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Bresser K, Popović B, Wolkers MC. What's in a name: the multifaceted function of DNA- and RNA-binding proteins in T cell responses. FEBS J 2025; 292:1853-1867. [PMID: 39304985 PMCID: PMC12001178 DOI: 10.1111/febs.17273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/12/2024] [Accepted: 09/02/2024] [Indexed: 04/17/2025]
Abstract
Cellular differentiation allows cells to transition between different functional states and adapt to various environmental cues. The diversity and plasticity of this process is beautifully exemplified by T cells responding to pathogens, which undergo highly specialized differentiation tailored to the ongoing infection. Such antigen-induced T cell differentiation is regulated at the transcriptional level by DNA-binding proteins and at the post-transcriptional level by RNA-binding proteins. Although traditionally defined as separate protein classes, a growing body of evidence indicates an overlap between these two groups of proteins, collectively coined DNA/RNA-binding proteins (DRBPs). In this review, we describe how DRBPs might bind both DNA and RNA, discuss the putative functional relevance of this dual binding, and provide an exploratory analysis into characteristics that are associated with DRBPs. To exemplify the significance of DRBPs in T cell biology, we detail the activity of several established and putative DRBPs during the T cell response. Finally, we highlight several methodologies that allow untangling of the distinct functionalities of DRBPs at the DNA and RNA level, including key considerations to take into account when applying such methods.
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Affiliation(s)
- Kaspar Bresser
- T Cell Differentiation Lab, Department of ResearchSanquin Blood Supply FoundationAmsterdamThe Netherlands
- Landsteiner LaboratoryAmsterdam UMC, University of AmsterdamThe Netherlands
- Cancer Immunology, Cancer Center AmsterdamAmsterdam Institute for Infection & ImmunityThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Branka Popović
- T Cell Differentiation Lab, Department of ResearchSanquin Blood Supply FoundationAmsterdamThe Netherlands
- Landsteiner LaboratoryAmsterdam UMC, University of AmsterdamThe Netherlands
- Cancer Immunology, Cancer Center AmsterdamAmsterdam Institute for Infection & ImmunityThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- T Cell Differentiation Lab, Department of ResearchSanquin Blood Supply FoundationAmsterdamThe Netherlands
- Landsteiner LaboratoryAmsterdam UMC, University of AmsterdamThe Netherlands
- Cancer Immunology, Cancer Center AmsterdamAmsterdam Institute for Infection & ImmunityThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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2
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Sun D, Cui X, Yang W, Wei M, Yan Z, Zhang M, Yu W. Simvastatin inhibits PD-L1 via ILF3 to induce ferroptosis in gastric cancer cells. Cell Death Dis 2025; 16:208. [PMID: 40140647 PMCID: PMC11947124 DOI: 10.1038/s41419-025-07562-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 03/09/2025] [Accepted: 03/18/2025] [Indexed: 03/28/2025]
Abstract
The treatment of gastric cancer remains challenging, with immunotherapy serving as a critical component of the holistic approach to its treatment. The results of this study indicated that statins could decrease the serum levels of interleukin-enhancing binding factor 3 (ILF3) and programmed cell death ligand 1(PD-L1) in GC patients and improve their prognosis. Functional experiments demonstrated that simvastatin induced ferroptosis by inhibiting ILF3 in GC cells and enhanced the killing effect of activated CD8+ T cells on GC cells. The CUT&Tag assay revealed that, mechanistically, simvastatin inhibited ILF3 expression by reducing the acetylation level at residue site H3K14 in ILF3. Next-generation sequencing and Kyoto Encyclopedia of Genes and Genomes analysis revealed that ILF3 regulated PD-L1 expression through the DEPTOR/mTOR signaling pathway. Overall, simvastatin induced ferroptosis in GC cells by inhibiting ILF3 expression while promoting the activation of CD8+ T cells to augment antitumor immune responses, thereby facilitating synergistic immunotherapy.
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Affiliation(s)
- Danping Sun
- Department of Gastrointestinal Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Xiaohan Cui
- Department of Gastrointestinal Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Wenshuo Yang
- Department of Gastrointestinal Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Meng Wei
- Department of Gastrointestinal Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Zhibo Yan
- Department of Gastrointestinal Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Mingxiang Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, Department of Cardiology, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Wenbin Yu
- Department of Gastrointestinal Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wen Hua Road, Jinan, 250012, China.
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3
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Zhou M, Yin X, Zhang L, Cui Z, Jiang X, Ji Q, Ma S, Chen C. RNA-Binding Protein Lin28B Promotes Chronic Myeloid Leukemia Blast Crisis by Transcriptionally Upregulating miR-181d. Mol Cancer Res 2024; 22:932-942. [PMID: 38847604 DOI: 10.1158/1541-7786.mcr-23-0928] [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: 11/07/2023] [Revised: 04/05/2024] [Accepted: 06/04/2024] [Indexed: 10/03/2024]
Abstract
The blast crisis (BC) of chronic myeloid leukemia (CML) has poor efficacy against existing treatments and extremely short survival. However, the molecular mechanism of CML-chronic phase (CP) transformation to CML-BC is not yet fully understood. Here, we show that Lin28B, an RNA-binding protein, acted as an activator enhancing the transformation to CML-BC by mediating excessive cell proliferation. The level of Lin28B expression was apparently elevated in patients with CML-BC compared with newly diagnosed patients with CML-CP. The overexpression of Lin28B promoted the proliferation of leukemia cells. Mechanistically, we identified Lin28B as a DNA-binding protein by binding to the promoter region of miR-181d and upregulating its expression, which inhibited the expression of programmed cell death 4 (PDCD4) by binding to the PDCD4 3'UTR region, thereby enhancing the proliferation of CML cells. Overall, the "Lin28B-miR-181d-PDCD4" regulatory axis promoted CML blast crisis. Implications: Our findings highlight the oncogenic role of Lin28B in CML blast crisis, acting as a DNA-binding protein that transcriptionally upregulates miR-181d expression.
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MESH Headings
- Humans
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/genetics
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Blast Crisis/genetics
- Blast Crisis/pathology
- Blast Crisis/metabolism
- Up-Regulation
- Cell Proliferation/genetics
- Mice
- Cell Line, Tumor
- Animals
- Apoptosis Regulatory Proteins/genetics
- Apoptosis Regulatory Proteins/metabolism
- Gene Expression Regulation, Leukemic
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Affiliation(s)
- Minran Zhou
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, P.R. China
| | - Xiaolin Yin
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, P.R. China
| | - Lu Zhang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, P.R. China
| | - Zelong Cui
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, P.R. China
| | - Xinwen Jiang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, P.R. China
| | - Qingli Ji
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, P.R. China
| | - Sai Ma
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, P.R. China
| | - Chunyan Chen
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, P.R. China
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4
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Nilsson M, Kozyrev SV, Saellström S, Johansson S, Andersson G, Lindblad-Toh K, Hansson-Hamlin H, Rönnberg H. Elevated levels of IL-12/IL-23p40 in Nova Scotia Duck Tolling Retrievers with autoimmune disease and lymphoma. Sci Rep 2024; 14:11624. [PMID: 38773194 PMCID: PMC11109178 DOI: 10.1038/s41598-024-62265-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 05/15/2024] [Indexed: 05/23/2024] Open
Abstract
The Nova Scotia Duck Tolling Retriever (NSDTR) is predisposed to immune mediated rheumatic disease (IMRD), steroid-responsive meningitis-arteritis (SRMA) and certain forms of cancer. Cytokines are the main regulators of the immune system. Interleukin 2 is a cytokine involved in activation of T regulatory cells, playing a role in central tolerance and tumor immunity. Interleukin 12 and interleukin 23 share the same subunit, p40, and are both pro-inflammatory cytokines. The aim of this study was to compare levels of IL-2 in healthy NSDTRs to those with cancer or autoimmune disease and to compare levels of IL-12/IL-23p40 in healthy NSDTRs and beagles versus NSDTRs with cancer or autoimmune disease. 62 dogs were included in the analysis of IL-12/IL-23p40; healthy NSDTRs (n = 16), healthy beagles (n = 16), NSDTRs autoimmune (n = 18) and NDSTRs lymphoma/mastocytoma (n = 12) and 68 dogs for IL-2; healthy (n = 20), autoimmune (n = 36) and lymphoma/mastocytoma/adenocarcinoma (n = 12). NSDTRs with autoimmune disease had higher levels of IL-12/IL-23p40 compared to healthy dogs (p = 0.008). NSDTRs with lymphoma also had higher levels of IL-12/IL-23p40 compared to healthy NSDTRs (p = 0.002). There was no difference in levels of IL-2 between healthy and diseased NSDTR. Statistical analysis was performed using Bonferroni corrections for multiple testing. These findings can contribute to the knowledge of autoimmune disease and cancer in dogs.
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Affiliation(s)
- Malin Nilsson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Sergey V Kozyrev
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Sara Saellström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Siri Johansson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Anicura Kalmarsund Animal Hospital, Kalmar, Sweden
| | - Göran Andersson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Helene Hansson-Hamlin
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Henrik Rönnberg
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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5
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Wang Z, Zhang C, Fan C, Liu Y. Post-translational modifications in stress granule and their implications in neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194989. [PMID: 37751804 DOI: 10.1016/j.bbagrm.2023.194989] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/21/2023] [Accepted: 09/21/2023] [Indexed: 09/28/2023]
Abstract
Stress granules (SGs) arise as formations of mRNAs and proteins in response to translation initiation inhibition during stress. These dynamic compartments adopt a fluidic nature through liquid-liquid phase separation (LLPS), exhibiting a composition subject to constant change within cellular contexts. Research has unveiled an array of post-translational modifications (PTMs) occurring on SG proteins, intricately orchestrating SG dynamics. In the realm of neurodegenerative diseases, pathological mutant proteins congregate into insoluble aggregates alongside numerous SG proteins, manifesting resilience against disassembly. Specific PTMs conspicuously label these aggregates, designating them for subsequent degradation. The strategic manipulation of aberrant SGs via PTMs emerges as a promising avenue for therapeutic intervention. This review discerns recent strides in comprehending the impact of PTMs on LLPS behavior and the assembly/disassembly kinetics of SGs. By delving into the roles of PTMs in governing SG dynamics, we augment our cognizance of the molecular underpinnings of neurodegeneration. Furthermore, we offer invaluable insights into potential targets for therapeutic intervention in neurodegenerative afflictions, encompassing conditions like amyotrophic lateral sclerosis and frontotemporal dementia.
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Affiliation(s)
- Zhangshun Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chen'ang Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chengyu Fan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yanfen Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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6
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Koh D, Bin Jeon H, Oh C, Noh JH, Kim KM. RNA-binding proteins in cellular senescence. Mech Ageing Dev 2023; 214:111853. [PMID: 37453659 DOI: 10.1016/j.mad.2023.111853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Cellular senescence is a state of irreversible cell cycle arrest that is triggered and controlled by various external and/or internal factors. Among them, the regulation of senescence-associated genes is an important molecular event that plays a role in senescence. The regulation of gene expression can be achieved by various types of modulating mechanisms, and RNA-binding proteins (RBPs) are commonly known as critical regulators targeting a global range of transcripts. RBPs bind to RNA-binding motifs of the target transcripts and are involved in post-transcriptional processes such as RNA transport, stabilization, splicing, and decay. These RBPs may also play critical roles in cellular senescence by regulating the expression of senescence-associated genes. The biological functions of RBPs in controlling cellular senescence are being actively studied. Herein, we summarized the RBPs that influence cellular senescence, particularly by regulating processes such as the senescence-associated secretory phenotype, cell cycle, and mitochondrial function.
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Affiliation(s)
- Dahyeon Koh
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, South Korea
| | - Hyeong Bin Jeon
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, South Korea
| | - Chaehwan Oh
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, South Korea
| | - Ji Heon Noh
- Department of Biochemistry, Chungnam National University, Daejeon 34134, South Korea
| | - Kyoung Mi Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, South Korea.
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7
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Zhang JJ, Shen Y, Chen XY, Jiang ML, Yuan FH, Xie SL, Zhang J, Xu F. Integrative network-based analysis on multiple Gene Expression Omnibus datasets identifies novel immune molecular markers implicated in non-alcoholic steatohepatitis. Front Endocrinol (Lausanne) 2023; 14:1115890. [PMID: 37008925 PMCID: PMC10061151 DOI: 10.3389/fendo.2023.1115890] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/02/2023] [Indexed: 03/17/2023] Open
Abstract
Introduction Non-alcoholic steatohepatitis (NASH), an advanced subtype of non-alcoholic fatty liver disease (NAFLD), has becoming the most important aetiology for end-stage liver disease, such as cirrhosis and hepatocellular carcinoma. This study were designed to explore novel genes associated with NASH. Methods Here, five independent Gene Expression Omnibus (GEO) datasets were combined into a single cohort and analyzed using network biology approaches. Results 11 modules identified by weighted gene co-expression network analysis (WGCNA) showed significant association with the status of NASH. Further characterization of four gene modules of interest demonstrated that molecular pathology of NASH involves the upregulation of hub genes related to immune response, cholesterol and lipid metabolic process, extracellular matrix organization, and the downregulation of hub genes related to cellular amino acid catabolic, respectively. After DEGs enrichment analysis and module preservation analysis, the Turquoise module associated with immune response displayed a remarkably correlation with NASH status. Hub genes with high degree of connectivity in the module, including CD53, LCP1, LAPTM5, NCKAP1L, C3AR1, PLEK, FCER1G, HLA-DRA and SRGN were further verified in clinical samples and mouse model of NASH. Moreover, single-cell RNA-seq analysis showed that those key genes were expressed by distinct immune cells such as microphages, natural killer, dendritic, T and B cells. Finally, the potential transcription factors of Turquoise module were characterized, including NFKB1, STAT3, RFX5, ILF3, ELF1, SPI1, ETS1 and CEBPA, the expression of which increased with NASH progression. Discussion In conclusion, our integrative analysis will contribute to the understanding of NASH and may enable the development of potential biomarkers for NASH therapy.
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Affiliation(s)
- Jun-jie Zhang
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Yan Shen
- Department of Publication Health and Health Management, Gannan Medical University, Ganzhou, China
| | - Xiao-yuan Chen
- Department of Publication Health and Health Management, Gannan Medical University, Ganzhou, China
| | - Man-lei Jiang
- Department of Hepatology, The Affiliated Fifth People’s Hospital of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Feng-hua Yuan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Shui-lian Xie
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Jie Zhang
- Department of Hepatology, The Affiliated Fifth People’s Hospital of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Fei Xu
- Department of Hepatology, The Affiliated Fifth People’s Hospital of Ganzhou, Gannan Medical University, Ganzhou, China
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8
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Afsari F, McIntyre TM. D-2-Hydroxyglutarate Inhibits Calcineurin Phosphatase Activity to Abolish NF-AT Activation and IL-2 Induction in Stimulated Lymphocytes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:504-514. [PMID: 36602551 PMCID: PMC11071645 DOI: 10.4049/jimmunol.2200050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023]
Abstract
Gliomas expressing mutant isocitrate dehydrogenases excessively synthesize d-2-hydroxyglutarate (D2HG), suppressing immune surveillance. A portion of this D2HG is released from these tumor cells, but the way environmental D2HG inhibits lymphocyte function is undefined. We incubated human PBLs or Jurkat T cells with D2HG at concentrations present within and surrounding gliomas or its obverse l-2-hydroxyglutarate (L2HG) stereoisomer. We quantified each 2HG stereoisomer within washed cells by N-(p-toluenesulfonyl)-l-phenylalanyl chloride derivatization with stable isotope-labeled D2HG and L2HG internal standards, HPLC separation, and mass spectrometry. D2HG was present in quiescent cells and was twice as abundant as L2HG. Extracellular 2HG rapidly increased intracellular levels of the provided stereoisomer by a stereoselective, concentration-dependent process. IL-2 expression, even when elicited by A23187 and PMA, was abolished by D2HG in a concentration-dependent manner, with significant reduction at just twice its basal level. In contrast, L2HG was only moderately inhibitory. IL-2 expression is regulated by increased intracellular Ca2+ that stimulates calcineurin to dephosphorylate cytoplasmic phospho-NF-AT, enabling its nuclear translocation. D2HG abolished stimulated expression of a stably integrated NF-AT-driven luciferase reporter that precisely paralleled its concentration-dependent inhibition of IL-2. D2HG did not affect intracellular Ca2+. Rather, surface plasmon resonance showed D2HG, but not L2HG, bound calcineurin, and D2HG, but not L2HG, inhibited Ca2+-dependent calcineurin phosphatase activity in stimulated Jurkat extracts. Thus, D2HG is a stereoselective calcineurin phosphatase inhibitor that prevents NF-AT dephosphorylation and so abolishes IL-2 transcription in stimulated lymphocytes. This occurs at D2HG concentrations found within and adjacent to gliomas independent of its metabolic or epigenetic transcriptional regulation.
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Affiliation(s)
- Faezeh Afsari
- Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
| | - Thomas M. McIntyre
- Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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9
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Korn SM, Von Ehr J, Dhamotharan K, Tants JN, Abele R, Schlundt A. Insight into the Structural Basis for Dual Nucleic Acid-Recognition by the Scaffold Attachment Factor B2 Protein. Int J Mol Sci 2023; 24:ijms24043286. [PMID: 36834708 PMCID: PMC9958909 DOI: 10.3390/ijms24043286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
The family of scaffold attachment factor B (SAFB) proteins comprises three members and was first identified as binders of the nuclear matrix/scaffold. Over the past two decades, SAFBs were shown to act in DNA repair, mRNA/(l)ncRNA processing and as part of protein complexes with chromatin-modifying enzymes. SAFB proteins are approximately 100 kDa-sized dual nucleic acid-binding proteins with dedicated domains in an otherwise largely unstructured context, but whether and how they discriminate DNA and RNA binding has remained enigmatic. We here provide the SAFB2 DNA- and RNA-binding SAP and RRM domains in their functional boundaries and use solution NMR spectroscopy to ascribe DNA- and RNA-binding functions. We give insight into their target nucleic acid preferences and map the interfaces with respective nucleic acids on sparse data-derived SAP and RRM domain structures. Further, we provide evidence that the SAP domain exhibits intra-domain dynamics and a potential tendency to dimerize, which may expand its specifically targeted DNA sequence range. Our data provide a first molecular basis of and a starting point towards deciphering DNA- and RNA-binding functions of SAFB2 on the molecular level and serve a basis for understanding its localization to specific regions of chromatin and its involvement in the processing of specific RNA species.
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Affiliation(s)
- Sophie M. Korn
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Julian Von Ehr
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Karthikeyan Dhamotharan
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Jan-Niklas Tants
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Rupert Abele
- Institute for Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
- Correspondence:
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10
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Li P, Mi Q, Yan S, Xie Y, Cui Z, Zhang S, Wang Y, Gao H, Wang Y, Li J, Du L, Wang C. Characterization of circSCL38A1 as a novel oncogene in bladder cancer via targeting ILF3/TGF-β2 signaling axis. Cell Death Dis 2023; 14:59. [PMID: 36697384 PMCID: PMC9876890 DOI: 10.1038/s41419-023-05598-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023]
Abstract
The regulatory role of circRNAs in cancer metastasis has become a focused issue in recent years. To date, however, the discovery of novel functional circRNAs and their regulatory mechanisms via binding with RBPs in bladder cancer (BC) are still lacking. Here, we screened out circSLC38A1 based on our sequencing data and followed validation with clinical tissue samples and cell lines. Functional assays showed that circSLC38A1 promoted BC cell invasion in vitro and lung metastasis of mice in vivo. By conducting RNA pull-down, mass spectrum, and RIP assays, circSLC38A1 was found to interact with Interleukin enhancer-binding factor 3 (ILF3), and stabilize ILF3 protein via modulating the ubiquitination process. By integrating our CUT&Tag-seq and RNA-seq data, TGF-β2 was identified as the functional target of the circSLC38A1-ILF3 complex. In addition, m6A methylation was enriched in circSLC38A1 and contributed to its upregulation. Clinically, circSLC38A1 was identified in serum exosomes of BC patients and could distinguish BC patients from healthy individuals with a diagnostic accuracy of 0.878. Thus, our study revealed an essential role and clinical significance of circSLC38A1 in BC via activating the transcription of TGF-β2 in an ILF3-dependent manner, extending the understanding of the importance of circRNA-mediated transcriptional regulation in BC metastasis.
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Affiliation(s)
- Peilong Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
| | - Qi Mi
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China
| | - Suzhen Yan
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
| | - Yan Xie
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China
| | - Zilian Cui
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Shujun Zhang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China
| | - Yifan Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China
| | - Huiru Gao
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China
| | - Yunshan Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Juan Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China.
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China.
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China.
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China.
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China.
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China.
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China.
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China.
- Shandong Technology Innovation Center for Big Data and Precision Medicine of Cancer, Jinan, 250033, Shandong, China.
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11
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Patrick MT, Li Q, Wasikowski R, Mehta N, Gudjonsson JE, Elder JT, Zhou X, Tsoi LC. Shared genetic risk factors and causal association between psoriasis and coronary artery disease. Nat Commun 2022; 13:6565. [PMID: 36323703 PMCID: PMC9630428 DOI: 10.1038/s41467-022-34323-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Psoriasis and coronary artery disease (CAD) are related comorbidities that are well established, but whether a genetic basis underlies this is not well studied. We apply trans-disease meta-analysis to 11,024 psoriasis and 60,801 CAD cases, along with their associated controls, identifying one opposing and three shared genetic loci, which are confirmed through colocalization analysis. Combining results from Bayesian credible interval analysis with independent information from genomic, epigenomic, and spatial chromatin organization, we prioritize genes (including IFIH1 and IL23A) that have implications for common molecular mechanisms involved in psoriasis and CAD inflammatory signaling. Chronic systemic inflammation has been associated with CAD and myocardial infarction, and Mendelian randomization analysis finds that CAD as an exposure can have a significant causal effect on psoriasis (OR = 1.11; p = 3×10-6) following adjustment for BMI and waist-hip ratio. Together, these findings suggest that systemic inflammation which causes CAD can increase the risk of psoriasis.
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Affiliation(s)
- Matthew T Patrick
- Department of Dermatology, Michigan Medicine, University of Michigan, Michigan, MI, USA
| | - Qinmengge Li
- Department of Biostatistics, School of Public Health, University of Michigan, Michigan, MI, USA
| | - Rachael Wasikowski
- Department of Dermatology, Michigan Medicine, University of Michigan, Michigan, MI, USA
| | - Nehal Mehta
- Section of Inflammation and Cardiometabolic Disease, National Heart, Lung, and Blood Institute, National Institutes of Health, Michigan, MD, USA
| | - Johann E Gudjonsson
- Department of Dermatology, Michigan Medicine, University of Michigan, Michigan, MI, USA
| | - James T Elder
- Department of Dermatology, Michigan Medicine, University of Michigan, Michigan, MI, USA
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Michigan, MI, USA
| | - Lam C Tsoi
- Department of Dermatology, Michigan Medicine, University of Michigan, Michigan, MI, USA.
- Department of Biostatistics, School of Public Health, University of Michigan, Michigan, MI, USA.
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, University of Michigan, Michigan, MI, USA.
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12
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Xie F, Cui QK, Wang ZY, Liu B, Qiao W, Li N, Cheng J, Hou YM, Dong XY, Wang Y, Zhang MX. ILF3 is responsible for hyperlipidemia-induced arteriosclerotic calcification by mediating BMP2 and STAT1 transcription. J Mol Cell Cardiol 2021; 161:39-52. [PMID: 34343541 DOI: 10.1016/j.yjmcc.2021.07.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/01/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
Calcification is common in atherosclerotic plaque and can induce vulnerability, which further leads to myocardial infarction, plaque rupture and stroke. The mechanisms of atherosclerotic calcification are poorly characterized. Interleukin enhancer binding factor 3 (ILF3) has been identified as a novel factor affecting dyslipidemia and stroke subtypes. However, the precise role of ILF3 in atherosclerotic calcification remains unclear. In this study, we used smooth muscle-conditional ILF3 knockout (ILF3SM-KO) and transgenic mice (ILF3SM-Tg) and macrophage-conditional ILF3 knockout (ILF3M-KO) and transgenic (ILF3M-Tg) mice respectively. Here we showed that ILF3 expression is increased in calcified human aortic vascular smooth muscle cells (HAVSMCs) and calcified atherosclerotic plaque in humans and mice. We then found that hyperlipidemia increases ILF3 expression and exacerbates calcification of VSMCs and macrophages by regulating bone morphogenetic protein 2 (BMP2) and signal transducer and activator of transcription 1 (STAT1) transcription. We further explored the molecular mechanisms of ILF3 in atherosclerotic calcification and revealed that ILF3 acts on the promoter regions of BMP2 and STAT1 and mediates BMP2 upregulation and STAT1 downregulation, which promotes atherosclerotic calcification. Our results demonstrate the effect of ILF3 in atherosclerotic calcification. Inhibition of ILF3 may be a useful therapy for preventing and even reversing atherosclerotic calcification.
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Affiliation(s)
- Fei Xie
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qing-Ke Cui
- Department of Neurosurgery, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Zhao-Yang Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bin Liu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wen Qiao
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Na Li
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Cheng
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ya-Min Hou
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xin-Ying Dong
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ying Wang
- Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
| | - Ming-Xiang Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
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13
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Xie Y, Wang L, Sun H, Shang Q, Wang Y, Zhang G, Yang W, Jiang S. A polysaccharide extracted from alfalfa activates splenic B cells by TLR4 and acts primarily via the MAPK/p38 pathway. Food Funct 2021; 11:9035-9047. [PMID: 33021613 DOI: 10.1039/d0fo01711f] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Alfalfa polysaccharide (APS) has been proposed to exhibit growth-promoting and immune-enhancing bodily functions in vivo. However, little is known about its downstream immunomodulatory and intrinsic molecular mechanisms. Herein, mouse splenic lymphocytes were isolated to characterize the immunomodulatory effects and molecular mechanisms of APS in vitro. The results demonstrated that APS selectively improved the cell viability and IgM production of B cells, but no effects on T cell viability or secretion of IL-2, IL-4 and IFN-γ were observed in vitro. The receptor blocking assay showed that TLR4 was the primary receptor involved in APS-mediated B cell activation, which was confirmed by the results obtained using C57BL/10ScNJ (TLR4 gene-deficient) mice. Moreover, APS activated the TLR4-MyD88 signaling pathway at the translational level by significantly increasing the protein expression of TLR4 and MyD88. Downstream pathway blocking assay demonstrated that both the MAPK and NF-κB pathways were involved in APS-induced B cell activation. Additionally, APS significantly enhanced the phosphorylation of p38, ERK, and JNK and activated the nuclear translocation of the NF-κB p65 subunit. Therefore, we concluded that APS specifically activates the immune functions of splenic B cells by TLR4, acting through the MAPK and NF-κB signaling pathways, and potently activates the p38 pathway.
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Affiliation(s)
- Yuhuai Xie
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Lixue Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Hua Sun
- Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, PR China
| | - Qinghui Shang
- Department of Animal Science and Technology, China Agricultural University, Beijing, 100083, PR China
| | - Yuxi Wang
- Lethbridge Research Centre, Agriculture and Agri-Food C, anadaLethbridge, Alberta T1J 4B1, Canada
| | - Guiguo Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Weiren Yang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Shuzhen Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
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14
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Dou S, Li G, Li G, Hou C, Zheng Y, Tang L, Gao Y, Mo R, Li Y, Wang R, Shen B, Zhang J, Han G. Ubiquitination and degradation of NF90 by Tim-3 inhibits antiviral innate immunity. eLife 2021; 10:66501. [PMID: 34110282 PMCID: PMC8225388 DOI: 10.7554/elife.66501] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022] Open
Abstract
Nuclear factor 90 (NF90) is a novel virus sensor that serves to initiate antiviral innate immunity by triggering stress granule (SG) formation. However, the regulation of the NF90-SG pathway remains largely unclear. We found that Tim-3, an immune checkpoint inhibitor, promotes the ubiquitination and degradation of NF90 and inhibits NF90-SG-mediated antiviral immunity. Vesicular stomatitis virus (VSV) infection induces the up-regulation and activation of Tim-3 in macrophages, which in turn recruit the E3 ubiquitin ligase TRIM47 to the zinc finger domain of NF90 and initiate a proteasome-dependent degradation via K48-linked ubiquitination at Lys297. Targeted inactivation of Tim-3 enhances the NF90 downstream SG formation by selectively increasing the phosphorylation of protein kinase R and eukaryotic translation initiation factor 2α, the expression of SG markers G3BP1 and TIA-1, and protecting mice from VSV challenge. These findings provide insights into the crosstalk between Tim-3 and other receptors in antiviral innate immunity and its related clinical significance.
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Affiliation(s)
- Shuaijie Dou
- Beijing Institute of Basic Medical Sciences, Beijing, China.,Anhui Medical University, Hefei, China
| | - Guoxian Li
- Beijing Institute of Basic Medical Sciences, Beijing, China.,Institute of Immunology, Medical School of Henan University, Kaifeng, China
| | - Ge Li
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Chunmei Hou
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yang Zheng
- Department of Oncology, First Hospital of Jilin University, Changchun, China
| | - Lili Tang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yang Gao
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Rongliang Mo
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yuxiang Li
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Renxi Wang
- Beijing Institute of Basic Medical Sciences, Beijing, China.,Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Beifen Shen
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jun Zhang
- Institute of Immunology, Medical School of Henan University, Kaifeng, China
| | - Gencheng Han
- Beijing Institute of Basic Medical Sciences, Beijing, China
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15
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Nazitto R, Amon LM, Mast FD, Aitchison JD, Aderem A, Johnson JS, Diercks AH. ILF3 Is a Negative Transcriptional Regulator of Innate Immune Responses and Myeloid Dendritic Cell Maturation. THE JOURNAL OF IMMUNOLOGY 2021; 206:2949-2965. [PMID: 34031149 DOI: 10.4049/jimmunol.2001235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/31/2021] [Indexed: 12/31/2022]
Abstract
APCs such as myeloid dendritic cells (DCs) are key sentinels of the innate immune system. In response to pathogen recognition and innate immune stimulation, DCs transition from an immature to a mature state that is characterized by widespread changes in host gene expression, which include the upregulation of cytokines, chemokines, and costimulatory factors to protect against infection. Several transcription factors are known to drive these gene expression changes, but the mechanisms that negatively regulate DC maturation are less well understood. In this study, we identify the transcription factor IL enhancer binding factor 3 (ILF3) as a negative regulator of innate immune responses and DC maturation. Depletion of ILF3 in primary human monocyte-derived DCs led to increased expression of maturation markers and potentiated innate responses during stimulation with viral mimetics or classic innate agonists. Conversely, overexpression of short or long ILF3 isoforms (NF90 and NF110) suppressed DC maturation and innate immune responses. Through mutagenesis experiments, we found that a nuclear localization sequence in ILF3, and not its dual dsRNA-binding domains, was required for this function. Mutation of the domain associated with zinc finger motif of ILF3's NF110 isoform blocked its ability to suppress DC maturation. Moreover, RNA-sequencing analysis indicated that ILF3 regulates genes associated with cholesterol homeostasis in addition to genes associated with DC maturation. Together, our data establish ILF3 as a transcriptional regulator that restrains DC maturation and limits innate immune responses through a mechanism that may intersect with lipid metabolism.
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Affiliation(s)
- Rodolfo Nazitto
- Department of Immunology, University of Washington School of Medicine, Seattle, WA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Lynn M Amon
- Center for Infectious Disease Research, Seattle, WA; and
| | - Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Alan Aderem
- Department of Immunology, University of Washington School of Medicine, Seattle, WA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Jarrod S Johnson
- Center for Infectious Disease Research, Seattle, WA; and.,Department of Biochemistry, University of Utah, Salt Lake City, UT
| | - Alan H Diercks
- Department of Immunology, University of Washington School of Medicine, Seattle, WA;
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16
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Freen-van Heeren JJ. Post-transcriptional control of T-cell cytokine production: Implications for cancer therapy. Immunology 2021; 164:57-72. [PMID: 33884612 DOI: 10.1111/imm.13339] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/22/2021] [Accepted: 03/30/2021] [Indexed: 01/05/2023] Open
Abstract
As part of the adaptive immune system, T cells are vital for the eradication of infected and malignantly transformed cells. To perform their protective function, T cells produce effector molecules that are either directly cytotoxic, such as granzymes, perforin, interferon-γ and tumour necrosis factor α, or attract and stimulate (immune) cells, such as interleukin-2. As these molecules can also induce immunopathology, tight control of their production is required. Indeed, inflammatory cytokine production is regulated on multiple levels. Firstly, locus accessibility and transcription factor availability and activity determine the amount of mRNA produced. Secondly, post-transcriptional mechanisms, influencing mRNA splicing/codon usage, stability, decay, localization and translation rate subsequently determine the amount of protein that is produced. In the immune suppressive environments of tumours, T cells gradually lose the capacity to produce effector molecules, resulting in tumour immune escape. Recently, the role of post-transcriptional regulation in fine-tuning T-cell effector function has become more appreciated. Furthermore, several groups have shown that exhausted or dysfunctional T cells from cancer patients or murine models possess mRNA for inflammatory mediators, but fail to produce effector molecules, hinting that post-transcriptional events also play a role in hampering tumour-infiltrating lymphocyte effector function. Here, the post-transcriptional regulatory events governing T-cell cytokine production are reviewed, with a specific focus on the importance of post-transcriptional regulation in anti-tumour responses. Furthermore, potential approaches to circumvent tumour-mediated dampening of T-cell effector function through the (dis)engagement of post-transcriptional events are explored, such as CRISPR/Cas9-mediated genome editing or chimeric antigen receptors.
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17
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McKellar J, Rebendenne A, Wencker M, Moncorgé O, Goujon C. Mammalian and Avian Host Cell Influenza A Restriction Factors. Viruses 2021; 13:522. [PMID: 33810083 PMCID: PMC8005160 DOI: 10.3390/v13030522] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/27/2022] Open
Abstract
The threat of a new influenza pandemic is real. With past pandemics claiming millions of lives, finding new ways to combat this virus is essential. Host cells have developed a multi-modular system to detect incoming pathogens, a phenomenon called sensing. The signaling cascade triggered by sensing subsequently induces protection for themselves and their surrounding neighbors, termed interferon (IFN) response. This response induces the upregulation of hundreds of interferon-stimulated genes (ISGs), including antiviral effectors, establishing an antiviral state. As well as the antiviral proteins induced through the IFN system, cells also possess a so-called intrinsic immunity, constituted of antiviral proteins that are constitutively expressed, creating a first barrier preceding the induction of the interferon system. All these combined antiviral effectors inhibit the virus at various stages of the viral lifecycle, using a wide array of mechanisms. Here, we provide a review of mammalian and avian influenza A restriction factors, detailing their mechanism of action and in vivo relevance, when known. Understanding their mode of action might help pave the way for the development of new influenza treatments, which are absolutely required if we want to be prepared to face a new pandemic.
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Affiliation(s)
- Joe McKellar
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Antoine Rebendenne
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Mélanie Wencker
- Centre International de Recherche en Infectiologie, INSERM/CNRS/UCBL1/ENS de Lyon, 69007 Lyon, France;
| | - Olivier Moncorgé
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Caroline Goujon
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
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18
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Tsai H, Zeng X, Liu L, Xin S, Wu Y, Xu Z, Zhang H, Liu G, Bi Z, Su D, Yang M, Tao Y, Wang C, Zhao J, Eriksson JE, Deng W, Cheng F, Chen H. NF45/NF90-mediated rDNA transcription provides a novel target for immunosuppressant development. EMBO Mol Med 2021; 13:e12834. [PMID: 33555115 PMCID: PMC7933818 DOI: 10.15252/emmm.202012834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 12/26/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022] Open
Abstract
Herein, we demonstrate that NFAT, a key regulator of the immune response, translocates from cytoplasm to nucleolus and interacts with NF45/NF90 complex to collaboratively promote rDNA transcription via triggering the directly binding of NF45/NF90 to the ARRE2-like sequences in rDNA promoter upon T-cell activation in vitro. The elevated pre-rRNA level of T cells is also observed in both mouse heart or skin transplantation models and in kidney transplanted patients. Importantly, T-cell activation can be significantly suppressed by inhibiting NF45/NF90-dependent rDNA transcription. Amazingly, CX5461, a rDNA transcription-specific inhibitor, outperformed FK506, the most commonly used immunosuppressant, both in terms of potency and off-target activity (i.e., toxicity), as demonstrated by a series of skin and heart allograft models. Collectively, this reveals NF45/NF90-mediated rDNA transcription as a novel signaling pathway essential for T-cell activation and as a new target for the development of safe and effective immunosuppressants.
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Affiliation(s)
- Hsiang‐i Tsai
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Xiaobin Zeng
- Center Lab of Longhua Branch and Department of Infectious DiseaseShenzhen People's Hospital2 Clinical Medical College of Jinan UniversityShenzhenChina
- Guangdong Provincial Key Laboratory of Regional Immunity and DiseasesMedicine School of Shenzhen UniversityShenzhenChina
| | - Longshan Liu
- Organ Transplant CentermThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Shengchang Xin
- State Key Laboratory of Coordination ChemistryInstitute of Chemistry and Biomedical SciencesSchool of Life SciencesNanjing UniversityNanjingChina
| | - Yingyi Wu
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Zhanxue Xu
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Huanxi Zhang
- Organ Transplant CentermThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Gan Liu
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Zirong Bi
- Organ Transplant CentermThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Dandan Su
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Min Yang
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Yijing Tao
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Changxi Wang
- Organ Transplant CentermThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Jing Zhao
- State Key Laboratory of Coordination ChemistryInstitute of Chemistry and Biomedical SciencesSchool of Life SciencesNanjing UniversityNanjingChina
| | - John E Eriksson
- Cell BiologyBiosciencesFaculty of Science and EngineeringÅbo Akademi UniversityTurkuFinland
- Turku Centre for BiotechnologyUniversity of Turku and Åbo Akademi UniversityTurkuFinland
| | - Wenbin Deng
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Fang Cheng
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Hongbo Chen
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
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19
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Ding D, Huang H, Li Q, Yu W, Wang C, Ma H, Wu J, Dang Y, Yu L, Jiang W. NF90 stabilizes cyclin E1 mRNA through phosphorylation of NF90-Ser382 by CDK2. Cell Death Discov 2020; 6:3. [PMID: 32123579 PMCID: PMC7026180 DOI: 10.1038/s41420-020-0236-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/17/2019] [Accepted: 01/02/2020] [Indexed: 12/19/2022] Open
Abstract
Nuclear factor 90 (NF90), an RNA-binding protein, has been implicated in regulating interleukin-2 (IL-2) and the immune response. It was recently reported that NF90 is upregulated in hepatocellular carcinoma (HCC) tissues and promotes HCC proliferation through upregulating cyclin E1 at the posttranscription level. However, the regulation of NF90 in HCC remains unclear. We demonstrate here that cyclin-dependent kinase (CDK) 2 interacts with NF90 and phosphorylated it at serine382. Mechanistically, phosphorylation of NF90-Ser382 determines the nuclear export of NF90 and stabilization of cyclin E1 mRNA. We also demonstrate that the phosphorylation deficient mutant NF90-S382A inhibits cell growth and induces cell cycle arrest at the G1 phase in HCC cells. Moreover, an NF90-S382A xenograft tumor had a decreased size and weight compared with the wildtype NF90. The NF90-S382A xenograft contained a significantly lower level of the proliferation marker Ki-67. Additionally, in HCC patients, NF90-Ser382 phosphorylation was stronger in tumor than in non-tumor tissues. Clinically, phosphorylation of NF90-Ser382 is significantly associated with larger tumor sizes, higher AFP levels, and shorter overall survival rates. These results suggest NF90-Ser382 phosphorylation serves as a potential diagnosis and prognostic marker and a promising pharmacological target for HCC.
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Affiliation(s)
- Donglin Ding
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN USA
| | - Huixing Huang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Quanfu Li
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wenbo Yu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Chenji Wang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Haijie Ma
- Laboratory of Cytobiology and Molecular Biology, The Affiliated Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang China
| | - Jiaxue Wu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Long Yu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Wei Jiang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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20
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ILF3 is a substrate of SPOP for regulating serine biosynthesis in colorectal cancer. Cell Res 2019; 30:163-178. [PMID: 31772275 PMCID: PMC7015059 DOI: 10.1038/s41422-019-0257-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/02/2019] [Indexed: 01/22/2023] Open
Abstract
The Serine–Glycine–One-Carbon (SGOC) pathway is pivotal in multiple anabolic processes. Expression levels of SGOC genes are deregulated under tumorigenic conditions, suggesting participation of oncogenes in deregulating the SGOC biosynthetic pathway. However, the underlying mechanism remains elusive. Here, we identified that Interleukin enhancer-binding factor 3 (ILF3) is overexpressed in primary CRC patient specimens and correlates with poor prognosis. ILF3 is critical in regulating the SGOC pathway by directly regulating the mRNA stability of SGOC genes, thereby increasing SGOC genes expression and facilitating tumor growth. Mechanistic studies showed that the EGF–MEK–ERK pathway mediates ILF3 phosphorylation, which hinders E3 ligase speckle-type POZ protein (SPOP)-mediated poly-ubiquitination and degradation of ILF3. Significantly, combination of SGOC inhibitor and the anti-EGFR monoclonal antibody cetuximab can hinder the growth of patient-derived xenografts that sustain high ERK-ILF3 levels. Taken together, deregulation of ILF3 via the EGF–ERK signaling plays an important role in systemic serine metabolic reprogramming and confers a predilection toward CRC development. Our findings indicate that clinical evaluation of SGOC inhibitor is warranted for CRC patients with ILF3 overexpression.
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21
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Zhuang Q, Ye B, Hui S, Du Y, Zhao RC, Li J, Wu Z, Li N, Zhang Y, Li H, Wang S, Yang Y, Li S, Zhao H, Fan Z, Qiu G, Zhang J. Long noncoding RNA lncAIS downregulation in mesenchymal stem cells is implicated in the pathogenesis of adolescent idiopathic scoliosis. Cell Death Differ 2019; 26:1700-1715. [PMID: 30464226 PMCID: PMC6748078 DOI: 10.1038/s41418-018-0240-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 09/15/2018] [Accepted: 11/05/2018] [Indexed: 12/24/2022] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is a complex, three dimensional deformity of the spine that commonly occurs in pubescent girls. Abnormal osteogenic differentiation of mesenchymal stem cells (MSCs) is implicated in the pathogenesis of AIS. However, the biological roles of long noncoding RNAs (lncRNAs) in the regulation of osteogenic differentiation of MSCs are unknown. Through microarray analyses of bone marrow (BM) MSCs from healthy donors and AIS patients, we identified 1483 differentially expressed lncRNAs in AIS BM-MSCs. We defined a novel lncAIS (gene symbol: ENST00000453347) is dramatically downregulated in AIS BM-MSCs. In normal BM-MSCs, lncAIS interacts with NF90 to promote HOXD8 mRNA stability that enhances RUNX2 transcription in BM-MSCs, leading to osteogenic differentiation of normal BM-MSCs. By contrast, lncAIS downregualtion in AIS BM-MSCs cannot recruit NF90 and abrogates HOXD8 mRNA stability, which impedes RUNX2 transcription for osteogenic differentiation. Thereby lncAIS downregualtion in BM-MSCs suppresses osteogenic differentiation that is implicated in the pathogenesis of AIS.
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Affiliation(s)
- Qianyu Zhuang
- Department of Orthopedics, Peking Union Medical College Hospital, Beijing, P.R. China
| | - Buqing Ye
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shangyi Hui
- Department of Anesthesiolgy, Peking Union Medical College Hospital, Beijing, China
| | - Ying Du
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Robert Chunhua Zhao
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Li
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhihong Wu
- Department of Orthopedics, Peking Union Medical College Hospital, Beijing, P.R. China
| | - Na Li
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanbin Zhang
- Department of Orthopedics, Peking Union Medical College Hospital, Beijing, P.R. China
| | - Hongling Li
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences and School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shengru Wang
- Department of Orthopedics, Peking Union Medical College Hospital, Beijing, P.R. China
| | - Yang Yang
- Department of Orthopedics, Peking Union Medical College Hospital, Beijing, P.R. China
| | - Shugang Li
- Department of Orthopedics, Peking Union Medical College Hospital, Beijing, P.R. China
| | - Hong Zhao
- Department of Orthopedics, Peking Union Medical College Hospital, Beijing, P.R. China
| | - Zusen Fan
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Guixing Qiu
- Department of Orthopedics, Peking Union Medical College Hospital, Beijing, P.R. China
| | - Jianguo Zhang
- Department of Orthopedics, Peking Union Medical College Hospital, Beijing, P.R. China.
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22
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Guarnerio J, Zhang Y, Cheloni G, Panella R, Mae Katon J, Simpson M, Matsumoto A, Papa A, Loretelli C, Petri A, Kauppinen S, Garbutt C, Nielsen GP, Deshpande V, Castillo-Martin M, Cordon-Cardo C, Dimitrios S, Clohessy JG, Batish M, Pandolfi PP. Intragenic antagonistic roles of protein and circRNA in tumorigenesis. Cell Res 2019; 29:628-640. [PMID: 31209250 PMCID: PMC6796857 DOI: 10.1038/s41422-019-0192-1] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 05/23/2019] [Indexed: 01/28/2023] Open
Abstract
circRNAs arise from back splicing events during mRNA processing, and when deregulated can play an active role in cancer. Here we characterize a new circRNA (circPOK) encoded by the Zbtb7a gene (also kown as POKEMON, LRF) in the context of mesenchymal tumor progression. circPOK functions as a non-coding proto-oncogenic RNA independently and antithetically to its linear transcript counterpart, which acts as a tumor suppressor by encoding the Pokemon transcription factor. We find that circPOK regulates pro-proliferative and pro-angiogenic factors by co-activation of the ILF2/3 complex. Importantly, the expression of Pokemon protein and circRNA is aberrantly uncoupled in cancer through differential post-transcriptional regulation. Thus, we identify a novel type of genetic unit, the iRegulon, that yields biochemically distinct RNA products, circular and linear, with diverse and antithetical functions. Our findings further expand the cellular repertoire towards the control of normal biological outputs, while aberrant expression of such components may underlie disease pathogenesis including cancer.
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Affiliation(s)
- Jlenia Guarnerio
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Cedars-Sinai Medical Center, Department of Radiation Oncology, Samuel Oschin Comprehensive Cancer Center, Los Angeles, CA, 90048, USA
| | - Yang Zhang
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Giulia Cheloni
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Riccardo Panella
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jesse Mae Katon
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Mark Simpson
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, Newark, NJ, 07103, USA
| | - Akinobu Matsumoto
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Antonella Papa
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Cristian Loretelli
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark; Department of Hematology, Aalborg University Hospital, Aalborg, Denmark
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark; Department of Hematology, Aalborg University Hospital, Aalborg, Denmark
| | - Cassandra Garbutt
- MGH Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, New York, USA
| | | | - Vikram Deshpande
- MGH Center for Sarcoma and Connective Tissue Oncology, Department of Pathology, New York, USA
| | - Mireia Castillo-Martin
- Department of Pathology, Mount Sinai School of Medicine, The Mount Sinai Medical Center, New York, NY, 10029, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Mount Sinai School of Medicine, The Mount Sinai Medical Center, New York, NY, 10029, USA
| | - Spentzos Dimitrios
- MGH Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, New York, USA
| | - John G Clohessy
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, Newark, NJ, 07103, USA
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
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23
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Jia R, Ajiro M, Yu L, McCoy P, Zheng ZM. Oncogenic splicing factor SRSF3 regulates ILF3 alternative splicing to promote cancer cell proliferation and transformation. RNA (NEW YORK, N.Y.) 2019; 25:630-644. [PMID: 30796096 PMCID: PMC6467003 DOI: 10.1261/rna.068619.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/21/2019] [Indexed: 05/28/2023]
Abstract
Alternative RNA splicing is an important focus in molecular and clinical oncology. We report here that SRSF3 regulates alternative RNA splicing of interleukin enhancer binding factor 3 (ILF3) and production of this double-strand RNA-binding protein. An increased coexpression of ILF3 isoforms and SRSF3 was found in various types of cancers. ILF3 isoform-1 and isoform-2 promote cell proliferation and transformation. Tumor cells with reduced SRSF3 expression produce aberrant isoform-5 and -7 of ILF3. By binding to RNA sequence motifs, SRSF3 regulates the production of various ILF3 isoforms by exclusion/inclusion of ILF3 exon 18 or by selection of an alternative 3' splice site within exon 18. ILF3 isoform-5 and isoform-7 suppress tumor cell proliferation and the isoform-7 induces cell apoptosis. Our data indicate that ILF3 isoform-1 and isoform-2 are two critical factors for cell proliferation and transformation. The increased SRSF3 expression in cancer cells plays an important role in maintaining the steady status of ILF3 isoform-1 and isoform-2.
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Affiliation(s)
- Rong Jia
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Ke Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Masahiko Ajiro
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Lulu Yu
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Philip McCoy
- Flow Cytometry Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
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24
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Wu TH, Shi L, Lowe AW, Nicolls MR, Kao PN. Inducible expression of immediate early genes is regulated through dynamic chromatin association by NF45/ILF2 and NF90/NF110/ILF3. PLoS One 2019; 14:e0216042. [PMID: 31022259 PMCID: PMC6483252 DOI: 10.1371/journal.pone.0216042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 04/14/2019] [Indexed: 12/11/2022] Open
Abstract
Immediate early gene (IEG) transcription is rapidly activated by diverse stimuli. This transcriptional regulation is assumed to involve constitutively expressed nuclear factors that are targets of signaling cascades initiated at the cell membrane. NF45 (encoded by ILF2) and its heterodimeric partner NF90/NF110 (encoded by ILF3) are chromatin-interacting proteins that are constitutively expressed and localized predominantly in the nucleus. Previously, NF90/NF110 chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) in K562 erythroleukemia cells revealed its enriched association with chromatin at active promoters and strong enhancers. NF90/NF110 specifically occupied the promoters of IEGs. Here, ChIP in serum-starved HEK293 cells demonstrated that NF45 and NF90/NF110 pre-exist and specifically occupy the promoters of IEG transcription factors EGR1, FOS and JUN. Cellular stimulation with phorbol myristyl acetate increased NF90/NF110 chromatin association, while decreasing NF45 chromatin association at promoters of EGR1, FOS and JUN. In HEK293 cells stably transfected with doxycycline-inducible shRNA vectors targeting NF90/NF110 or NF45, doxycycline-mediated knockdown of NF90/NF110 or NF45 attenuated the inducible expression of EGR1, FOS, and JUN at the levels of transcription, RNA and protein. Dynamic chromatin association of NF45 and NF90/NF110 at IEG promoters are observed upon stimulation, and NF45 and NF90/NF110 contribute to inducible transcription of IEGs. NF45 and NF90/NF110 operate as chromatin regulators of the immediate early response.
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Affiliation(s)
- Ting-Hsuan Wu
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lingfang Shi
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Anson W. Lowe
- Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mark R. Nicolls
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter N. Kao
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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25
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Masuda K, Kuwano Y. Diverse roles of RNA-binding proteins in cancer traits and their implications in gastrointestinal cancers. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1520. [PMID: 30479000 DOI: 10.1002/wrna.1520] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023]
Abstract
Gene expression patterns in cancer cells are strongly influenced by posttranscriptional mechanisms. RNA-binding proteins (RBPs) play key roles in posttranscriptional gene regulation; they can interact with target mRNAs in a sequence- and structure-dependent manner, and determine cellular behavior by manipulating the processing of these mRNAs. Numerous RBPs are aberrantly deregulated in many human cancers and hence, affect the functioning of mRNAs that encode proteins, implicated in carcinogenesis. Here, we summarize the key roles of RBPs in posttranscriptional gene regulation, describe RBPs disrupted in cancer, and lastly focus on RBPs that are responsible for implementing cancer traits in the digestive tract. These evidences may reveal a potential link between changes in expression/function of RBPs and malignant transformation, and a framework for new insights and potential therapeutic applications. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Kiyoshi Masuda
- Kawasaki Medical School at Kurashiki-City, Okayama, Japan
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School at Tokushima-City, Tokushima, Japan
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26
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Wu TH, Shi L, Adrian J, Shi M, Nair RV, Snyder MP, Kao PN. NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells. PLoS One 2018; 13:e0193126. [PMID: 29590119 PMCID: PMC5873942 DOI: 10.1371/journal.pone.0193126] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/05/2018] [Indexed: 11/19/2022] Open
Abstract
NF90 and splice variant NF110 are DNA- and RNA-binding proteins encoded by the Interleukin enhancer-binding factor 3 (ILF3) gene that have been established to regulate RNA splicing, stabilization and export. The roles of NF90 and NF110 in regulating transcription as chromatin-interacting proteins have not been comprehensively characterized. Here, chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) identified 9,081 genomic sites specifically occupied by NF90/NF110 in K562 cells. One third of NF90/NF110 peaks occurred at promoters of annotated genes. NF90/NF110 occupancy colocalized with chromatin marks associated with active promoters and strong enhancers. Comparison with 150 ENCODE ChIP-seq experiments revealed that NF90/NF110 clustered with transcription factors exhibiting preference for promoters over enhancers (POLR2A, MYC, YY1). Differential gene expression analysis following shRNA knockdown of NF90/NF110 in K562 cells revealed that NF90/NF110 activates transcription factors that drive growth and proliferation (EGR1, MYC), while attenuating differentiation along the erythroid lineage (KLF1). NF90/NF110 associates with chromatin to hierarchically regulate transcription factors that promote proliferation and suppress differentiation.
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Affiliation(s)
- Ting-Hsuan Wu
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (PNK.); (THW)
| | - Lingfang Shi
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jessika Adrian
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Minyi Shi
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ramesh V. Nair
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, California, United States of America
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter N. Kao
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (PNK.); (THW)
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27
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ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease. Sci Rep 2018; 8:4852. [PMID: 29556082 PMCID: PMC5859008 DOI: 10.1038/s41598-018-23034-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/05/2018] [Indexed: 12/12/2022] Open
Abstract
Dogs can spontaneously develop complex systemic autoimmune disorders, with similarities to human autoimmune disease. Autoantibodies directed at self-antigens are a key feature of these autoimmune diseases. Here we report the identification of interleukin enhancer-binding factors 2 and 3 (ILF2 and ILF3) as autoantigens in canine immune-mediated rheumatic disease. The ILF2 autoantibodies were discovered in a small, selected canine cohort through the use of human protein arrays; a method not previously described in dogs. Subsequently, ILF3 autoantibodies were also identified in the same cohort. The results were validated with an independent method in a larger cohort of dogs. ILF2 and ILF3 autoantibodies were found exclusively, and at a high frequency, in dogs that showed a speckled pattern of antinuclear antibodies on immunofluorescence. ILF2 and ILF3 autoantibodies were also found at low frequency in human patients with SLE and Sjögren's syndrome. These autoantibodies have the potential to be used as diagnostic biomarkers for canine, and possibly also human, autoimmune disease.
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28
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Nuclear factor 90 promotes angiogenesis by regulating HIF-1α/VEGF-A expression through the PI3K/Akt signaling pathway in human cervical cancer. Cell Death Dis 2018; 9:276. [PMID: 29449553 PMCID: PMC5833414 DOI: 10.1038/s41419-018-0334-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 01/17/2018] [Accepted: 01/19/2018] [Indexed: 01/28/2023]
Abstract
Vascular endothelial growth factor A (VEGF-A), a fundamental component of angiogenesis, provides nutrients and oxygen to solid tumors, and enhances tumor cell survival, invasion, and migration. Nuclear factor 90 (NF90), a double-stranded RNA-binding protein, is strongly expressed in several human cancers, promotes tumor growth by reducing apoptosis, and increasing cell cycle process. The mechanisms by which cervical cancer cells inducing VEGF-A expression and angiogenesis upon NF90 upregulation remain to be fully established. We demonstrated that NF90 is upregulated in human cervical cancer specimens and the expression of NF90 is paralleled with that of VEGF-A under hypoxia. The expressions of hypoxia inducible factor-1α (HIF-1α) and VEGF-A are downregulated upon NF90 knockdown, which can be rescued by ectopic expression of NF90. Suppression of NF90 decreases the tube formation and cell migration of HUVECs. Moreover, the PI3K/Akt signaling pathway participates in the regulation. Knockdown of NF90 also reduces the tumor growth and angiogenesis of cervical cancer cell line in the mouse xenograft model. Taken together, suppression of NF90 in cervical cancer cell lines can decrease VEGF-A expression, inhibit angiogenesis, and reduce tumorigenic capacity in vivo.
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29
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Fernández-Ponce C, Durán-Ruiz MC, Narbona-Sánchez I, Muñoz-Miranda JP, Arbulo-Echevarria MM, Serna-Sanz A, Baumann C, Litrán R, Aguado E, Bloch W, García-Cozar F. Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells. Front Microbiol 2018; 8:2595. [PMID: 29354102 PMCID: PMC5758585 DOI: 10.3389/fmicb.2017.02595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus core protein is a highly basic viral protein that multimerizes with itself to form the viral capsid. When expressed in CD4+ T lymphocytes, it can induce modifications in several essential cellular and biological networks. To shed light on the mechanisms underlying the alterations caused by the viral protein, we have analyzed HCV-core subcellular localization and its associations with host proteins in Jurkat T cells. In order to investigate the intracellular localization of Hepatitis C virus core protein, we have used a lentiviral system to transduce Jurkat T cells and subsequently localize the protein using immunoelectron microscopy techniques. We found that in Jurkat T cells, Hepatitis C virus core protein mostly localizes in the nucleus and specifically in the nucleolus. In addition, we performed pull-down assays combined with Mass Spectrometry Analysis, to identify proteins that associate with Hepatitis C virus core in Jurkat T cells. We found proteins such as NOLC1, PP1γ, ILF3, and C1QBP implicated in localization and/or traffic to the nucleolus. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4+ T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. Thus, in the current work, we show the ultrastructural localization of Hepatitis C virus core and the first profile of HCV core associated proteins in T cells, and we discuss the functions and interconnections of these proteins in molecular networks where relevant biological modifications have been described upon the expression of Hepatitis C virus core protein. Thereby, the current work constitutes a necessary step toward understanding the mechanisms underlying HCV core mediated alterations that had been described in relevant biological processes in CD4+ T cells.
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Affiliation(s)
- Cecilia Fernández-Ponce
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Maria C Durán-Ruiz
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Isaac Narbona-Sánchez
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Juan P Muñoz-Miranda
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Mikel M Arbulo-Echevarria
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | | | | | - Rocío Litrán
- Department of Condensed Matter Physics, University of Cádiz, Puerto Real, Spain
| | - Enrique Aguado
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Wilhelm Bloch
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiovascular Research and Sport Medicine, German Sport University Cologne, Cologne, Germany
| | - Francisco García-Cozar
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
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30
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Schmidt T, Friedrich S, