitative real-time PCR. Results We identified 16 and 15 PBMC subgroups in scRNA-seq and scATAC-seq datasets, respectively. Hemodialysis significantly suppressed the expression levels of T cell receptor (TCR) genes in CD4+ T cell subsets (e.g., TRAV4, CD45, CD3G, CD3D, CD3E) and major histocompatibility complex II (MHC-II) pathway-related genes in monocytes (HLA-DRB1, HLA-DQA2, HLA-DQA1, HLA-DPB1). Downstream pathways of TCR signaling, including PI3K-Akt-mTOR, MAPK, TNF, and NF-κB pathways, were also inhibited in CD4+ T cell subpopulations during the hemodialysis procedure. Hemodialysis altered cellular communication patterns between PBMC subgroups, particularly TGF-TGFBR, HVEM-BTLA, and IL16-CD4 signalings between CD4+ T cells and monocytes. Additionally, we found that hemodialysis inhibited the expression of AP-1 family transcription factors (JUN, JUND, FOS, FOSB) by interfering with the chromatin accessibility profile. Conclusions Our study provides a valuable framework for future investigations of hemodialysis-related immune dysregulation and identifies potential therapeutic targets for reconstituting the circulating immune system in maintenance hemodialysis patients.
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Affiliation(s)
- Hongwei Wu
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China.,Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Jingjing Dong
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China.,Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Haiyan Yu
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Kang Wang
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX, United States
| | - Xinzhou Zhang
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Nan Hu
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Lianghong Yin
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Donge Tang
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Fanna Liu
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Yong Dai
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
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11
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Li YR, Zhou Y, Kim YJ, Zhu Y, Ma F, Yu J, Wang YC, Chen X, Li Z, Zeng S, Wang X, Lee D, Ku J, Tsao T, Hardoy C, Huang J, Cheng D, Montel-Hagen A, Seet CS, Crooks GM, Larson SM, Sasine JP, Wang X, Pellegrini M, Ribas A, Kohn DB, Witte O, Wang P, Yang L. Development of allogeneic HSC-engineered iNKT cells for off-the-shelf cancer immunotherapy. Cell Rep Med 2021; 2:100449. [PMID: 34841295 PMCID: PMC8607011 DOI: 10.1016/j.xcrm.2021.100449] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/12/2021] [Accepted: 10/19/2021] [Indexed: 01/19/2023]
Abstract
Cell-based immunotherapy has become the new-generation cancer medicine, and "off-the-shelf" cell products that can be manufactured at large scale and distributed readily to treat patients are necessary. Invariant natural killer T (iNKT) cells are ideal cell carriers for developing allogeneic cell therapy because they are powerful immune cells targeting cancers without graft-versus-host disease (GvHD) risk. However, healthy donor blood contains extremely low numbers of endogenous iNKT cells. Here, by combining hematopoietic stem cell (HSC) gene engineering and in vitro differentiation, we generate human allogeneic HSC-engineered iNKT (AlloHSC-iNKT) cells at high yield and purity; these cells closely resemble endogenous iNKT cells, effectively target tumor cells using multiple mechanisms, and exhibit high safety and low immunogenicity. These cells can be further engineered with chimeric antigen receptor (CAR) to enhance tumor targeting or/and gene edited to ablate surface human leukocyte antigen (HLA) molecules and further reduce immunogenicity. Collectively, these preclinical studies demonstrate the feasibility and cancer therapy potential of AlloHSC-iNKT cell products and lay a foundation for their translational and clinical development.
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Affiliation(s)
- Yan-Ruide Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yang Zhou
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yu Jeong Kim
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yanni Zhu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Feiyang Ma
- Department of Molecular, Cell and Developmental Biology, College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jiaji Yu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yu-Chen Wang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xianhui Chen
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Zhe Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samuel Zeng
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xi Wang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Derek Lee
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Josh Ku
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tasha Tsao
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christian Hardoy
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jie Huang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amélie Montel-Hagen
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher S. Seet
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gay M. Crooks
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sarah M. Larson
- Department of Internal Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joshua P. Sasine
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Division of Hematology/Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiaoyan Wang
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Antoni Ribas
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Donald B. Kohn
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Division of Hematology/Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Owen Witte
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Pin Wang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Lili Yang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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12
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Novoszel P, Drobits B, Holcmann M, Fernandes CDS, Tschismarov R, Derdak S, Decker T, Wagner EF, Sibilia M. The AP-1 transcription factors c-Jun and JunB are essential for CD8α conventional dendritic cell identity. Cell Death Differ 2021; 28:2404-2420. [PMID: 33758366 PMCID: PMC8329169 DOI: 10.1038/s41418-021-00765-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/17/2021] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
Dendritic cell (DC) development is orchestrated by lineage-determining transcription factors (TFs). Although, members of the activator-protein-1 (AP-1) family, including Batf3, have been implicated in conventional (c)DC specification, the role of Jun proteins is poorly understood. Here, we identified c-Jun and JunB as essential for cDC1 fate specification and function. In mice, Jun proteins regulate extrinsic and intrinsic pathways, which control CD8α cDC1 diversification, whereas CD103 cDC1 development is unaffected. The loss of c-Jun and JunB in DC progenitors diminishes the CD8α cDC1 pool and thus confers resistance to Listeria monocytogenes infection. Their absence in CD8α cDC1 results in impaired TLR triggering and antigen cross-presentation. Both TFs are required for the maintenance of the CD8α cDC1 subset and suppression of cDC2 identity on a transcriptional and phenotypic level. Taken together, these results demonstrate the essential role of c-Jun and JunB in CD8α cDC1 diversification, function, and maintenance of their identity.
