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Piatek P, Namiecinska M, Lewkowicz N, Kulińska-Michalska M, Jabłonowski Z, Matysiak M, Michlewska S, Wieczorek M, Lewkowicz P. Histone H3 posttranslational modified enzymes defined neutrophil plasticity and their vulnerability to IL-10 in the course of the inflammation. J Inflamm (Lond) 2024; 21:16. [PMID: 38745328 PMCID: PMC11095086 DOI: 10.1186/s12950-024-00389-8] [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: 10/30/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Neutrophils are a heterogeneous population capable of antimicrobial functions associated with pre-activation/activation and tissue regeneration. The specific polarisation of immune cells is mediated by the modification of 'chromatin landscapes', which enables differentiated access and activity of regulatory elements that guarantee their plasticity during inflammation No specific pattern within histone posttranslational modifications (PTMs) controlling this plasticity has been identified. METHODS Using the in vitro model of inflammation, reflecting different states of neutrophils from resting, pre-activated cells to activated and reducing tissue regeneration, we have analysed 11 different histone posttranslational modifications (PTMs), PTM enzymes associated with remodelling neutrophil chromatin, and H3K4me3 ChIP-Seq Gene Ontology analysis focusing on the processes related to histone PTMs. These findings were verified by extrapolation to adequate clinical status, using neutrophils derived from the patients with sepsis (systemic septic inflammation with LPS-stimulated neutrophils), neuromyelitis optical spectrum disorders (aseptic inflammation with pre-activated neutrophils) and periodontitis (local self-limiting septic inflammation with IL-10-positive neutrophils). RESULTS Physiological activation of neutrophils comprises a pre-activation characterised by histone H3K27ac and H3K4me1, which position enhancers; direct LPS exposure is induced explicitly by H3K4me3 which marked Transcription Start Site (TSS) regions and low-level of H3K9me3, H3K79me2 and H3K27me3 which, in turn, marked repressed genes. Contrary to antimicrobial action, IL-10 positively induced levels of H3S10p and negatively H3K9me3, which characterised processes related to the activation of genes within heterochromatin mediated by CHD1 and H3K9me3 specific demethylase JMJD2A. IL-10 protects changes within histone PTMs induced by TNF or LPS that affected H3K4me3-specific methyltransferase SETD1A and MLL1. Neutrophils previously exposed to inflammatory factors become unvulnerable to IL-10 because previous LPS stimulation interrupts TSS regions marked by H3K4me3 of CHD1 and JMJD2A genes. Therefore, LPS-activated neutrophils are disabled to induce CHD1/JMJD2A enzymes by IL-10, making this process irreversible. Because transcription of JMJD2A and CHD1 also depends on TSS positioning by H3K4me3, neutrophils before LPS stimulation become insensitive to IL-10. CONCLUSION Neutrophils, once pre-activated by TNF or directly stimulated by LPS, become insensitive to the anti-inflammatory effects of IL-10, and vice versa; IL-10 protects neutrophils against these proinflammatory stimuli. This phenomenon is responsible for disturbing the natural process of resolving inflammation and tissue regeneration.
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Affiliation(s)
- Paweł Piatek
- Department of Immunogenetics, Medical University of Lodz, ul. Pomorska 251/A4, 92- 213, Lodz, Poland
| | - Magdalena Namiecinska
- Department of Immunogenetics, Medical University of Lodz, ul. Pomorska 251/A4, 92- 213, Lodz, Poland
| | - Natalia Lewkowicz
- Department of Periodontology and Oral Mucosal Diseases, Medical University of Lodz, 90-419, Lodz, Poland
| | | | | | - Mariola Matysiak
- Department of Neurology, Medical University of Lodz, 90-153, Lodz, Poland
| | - Sylwia Michlewska
- Laboratory of Microscopic Imaging and Specialized Biological Techniques, Faculty of Biology and Environmental Protection, University of Lodz, 90-237, Lodz, Poland
| | - Marek Wieczorek
- Department of Neurobiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland
| | - Przemysław Lewkowicz
- Department of Immunogenetics, Medical University of Lodz, ul. Pomorska 251/A4, 92- 213, Lodz, Poland.
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Bártová E. Epigenetic and gene therapy in human and veterinary medicine. ENVIRONMENTAL EPIGENETICS 2024; 10:dvae006. [PMID: 38751572 PMCID: PMC11095531 DOI: 10.1093/eep/dvae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/12/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
Gene therapy is a focus of interest in both human and veterinary medicine, especially in recent years due to the potential applications of CRISPR/Cas9 technology. Another relatively new approach is that of epigenetic therapy, which involves an intervention based on epigenetic marks, including DNA methylation, histone post-translational modifications, and post-transcription modifications of distinct RNAs. The epigenome results from enzymatic reactions, which regulate gene expression without altering DNA sequences. In contrast to conventional CRISP/Cas9 techniques, the recently established methodology of epigenetic editing mediated by the CRISPR/dCas9 system is designed to target specific genes without causing DNA breaks. Both natural epigenetic processes and epigenetic editing regulate gene expression and thereby contribute to maintaining the balance between physiological functions and pathophysiological states. From this perspective, knowledge of specific epigenetic marks has immense potential in both human and veterinary medicine. For instance, the use of epigenetic drugs (chemical compounds with therapeutic potential affecting the epigenome) seems to be promising for the treatment of cancer, metabolic, and infectious diseases. Also, there is evidence that an epigenetic diet (nutrition-like factors affecting epigenome) should be considered as part of a healthy lifestyle and could contribute to the prevention of pathophysiological processes. In summary, epigenetic-based approaches in human and veterinary medicine have increasing significance in targeting aberrant gene expression associated with various diseases. In this case, CRISPR/dCas9, epigenetic targeting, and some epigenetic nutrition factors could contribute to reversing an abnormal epigenetic landscape to a healthy physiological state.
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Affiliation(s)
- Eva Bártová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 612 00, the Czech Republic
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3
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Ren X, Wang R, Yu XT, Cai B, Guo F. Regulation of histone H3 lysine 9 methylation in inflammation. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1931477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Xin Ren
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Rong Wang
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Xiao-ting Yu
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Bo Cai
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Fei Guo
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
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Sheikh T, Sen E. p53 affects epigenetic signature on SOCS1 promoter in response to TLR4 inhibition. Cytokine 2021; 140:155418. [PMID: 33476981 DOI: 10.1016/j.cyto.2020.155418] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 12/26/2020] [Indexed: 02/06/2023]
Abstract
Suppressor of cytokine signaling (SOCS1) functions as a negative regulator of toll-like receptor (TLR) induced inflammatory signaling. As silencing of SOCS1 is concomitant with elevated TLR4 levels in glioblastoma, we investigated the effect of TLR4 inhibition on SOCS1 expression. Pharmacological inhibition of TLR4 signaling by TAK242 or its siRNA-mediated knockdown in p53 mutant or wild-type glioma cells resulted in either increased or decreased SOCS1 expression and promoter activity, respectively. Genetic manipulation of p53 indicated that SOCS1 expression upon TLR4 inhibition is dependent on p53 mutational status. Increased SOCS1 level was concomitant with diminished nucleosomal occupancy around p53-binding site on SOCS1 promoter. This altered nucleosomal landscape was accompanied by (i) diminished nuclear H3K9me3 and (ii) increased JMJD2A and Brg1 levels. JMJD2A inhibition or ectopic expression of ATPase-deficient BRG1 prevented TAK242 mediated increase in SOCS1 expression. Recruitment of Brg1-p53-JMJD2A complex on p53 binding sites of SOCS1 promoter upon TLR4 inhibition was concomitant with increased SOCS1 expression in p53-mutant cells. The Cancer Genome Atlas (TCGA) dataset indicated an inverse correlation between TLR4 and SOCS1 levels in p53 mutant but not in p53WT GBM. Taken together, p53 mutational status regulates transcriptional plasticity of SOCS1 promoter through differential recruitment of chromatin remodelers and epigenetic regulators in response to TLR4 inhibition.
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Affiliation(s)
- Touseef Sheikh
- National Brain Research Centre, Manesar, Haryana 122 052, India
| | - Ellora Sen
- National Brain Research Centre, Manesar, Haryana 122 052, India.
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Lin H, Li Q, Li Q, Zhu J, Gu K, Jiang X, Hu Q, Feng F, Qu W, Chen Y, Sun H. Small molecule KDM4s inhibitors as anti-cancer agents. J Enzyme Inhib Med Chem 2018; 33:777-793. [PMID: 29651880 PMCID: PMC6010108 DOI: 10.1080/14756366.2018.1455676] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Histone demethylation is a vital process in epigenetic regulation of gene expression. A number of histone demethylases are present to control the methylated states of histone. Among these enzymes, KDM4s are one subfamily of JmjC KDMs and play important roles in both normal and cancer cells. The discovery of KDM4s inhibitors is a potential therapeutic strategy against different diseases including cancer. Here, we summarize the development of KDM4s inhibitors and some related pharmaceutical information to provide an update of recent progress in KDM4s inhibitors.
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Affiliation(s)
- Hongzhi Lin
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qihang Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qi Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Jie Zhu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Kai Gu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Xueyang Jiang
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qianqian Hu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Feng Feng
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Wei Qu
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Yao Chen
- c School of Pharmacy , Nanjing University of Chinese Medicine , Nanjing , China
| | - Haopeng Sun
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
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Jang SM, Redon CE, Aladjem MI. Chromatin-Bound Cullin-Ring Ligases: Regulatory Roles in DNA Replication and Potential Targeting for Cancer Therapy. Front Mol Biosci 2018; 5:19. [PMID: 29594129 PMCID: PMC5859106 DOI: 10.3389/fmolb.2018.00019] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/12/2018] [Indexed: 12/14/2022] Open
Abstract
Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligases (CRLs), the largest family of E3 ubiquitin ligases, are functional multi-subunit complexes including substrate receptors, adaptors, cullin scaffolds, and RING-box proteins. CRLs are responsible for ubiquitination of ~20% of cellular proteins and are involved in diverse biological processes including cell cycle progression, genome stability, and oncogenesis. Not surprisingly, cullins are deregulated in many diseases and instances of cancer. Recent studies have highlighted the importance of CRL-mediated ubiquitination in the regulation of DNA replication/repair, including specific roles in chromatin assembly and disassembly of the replication machinery. The development of novel therapeutics targeting the CRLs that regulate the replication machinery and chromatin in cancer is now an attractive therapeutic strategy. In this review, we summarize the structure and assembly of CRLs and outline their cellular functions and their diverse roles in cancer, emphasizing the regulatory functions of nuclear CRLs in modulating the DNA replication machinery. Finally, we discuss the current strategies for targeting CRLs against cancer in the clinic.
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Affiliation(s)
- Sang-Min Jang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
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Zheng N, Wang Z, Wei W. Ubiquitination-mediated degradation of cell cycle-related proteins by F-box proteins. Int J Biochem Cell Biol 2016; 73:99-110. [PMID: 26860958 PMCID: PMC4798898 DOI: 10.1016/j.biocel.2016.02.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/05/2016] [Accepted: 02/05/2016] [Indexed: 02/06/2023]
Abstract
F-box proteins, subunits of SKP1-cullin 1-F-box protein (SCF) type of E3 ubiquitin ligase complexes, have been validated to play a crucial role in governing various cellular processes such as cell cycle, cell proliferation, apoptosis, migration, invasion and metastasis. Recently, a wealth of evidence has emerged that F-box proteins is critically involved in tumorigenesis in part through governing the ubiquitination and subsequent degradation of cell cycle proteins, and dysregulation of this process leads to aberrant cell cycle progression and ultimately, tumorigenesis. Therefore, in this review, we describe the critical role of F-box proteins in the timely regulation of cell cycle. Moreover, we discuss how F-box proteins involve in tumorigenesis via targeting cell cycle-related proteins using biochemistry studies, engineered mouse models, and pathological gene alternations. We conclude that inhibitors of F-box proteins could have promising therapeutic potentials in part through controlling of aberrant cell cycle progression for cancer therapies.
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Affiliation(s)
- Nana Zheng
- The Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, The First Affiliated Hospital, Soochow University, Suzhou 215123, China
| | - Zhiwei Wang
- The Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, The First Affiliated Hospital, Soochow University, Suzhou 215123, China; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA 02215, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA 02215, USA.
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Das A, Chai JC, Yang CS, Lee YS, Das ND, Jung KH, Chai YG. Dual transcriptome sequencing reveals resistance of TLR4 ligand-activated bone marrow-derived macrophages to inflammation mediated by the BET inhibitor JQ1. Sci Rep 2015; 5:16932. [PMID: 26582142 PMCID: PMC4652239 DOI: 10.1038/srep16932] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 10/05/2015] [Indexed: 01/08/2023] Open
Abstract
Persistent macrophage activation is associated with the expression of various pro-inflammatory genes, cytokines and chemokines, which may initiate or amplify inflammatory disorders. A novel synthetic BET inhibitor, JQ1, was proven to exert immunosuppressive activities in macrophages. However, a genome-wide search for JQ1 molecular targets has not been undertaken. The present study aimed at evaluating the anti-inflammatory function and underlying genes that are targeted by JQ1 in LPS-stimulated primary bone marrow-derived macrophages (BMDMs) using global transcriptomic RNA sequencing and quantitative real-time PCR. Among the annotated genes, transcriptional sequencing of BMDMs that were treated with JQ1 revealed a selective effect on LPS-induced gene expression in which the induction of cytokines/chemokines, interferon-stimulated genes, and prominent (transcription factors) TFs was suppressed. Additionally, we found that JQ1 reduced the expression of previously unidentified genes that are important in inflammation. Importantly, these inflammatory genes were not affected by JQ1 treatment alone. Furthermore, we confirmed that JQ1 reduced cytokines/chemokines in the supernatants of LPS treated BMDMs. Moreover, the biological pathways and gene ontology of the differentially expressed genes were determined in the JQ1 treatment of BMDMs. These unprecedented results suggest that the BET inhibitor JQ1 is a candidate for the prevention or therapeutic treatment of inflammatory disorders.
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Affiliation(s)
- Amitabh Das
- Department of Bionanotechnology, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Jin Choul Chai
- Department of Molecular &Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Chul-Su Yang
- Department of Molecular &Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Young Seek Lee
- Department of Molecular &Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Nando Dulal Das
- Epigenetics Drug Discovery Unit, Division of Structural &Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Yokohama 230-0045, Japan
| | - Kyoung Hwa Jung
- Institute of Natural Science &Technology, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Young Gyu Chai
- Department of Bionanotechnology, Hanyang University, Seoul, 133-791, Republic of Korea.,Department of Molecular &Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea
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Xu W, Jiang K, Shen M, Chen Y, Huang HY. Jumonji domain containing 2A predicts prognosis and regulates cell growth in lung cancer depending on miR-150. Oncol Rep 2015; 35:352-8. [PMID: 26498874 DOI: 10.3892/or.2015.4349] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/20/2015] [Indexed: 11/06/2022] Open
Abstract
Lung cancer has become the most common cancer worldwide, of which non-small cell lung cancer (NSCLC) accounts for over 80%. Previous studies have shown that the Jumonji domain containing 2A (JMJD2A) was aberrantly expressed in various tumors and involved in the regulation of tumor progression, but the role of JMJD2A on the tumorigenesis in NSCLC and the underlying mechanisms are still unclear. In the present study, we first identified the expression of JMJD2A in NSCLC tissues and cell lines through quantitative RT-PCR (qRT-PCR) and western blotting. Next, the effects of JMJD2A on the progression of NSCLC were analyzed. MTT assay was performed to measure the cell numbers and fluorescence-activated cell sorting (FACS) was adopted to evaluate cell apoptosis. Finally, the relationship between JMJD2A and miR-150 involved in NSCLC was studied. Our results suggested that JMJD2A was significantly overexpressed in NSCLC samples and cell lines. Kaplan-Meier analysis showed that high level of JMJD2A predicted a poor prognosis. Knockdown of JMJD2A inhibited tumor growth and promoted cell apoptosis in NSCLC cells. Additionally, miR-150 was upregulated in NSCLC tissues and positively related with JMJD2A expression. Significant downregulation of miR-150 was observed with JMJD2A knockdown. Furthermore, JMJD2A knockdown inhibited NSCLC cell proliferation while the silencing of miR-150 attenuated the inhibition effect on cell proliferation, suggesting that the effect of JMJD2A on NSCLC cell growth was dependent on miR-150. Thus, our findings identified that JMJD2A played an oncogenic role in NSCLC via regulating miR-150. JMJD2A could possibly serve as a prognostic factor and potential target for NSCLC therapy.
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Affiliation(s)
- Weihua Xu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Kanqiu Jiang
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Mingjing Shen
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Yongbing Chen
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Hao-Yue Huang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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Das A, Chai JC, Kim SH, Lee YS, Park KS, Jung KH, Chai YG. Transcriptome sequencing of microglial cells stimulated with TLR3 and TLR4 ligands. BMC Genomics 2015; 16:517. [PMID: 26159724 PMCID: PMC4497376 DOI: 10.1186/s12864-015-1728-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 06/26/2015] [Indexed: 01/07/2023] Open
Abstract
Background Resident macrophages in the CNS microglia become activated and produce proinflammatory molecules upon encountering bacteria or viruses. TLRs are a phylogenetically conserved diverse family of sensors that drive innate immune responses following interactions with PAMPs. TLR3 and TLR4 recognize viral dsRNA Poly (I:C) and bacterial endotoxin LPS, respectively. Importantly, these receptors differ in their downstream adaptor molecules. Thus far, only a few studies have investigated the effects of TLR3 and TLR4 in macrophages. However, a genome-wide search for the effects of these TLRs has not been performed in microglia using RNA-seq. Gene expression patterns were determined for the BV-2 microglial cell line when stimulated with viral dsRNA Poly (I:C) or bacterial endotoxin LPS to identify novel transcribed genes, as well as investigate how differences in downstream signaling could influence gene expression in innate immunity. Results Sequencing assessment and quality evaluation revealed that common and unique patterns of proinflammatory genes were significantly up-regulated in response to TLR3 and TLR4 stimulation. However, the IFN/viral response gene showed a stronger response to TLR3 stimulation than to TLR4 stimulation. Unexpectedly, TLR3 and TLR4 stimulation did not activate IFN-ß and IRF3 in BV-2 microglia. Most importantly, we observed that previously unidentified transcription factors (TFs) (i.e., IRF1, IRF7, and IRF9) and the epigenetic regulators KDM4A and DNMT3L were significantly up-regulated in both TLR3- and TLR4-stimulated microglia. We also identified 29 previously unidentified genes that are important in immune regulation. In addition, we confirmed the expressions of key inflammatory genes as well as pro-inflammatory mediators in the supernatants were significantly induced in TLR3-and TLR4-stimulated primary microglial cells. Moreover, transcriptional start sites (TSSs) and isoforms, as well as differential promoter usage, revealed a complex pattern of transcriptional and post-transcriptional gene regulation upon infection with TLR3 and TLR4. Furthermore, TF motif analysis (-950 to +50 bp of the 5′ upstream promoters) revealed that the DNA sequences for NF-κB, IRF1, and STAT1 were significantly enriched in TLR3- and TLR4-stimulated microglia. Conclusions These unprecedented findings not only permit a comparison of TLR3-and TLR4-stimulated genes but also identify new genes that have not been previously implicated in innate immunity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1728-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amitabh Das
- Department of Bionanotechnology, Hanyang University, Seoul, 133-791, Republic of Korea.
| | - Jin Choul Chai
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea.
| | - Sun Hwa Kim
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea.
| | - Young Seek Lee
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea.
| | - Kyoung Sun Park
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea.
| | - Kyoung Hwa Jung
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea. .,Institute of Natural Science & Technology, Hanyang University, Ansan, 426-791, South Korea.
| | - Young Gyu Chai
- Department of Bionanotechnology, Hanyang University, Seoul, 133-791, Republic of Korea. .,Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea.
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Dual RNA sequencing reveals the expression of unique transcriptomic signatures in lipopolysaccharide-induced BV-2 microglial cells. PLoS One 2015; 10:e0121117. [PMID: 25811458 PMCID: PMC4374676 DOI: 10.1371/journal.pone.0121117] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/28/2015] [Indexed: 11/26/2022] Open
Abstract
Microglial cells become rapidly activated through interactions with pathogens, and the persistent activation of these cells is associated with various neurodegenerative diseases. Previous studies have investigated the transcriptomic signatures in microglia or macrophages using microarray technologies. However, this method has numerous restrictions, such as spatial biases, uneven probe properties, low sensitivity, and dependency on the probes spotted. To overcome this limitation and identify novel transcribed genes in response to LPS, we used RNA Sequencing (RNA-Seq) to determine the novel transcriptomic signatures in BV-2 microglial cells. Sequencing assessment and quality evaluation showed that approximately 263 and 319 genes (≥ 1.5 log2-fold), such as cytokines and chemokines, were strongly induced after 2 and 4 h, respectively, and the induction of several genes with unknown immunological functions was also observed. Importantly, we observed that previously unidentified transcription factors (TFs) (irf1, irf7, and irf9), histone demethylases (kdm4a) and DNA methyltransferases (dnmt3l) were significantly and selectively expressed in BV-2 microglial cells. The gene expression levels, transcription start sites (TSS), isoforms, and differential promoter usage revealed a complex pattern of transcriptional and post-transcriptional gene regulation upon infection with LPS. In addition, gene ontology, molecular networks and pathway analyses identified the top significantly regulated functional classification, canonical pathways and network functions at each activation status. Moreover, we further analyzed differentially expressed genes to identify transcription factor (TF) motifs (−950 to +50 bp of the 5’ upstream promoters) and epigenetic mechanisms. Furthermore, we confirmed that the expressions of key inflammatory genes as well as pro-inflammatory mediators in the supernatants were significantly induced in LPS treated primary microglial cells. This transcriptomic analysis is the first to show a comparison of the family-wide differential expression of most known immune genes and also reveal transcription evidence of multiple gene families in BV-2 microglial cells. Collectively, these findings reveal unique transcriptomic signatures in BV-2 microglial cells required for homeostasis and effective immune responses.
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