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Affiliation(s)
- Philipp Novoszel
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Barbara Drobits
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Martin Holcmann
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Cristiano De Sa Fernandes
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Roland Tschismarov
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Sophia Derdak
- Core Facilities, Medical University of Vienna, Vienna, Austria
| | - Thomas Decker
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Erwin F Wagner
- Department of Dermatology and Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Maria Sibilia
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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13
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Novoszel P, Holcmann M, Stulnig G, De Sa Fernandes C, Zyulina V, Borek I, Linder M, Bogusch A, Drobits B, Bauer T, Tam‐Amersdorfer C, Brunner PM, Stary G, Bakiri L, Wagner EF, Strobl H, Sibilia M. Psoriatic skin inflammation is promoted by c-Jun/AP-1-dependent CCL2 and IL-23 expression in dendritic cells. EMBO Mol Med 2021; 13:e12409. [PMID: 33724710 PMCID: PMC8033525 DOI: 10.15252/emmm.202012409] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
Toll-like receptor (TLR) stimulation induces innate immune responses involved in many inflammatory disorders including psoriasis. Although activation of the AP-1 transcription factor complex is common in TLR signaling, the specific involvement and induced targets remain poorly understood. Here, we investigated the role of c-Jun/AP-1 protein in skin inflammation following TLR7 activation using human psoriatic skin, dendritic cells (DC), and genetically engineered mouse models. We show that c-Jun regulates CCL2 production in DCs leading to impaired recruitment of plasmacytoid DCs to inflamed skin after treatment with the TLR7/8 agonist Imiquimod. Furthermore, deletion of c-Jun in DCs or chemical blockade of JNK/c-Jun signaling ameliorates psoriasis-like skin inflammation by reducing IL-23 production in DCs. Importantly, the control of IL-23 and CCL2 by c-Jun is most pronounced in murine type-2 DCs. CCL2 and IL-23 expression co-localize with c-Jun in type-2/inflammatory DCs in human psoriatic skin and JNK-AP-1 inhibition reduces the expression of these targets in TLR7/8-stimulated human DCs. Therefore, c-Jun/AP-1 is a central driver of TLR7-induced immune responses by DCs and JNK/c-Jun a potential therapeutic target in psoriasis.
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Affiliation(s)
- Philipp Novoszel
- Department of Medicine IComprehensive Cancer CenterInstitute of Cancer ResearchMedical University of ViennaViennaAustria
| | - Martin Holcmann
- Department of Medicine IComprehensive Cancer CenterInstitute of Cancer ResearchMedical University of ViennaViennaAustria
| | - Gabriel Stulnig
- Department of Medicine IComprehensive Cancer CenterInstitute of Cancer ResearchMedical University of ViennaViennaAustria
| | - Cristiano De Sa Fernandes
- Department of Medicine IComprehensive Cancer CenterInstitute of Cancer ResearchMedical University of ViennaViennaAustria
| | - Victoria Zyulina
- Division of Immunology and PathophysiologyOtto Loewi Research CenterMedical University of GrazGrazAustria
| | - Izabela Borek
- Division of Immunology and PathophysiologyOtto Loewi Research CenterMedical University of GrazGrazAustria
| | - Markus Linder
- Department of Medicine IComprehensive Cancer CenterInstitute of Cancer ResearchMedical University of ViennaViennaAustria
| | - Alexandra Bogusch
- Department of Medicine IComprehensive Cancer CenterInstitute of Cancer ResearchMedical University of ViennaViennaAustria
| | - Barbara Drobits
- Department of Medicine IComprehensive Cancer CenterInstitute of Cancer ResearchMedical University of ViennaViennaAustria
| | - Thomas Bauer
- Department of Medicine IComprehensive Cancer CenterInstitute of Cancer ResearchMedical University of ViennaViennaAustria
| | - Carmen Tam‐Amersdorfer
- Division of Immunology and PathophysiologyOtto Loewi Research CenterMedical University of GrazGrazAustria
| | - Patrick M Brunner
- Division of Immunology, Allergy and Infectious DiseasesDepartment of DermatologyMedical University of ViennaViennaAustria
| | - Georg Stary
- Division of Immunology, Allergy and Infectious DiseasesDepartment of DermatologyMedical University of ViennaViennaAustria
| | - Latifa Bakiri
- Division of Immunology, Allergy and Infectious DiseasesDepartment of DermatologyMedical University of ViennaViennaAustria
- Department of Laboratory MedicineMedical University of ViennaViennaAustria
| | - Erwin F Wagner
- Division of Immunology, Allergy and Infectious DiseasesDepartment of DermatologyMedical University of ViennaViennaAustria
- Department of Laboratory MedicineMedical University of ViennaViennaAustria
| | - Herbert Strobl
- Division of Immunology and PathophysiologyOtto Loewi Research CenterMedical University of GrazGrazAustria
| | - Maria Sibilia
- Department of Medicine IComprehensive Cancer CenterInstitute of Cancer ResearchMedical University of ViennaViennaAustria
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14
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Identifying the Immunological Gene Signatures of Immune Cell Subtypes. BIOMED RESEARCH INTERNATIONAL 2021. [DOI: 10.1155/2021/6639698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The immune system is a complicated defensive system that comprises multiple functional cells and molecules acting against endogenous and exogenous pathogenic factors. Identifying immune cell subtypes and recognizing their unique immunological functions are difficult because of the complicated cellular components and immunological functions of the immune system. With the development of transcriptomics and high-throughput sequencing, the gene expression profiling of immune cells can provide a new strategy to explore the immune cell subtyping. On the basis of the new profiling data of mouse immune cell gene expression from the Immunological Genome Project (ImmGen), a novel computational pipeline was applied to identify different immune cell subtypes, including αβ T cells, B cells, γδ T cells, and innate lymphocytes. First, the profiling data was analyzed by a powerful feature selection method, Monte-Carlo Feature Selection, resulting in a feature list and some informative features. For the list, the two-stage incremental feature selection method, incorporating random forest as the classification algorithm, was applied to extract essential gene signatures and build an efficient classifier. On the other hand, a rule learning scheme was applied on the informative features to construct quantitative expression rules. A group of gene signatures was found as qualitatively related to the biological processes of four immune cell subtypes. The quantitative expression rules can efficiently cluster immune cells. This work provides a novel computational tool for immune cell quantitative subtyping and biomarker recognition.
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15
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Ge B, Guo C, Liang Y, Liu M, Wu K. Network analysis, and human and animal studies disclose the anticystitis glandularis effects of vitamin C. Biofactors 2019; 45:912-919. [PMID: 31469455 DOI: 10.1002/biof.1558] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Our present study aimed to unravel the therapeutic biotargets of vitamin C (VC) against cystitis glandularis (CG), and to elucidate the molecular mechanisms for VC treating CG. METHODS Network pharmacology was used to predict therapeutic targets of VC against CG, and to identify molecular mechanisms. In addition, further human and animal studies were designed to validate the bioinformatic findings through biochemical tests, computerized tomography scans, and immunostaining assays. RESULTS In bioinformatic analyses, pathogenic targets of CG and putative targets of VC were identified, respectively. An interaction network between biological target and functional protein was produced before screening and collecting the key therapeutic targets of VC against CG, biological processes, and signaling pathways. In addition, ingenuity pathway analysis with cloud platform indicated that anti-CG mechanisms of VC were achieved through modulating a cluster of molecular pathways, such as tumor necrosis factor (TNF) pathway. Meanwhile, 18 core targets of VC against CG were identified, and the most important TNF, interleukin-6 (IL6), and Jun biotargets were obtained, respectively. In further validation in human study, cellular TNF-α, IL6, and c-Jun expressions in patient's CG samples were elevated significantly, accompanied with detectable urinary tract infection. Beneficially, VC-dosed CG mice resulted in downregulated expressions of endogenous TNF-α, IL6, and c-Jun in blood and bladder samples. CONCLUSION Collectively, these bioinformatic findings and experimentative data uncover the therapeutic targets and biological mechanisms of VC for treating CG, in which the key biomarkers of TNF-α, IL6, and c-Jun may be the potential molecules for treating CG in clinical application.
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Affiliation(s)
- Bo Ge
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Chao Guo
- Department of Pharmacy, Guigang City People's Hospital, The Eighth Affiliated Hospital of Guangxi Medical University, Guigang, Guangxi, China
| | - Yujia Liang
- College of Pharmacy, Guangxi Medical University, Nanning, China
| | - Meizhen Liu
- College of Pharmacy, Guangxi Medical University, Nanning, China
| | - Ka Wu
- Department of Pharmacy, The Second People's Hospital of Nanning City, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
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16
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Fiala GJ, Schaffer AM, Merches K, Morath A, Swann J, Herr LA, Hils M, Esser C, Minguet S, Schamel WWA. Proximal Lck Promoter–Driven Cre Function Is Limited in Neonatal and Ineffective in Adult γδ T Cell Development. THE JOURNAL OF IMMUNOLOGY 2019; 203:569-579. [DOI: 10.4049/jimmunol.1701521] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/08/2019] [Indexed: 01/13/2023]
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17
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Stage-specific roles for Zmiz1 in Notch-dependent steps of early T-cell development. Blood 2018; 132:1279-1292. [PMID: 30076146 DOI: 10.1182/blood-2018-02-835850] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/29/2018] [Indexed: 12/15/2022] Open
Abstract
Notch1 signaling must elevate to high levels in order to drive the proliferation of CD4-CD8- double-negative (DN) thymocytes and progression to the CD4+CD8+ double-positive (DP) stage through β-selection. During this critical phase of pre-T-cell development, which is also known as the DN-DP transition, it is unclear whether the Notch1 transcriptional complex strengthens its signal output as a discrete unit or through cofactors. We previously showed that the protein inhibitor of activated STAT-like coactivator Zmiz1 is a context-dependent cofactor of Notch1 in T-cell leukemia. We also showed that withdrawal of Zmiz1 generated an early T-lineage progenitor (ETP) defect. Here, we show that this early defect seems inconsistent with loss-of-Notch1 function. In contrast, at the later pre-T-cell stage, withdrawal of Zmiz1 impaired the DN-DP transition by inhibiting proliferation, like withdrawal of Notch. In pre-T cells, but not ETPs, Zmiz1 cooperatively regulated Notch1 target genes Hes1, Lef1, and Myc. Enforced expression of either activated Notch1 or Myc partially rescued the Zmiz1-deficient DN-DP defect. We identified residues in the tetratricopeptide repeat (TPR) domain of Zmiz1 that bind Notch1. Mutating only a single residue impaired the Zmiz1-Notch1 interaction, Myc induction, the DN-DP transition, and leukemic proliferation. Similar effects were seen using a dominant-negative TPR protein. Our studies identify stage-specific roles of Zmiz1. Zmiz1 is a context-specific cofactor for Notch1 during Notch/Myc-dependent thymocyte proliferation, whether normal or malignant. Finally, we highlight a vulnerability in leukemic cells that originated from a developmentally important Zmiz1-Notch1 interaction that is hijacked during transformation from normal pre-T cells.
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18
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Valeri M, Raffatellu M. Cytokines IL-17 and IL-22 in the host response to infection. Pathog Dis 2016; 74:ftw111. [PMID: 27915228 PMCID: PMC5975231 DOI: 10.1093/femspd/ftw111] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/13/2016] [Accepted: 11/17/2016] [Indexed: 12/12/2022] Open
Abstract
Cytokines IL-17 and IL-22 play pivotal roles in host defense against microbes and in the development of chronic inflammatory diseases. These cytokines are produced by cells that are often located in epithelial barriers, including subsets of T cells and innate lymphoid cells. In general, IL-17 and IL-22 can be characterized as important cytokines in the rapid response to infectious agents, both by recruiting neutrophils and by inducing the production of antimicrobial peptides. Although each cytokine induces an innate immune response in epithelial cells, their functional spectra are generally distinct: IL-17 mainly induces an inflammatory tissue response and is involved in the pathogenesis of several autoimmune diseases, whereas IL-22 is largely protective and regenerative. In this review, we compare IL-17 and IL-22, describing overlaps and differences in their cellular sources as well as their regulation, signaling, biological functions and roles during disease, with a focus on the contribution of these cytokines to the gut mucosal barrier during bacterial infection.
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Affiliation(s)
- Maria Valeri
- Department of Microbiology and Molecular Genetics, University of California Irvine School of Medicine, Irvine, CA 92697-4025, USA
- Institute for Immunology, University of California Irvine School of Medicine, Irvine, CA 92697-4025, USA
| | - Manuela Raffatellu
- Department of Microbiology and Molecular Genetics, University of California Irvine School of Medicine, Irvine, CA 92697-4025, USA
- Institute for Immunology, University of California Irvine School of Medicine, Irvine, CA 92697-4025, USA
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19
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Hrdinka M, Sudan K, Just S, Drobek A, Stepanek O, Schlüter D, Reinhold D, Jordan BA, Gintschel P, Schraven B, Kreutz MR. Normal Development and Function of T Cells in Proline Rich 7 (Prr7) Deficient Mice. PLoS One 2016; 11:e0162863. [PMID: 27657535 PMCID: PMC5033326 DOI: 10.1371/journal.pone.0162863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/30/2016] [Indexed: 11/18/2022] Open
Abstract
Transmembrane adaptor proteins (TRAPs) are important organisers for the transduction of immunoreceptor-mediated signals. Prr7 is a TRAP that regulates T cell receptor (TCR) signalling and potently induces cell death when overexpressed in human Jurkat T cells. Whether endogenous Prr7 has a similar functional role is currently unknown. To address this issue, we analysed the development and function of the immune system in Prr7 knockout mice. We found that loss of Prr7 partially impairs development of single positive CD4+ T cells in the thymus but has no effect on the development of other T cell subpopulations, B cells, NK cells, or NKT cells. Moreover, Prr7 does not affect the TCR signalling pathway as T cells derived from Prr7 knockout and wild-type animals and stimulated in vitro express the same levels of the activation marker CD69, and retain their ability to proliferate and activate induced cell death programs. Importantly, Prr7 knockout mice retained the capacity to mount a protective immune response when challenged with Listeria monocytogenes infection in vivo. In addition, T cell effector functions (activation, migration, and reactivation) were normal following induction of experimental autoimmune encephalomyelitis (EAE) in Prr7 knockout mice. Collectively, our work shows that loss of Prr7 does not result in a major immune system phenotype and suggests that Prr7 has a dispensable function for TCR signalling.
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Affiliation(s)
- Matous Hrdinka
- RG Neuroplasticity, Leibniz-Institute for Neurobiology, Magdeburg, Germany
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
- * E-mail: (MH); (BS); (MRK)
| | - Kritika Sudan
- RG Neuroplasticity, Leibniz-Institute for Neurobiology, Magdeburg, Germany
| | - Sissy Just
- Institute of Medical Microbiology, Otto-von-Guericke University, Germany
| | - Ales Drobek
- Group of Adaptive Immunity, Institute of Molecular Genetics, CAS, Prague, Czech Republic
| | - Ondrej Stepanek
- Group of Adaptive Immunity, Institute of Molecular Genetics, CAS, Prague, Czech Republic
| | - Dirk Schlüter
- Institute of Medical Microbiology, Otto-von-Guericke University, Germany
- Organ-Specific Immune Regulation, Helmholtz-Center of Infection Research (HZI). Braunschweig, Germany
| | - Dirk Reinhold
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
| | - Bryen A. Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Patricia Gintschel
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
| | - Burkhart Schraven
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
- Department of Immune Control, Helmholtz-Center of Infection Research (HZI). Braunschweig, Germany
- * E-mail: (MH); (BS); (MRK)
| | - Michael R. Kreutz
- RG Neuroplasticity, Leibniz-Institute for Neurobiology, Magdeburg, Germany
- Leibniz Group 'Dendritic Organelles and Synaptic Function', University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology, Hamburg, Germany
- * E-mail: (MH); (BS); (MRK)
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Carow B, Gao Y, Coquet J, Reilly M, Rottenberg ME. lck-Driven Cre Expression Alters T Cell Development in the Thymus and the Frequencies and Functions of Peripheral T Cell Subsets. THE JOURNAL OF IMMUNOLOGY 2016; 197:2261-8. [PMID: 27503210 DOI: 10.4049/jimmunol.1600827] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/05/2016] [Indexed: 11/19/2022]
Abstract
Conditional gene targeting using the bacteriophage-derived Cre recombinase is widely applied for functional gene studies in mice. Mice transgenic for Cre under the control of the lck gene promoter are used to study the role of loxP-targeted genes in T cell development and function. In this article, we show a striking 65% reduction in cellularity, preferential development of γδ versus αβ T cells, and increased expression of IL-7R in the thymus of mice expressing Cre under the proximal lck promoter (lck-cre(+) mice). The transition from CD4/CD8 double-negative to double-positive cells was blocked, and lck-cre(+) double-positive cells were more prone to apoptosis and showed higher levels of Cre expression. Importantly, numbers of naive T cells were reduced in spleens and lymph nodes of lck-cre(+) mice. In contrast, frequencies of γδ T cells, CD44(+)CD62L(-) effector T cells, and Foxp3(+) regulatory T cells were elevated, as was the frequency of IFN-γ-secreting CD4(+) and CD8(+) T cells. A literature survey of 332 articles that used lck-cre(+) mice for deletion of floxed genes indicated that results are statistically influenced by the control used (lck-cre(+) or lck-cre(-)), more frequently resembling the lck-cre(+) phenotype described in this article if lck-cre(-) controls were used. Altogether, care should be taken when interpreting published results and to properly control targeted gene deletions using the lck-cre(+) strain.
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Affiliation(s)
- Berit Carow
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, S 171 77 Stockholm, Sweden; and
| | - Yu Gao
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, S 171 77 Stockholm, Sweden; and
| | - Jonathan Coquet
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, S 171 77 Stockholm, Sweden; and
| | - Marie Reilly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, S 171 77 Stockholm, Sweden
| | - Martin E Rottenberg
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, S 171 77 Stockholm, Sweden; and
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21
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St-Jean JR, Ounissi-Benkalha H, Polychronakos C. Yeast one-hybrid screen of a thymus epithelial library identifies ZBTB7A as a regulator of thymic insulin expression. Mol Immunol 2013; 56:637-42. [PMID: 23911422 DOI: 10.1016/j.molimm.2013.05.238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/28/2013] [Accepted: 05/28/2013] [Indexed: 12/20/2022]
Abstract
Insulin self-tolerance is, to a large extent, assured by the expression of small quantities of insulin by medullary thymic epithelial cells (mTECs). Regulation of thymic insulin expression differs from that in pancreas and its therapeutic manipulation could play an important role in the prevention of type 1 diabetes (T1D). Knowledge of the transcriptional regulators involved in the mTEC nuclear environment is essential for the development of such therapeutics. The yeast one-hybrid (Y1H) approach was used in order to identify such mTEC-specific nuclear proteins. We used a target composed of the human insulin gene promoter joined to the upstream class III VNTR allele, which is associated with both protection from T1D and higher thymic insulin expression, and a cDNA library from our insulin-producing mouse mTEC line. The Y1H screening allowed the identification of eleven proteins. An in vitro assay was used to confirm and quantify protein-DNA binding to the human insulin gene promoter alone or joined to a class I or class III VNTR allele, and identified the transcription factors ZBTB7A, JUN and EWSR1 as strong interacting partners. All three proteins could induce insulin expression in transfected HEK-293 cells, but ZBTB7A provided the most robust results especially in the presence of AIRE, with an additional 11-fold increase of the insulin mRNA levels from a co-transfected reporter driven by the class III VNTR allele. Thus, ZBTB7A is identified as a strong candidate for regulation of thymic insulin expression.
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Affiliation(s)
- Julien R St-Jean
- Laboratory of Endocrine Genetics, Department of Pediatrics, The McGill University Health Center, 4060 Ste-Catherine West, Montreal, Quebec, Canada H3Z 2Z3
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22
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Khalaf H, Demirel I, Bengtsson T. Suppression of inflammatory gene expression in T cells by Porphyromonas gingivalis is mediated by targeting MAPK signaling. Cell Mol Immunol 2013; 10:413-22. [PMID: 23892429 DOI: 10.1038/cmi.2013.23] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 04/30/2013] [Accepted: 05/16/2013] [Indexed: 12/29/2022] Open
Abstract
There is increasing awareness of the effects of Porphyromonas gingivalis on host immune responses. Degradation of cytokines and chemokines by cysteine proteinases has previously been reported. However, the precise mechanisms by which P. gingivalis is able to alter intracellular signaling, and thus proliferation and inflammation, have not been described. We have previously reported suppression of activator protein-1 (AP-1) and degradation of IL-2 by proteinases from P. gingivalis. In the present study, we have analyzed the effects of P. gingivalis on Jurkat T-cell signal transduction and subsequent IL-2 and CXCL8 expression. We found that CXCL8, but not IL-2, gene expression levels were significantly suppressed by viable P. gingivalis. Analysis of intracellular signaling revealed an inhibitory effect of P. gingivalis on c-Jun and c-Fos, but not NFκB (p50 and p65), NFAT or STAT5 expression. This inhibitory effect was not due to suppression of mitogen-activated protein kinase (MAPK) (p38, erk and JNK) gene expression, but was rather due to prevention of protein kinase C (PKC) and p38 phosphorylation, as demonstrated by western blot analysis. Furthermore, SOCS1 and SOCS3 expression levels decreased following treatment of Jurkat T cells with viable P. gingivalis. The results indicate that P. gingivalis is able to suppress inflammatory gene expression by targeting the activity of MAPK pathways in T cells, which was confirmed by using specific inhibitors of NF-κB, PKC, ERK, p38 and JNK.
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Affiliation(s)
- Hazem Khalaf
- Division of Clinical Medicine, School of Health and Medical Sciences, Örebro University, Örebro, Sweden
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Ma Y, Tian J, Cen H, Li J, Xu WD, Wang DG, Pan HF, Ye DQ. Association of c-Jun gene polymorphism with susceptibility to systemic lupus erythematosus in a Chinese population. DNA Cell Biol 2012; 31:1274-8. [PMID: 22489574 DOI: 10.1089/dna.2011.1536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
C-Jun has been proved as playing an important role in the pathogenesis of tumors, as a main component of Activator protein 1 and c-Jun gene polymorphisms are associated with colorectal cancer. However, the relationship between the c-Jun gene polymorphism and the susceptibility to systemic lupus erythematosus (SLE) has not been known. Our purpose is to evaluate whether the c-Jun gene polymorphism (SNP rs3748814) is associated with susceptibility to SLE in a Chinese population. In this study, we enrolled 502 SLE patients and 652 healthy controls. The c-Jun polymorphism (rs3748814) was specified from genomic DNA using the TaqMan genotyping assay on a 7300 real-time reverse transcription polymerase chain reaction system. We found that the frequency of the A/G genotype in SLE patients was lower than in healthy controls, whereas the frequency of the G/G genotype was significantly higher in SLE patients than in healthy controls (A/G vs. G/G p = 8.670e-08, odds ratio [OR] = 0.290, 95% confidence interval [CI] = 0.184-0.456). In addition, the frequency of allele A in the patients group was significantly lower than in the control group (A vs. G p=5.221e-09, OR = 0.308, 95% CI = 0.212-0.466). The distribution of genotype and allele frequency in SLE patients with lupus nephritis (LN) compared with SLE patients without LN was not statistically significant (A/G vs. G/G p = 0.744, OR = 1.157, 95% CI=0.481-2.785; A vs. G p = 0.748, OR = 1.152, 95% CI = 0.486-2.734; A/A+A/G vs. G/G p = 0.744, OR = 1.157, 95% CI = 0.481-2.785). Furthermore, we did not find any significant association between other clinical features and genotypes. Our findings suggest that the c-Jun polymorphism (rs3748814) may be significantly associated with the susceptibility to SLE in a Chinese population.
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Affiliation(s)
- Yan Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, PR China
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del Blanco B, García-Mariscal A, Wiest DL, Hernández-Munain C. Tcra enhancer activation by inducible transcription factors downstream of pre-TCR signaling. THE JOURNAL OF IMMUNOLOGY 2012; 188:3278-93. [PMID: 22357628 DOI: 10.4049/jimmunol.1100271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Tcra enhancer (Eα) is essential for pre-TCR-mediated activation of germline transcription and V(D)J recombination. Eα is considered an archetypical enhanceosome that acts through the functional synergy and cooperative binding of multiple transcription factors. Based on dimethylsulfate genomic footprinting experiments, there has been a long-standing paradox regarding Eα activation in the absence of differences in enhancer occupancy. Our data provide the molecular mechanism of Eα activation and an explanation of this paradox. We found that germline transcriptional activation of Tcra is dependent on constant phospholipase Cγ, as well as calcineurin- and MAPK/ERK-mediated signaling, indicating that inducible transcription factors are crucially involved. NFAT, AP-1, and early growth response factor 1, together with CREB-binding protein/p300 coactivators, bind to Eα as part of an active enhanceosome assembled during pre-TCR signaling. We favor a scenario in which the binding of lymphoid-restricted and constitutive transcription factors to Eα prior to its activation forms a regulatory scaffold to recruit factors induced by pre-TCR signaling. Thus, the combinatorial assembly of tissue- and signal-specific transcription factors dictates the Eα function. This mechanism for enhancer activation may represent a general paradigm in tissue-restricted and stimulus-responsive gene regulation.
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Affiliation(s)
- Beatriz del Blanco
- Departamento de Biología Celular e Inmunología, Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), Consejo Superior de Investigaciones Científicas, 18100-Armilla, Granada, Spain
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The transcription factor PU.1 regulates γδ T cell homeostasis. PLoS One 2011; 6:e22189. [PMID: 21779390 PMCID: PMC3136513 DOI: 10.1371/journal.pone.0022189] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 06/17/2011] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND T cell development results in the generation of both mature αβ and γδ T cells. While αβ T cells predominate in secondary lymphoid organs, γδ T cells are more abundant in mucosal tissues. PU.1, an Ets family transcription factor, also identified as the spleen focus forming virus proviral integration site-1 (Sfpi1) is essential for early stages of T cell development, but is down regulated during the DN T-cell stage. METHODOLOGY/PRINCIPAL FINDINGS In this study, we show that in mice specifically lacking PU.1 in T cells using an lck-Cre transgene with a conditional Sfpi1 allele (Sfpi1(lck-/-)) there are increased numbers of γδ T cells in spleen, thymus and in the intestine when compared to wild-type mice. The increase in γδ T cell numbers in PU.1-deficient mice is consistent in γδ T cell subsets identified by TCR variable regions. PU.1-deficient γδ T cells demonstrate greater proliferation in vivo and in vitro. CONCLUSIONS/SIGNIFICANCE The increase of γδ T cell numbers in Lck-Cre deleter strains, where deletion occurs after PU.1 expression is diminished, as well as the observation that PU.1-deficient γδ T cells have greater proliferative responses than wild type cells, suggests that PU.1 effects are not developmental but rather at the level of homeostasis. Thus, our data shows that PU.1 has a negative influence on γδ T cell expansion.
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26
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Das R, Sant'Angelo DB, Nichols KE. Transcriptional control of invariant NKT cell development. Immunol Rev 2011; 238:195-215. [PMID: 20969594 DOI: 10.1111/j.1600-065x.2010.00962.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Invariant natural killer T (iNKT) cells comprise a rare lymphocyte sublineage with phenotypic and functional properties similar to T and NK cells. Akin to conventional αβ T cells, their development occurs primarily in the thymus, where they originate from CD4(+) CD8(+) double positive (DP) progenitors. However, the selection of iNKT cells is unique in that it is mediated by homotypic interactions of DP cells and recognition of glycolipid antigen-CD1d complexes. Additionally, iNKT cells acquire an activated innate-like phenotype during development that allows them to release cytokines rapidly following antigen exposure. Given their hybrid features, it is not surprising that the developmental program of iNKT cells partially overlaps with that of T and NK cells. Several recent reports have provided new and exciting insights into the developmental mechanisms that direct natural killer T (NKT) cell lineage commitment and maturation. In this review, we provide a discussion of the NKT cell developmental program with an emphasis on the signaling mechanisms and transcription factors that influence the ontogeny of this lineage. Continued investigations into the complex interplay of these transcription factors and their relationship with other extracellular and intracellular signaling molecules will undoubtedly provide important clues into the biology of this unusual T-cell lineage.
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Affiliation(s)
- Rupali Das
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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27
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Taghon T, Rothenberg EV. Molecular mechanisms that control mouse and human TCR-alphabeta and TCR-gammadelta T cell development. Semin Immunopathol 2008; 30:383-98. [PMID: 18925397 DOI: 10.1007/s00281-008-0134-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 09/30/2008] [Indexed: 12/22/2022]
Abstract
Following specification of hematopoietic precursor cells into the T cell lineage, several developmental options remain available to the immature thymocytes. The paradigm is that the outcome of the T cell receptor rearrangements and the corresponding T cell receptor signaling events will be predominant to determine the first of these choices: the alphabeta versus gammadelta T cell pathways. Here, we review the thymus-derived environmental signals, the transcriptional mediators, and other molecular mechanisms that are also involved in this decision in both the mouse and human. We discuss the differences in cellular events between the alphabeta and gammadelta developmental pathways and try to correlate these with a corresponding complexity of the molecular mechanisms that support them.
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Affiliation(s)
- Tom Taghon
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University Hospital, Ghent University, De Pintelaan 185, 4 Blok A, 9000, Ghent, Belgium.
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Zenz R, Eferl R, Scheinecker C, Redlich K, Smolen J, Schonthaler HB, Kenner L, Tschachler E, Wagner EF. Activator protein 1 (Fos/Jun) functions in inflammatory bone and skin disease. Arthritis Res Ther 2008; 10:201. [PMID: 18226189 PMCID: PMC2374460 DOI: 10.1186/ar2338] [Citation(s) in RCA: 256] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Activator protein 1 (AP-1) (Fos/Jun) is a transcriptional regulator composed of members of the Fos and Jun families of DNA binding proteins. The functions of AP-1 were initially studied in mouse development as well as in the whole organism through conventional transgenic approaches, but also by gene targeting using knockout strategies. The importance of AP-1 proteins in disease pathways including the inflammatory response became fully apparent through conditional mutagenesis in mice, in particular when employing gene inactivation in a tissue-specific and inducible fashion. Besides the well-documented roles of Fos and Jun proteins in oncogenesis, where these genes can function both as tumor promoters or tumor suppressors, AP-1 proteins are being recognized as regulators of bone and immune cells, a research area termed osteoimmunology. In the present article, we review recent data regarding the functions of AP-1 as a regulator of cytokine expression and an important modulator in inflammatory diseases such as rheumatoid arthritis, psoriasis and psoriatic arthritis. These new data provide a better molecular understanding of disease pathways and should pave the road for the discovery of new targets for therapeutic applications.
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Affiliation(s)
- Rainer Zenz
- Ludwig Boltzmann Institute for Cancer Research, Währinger Strasse 13a, A-1090 Vienna, Austria
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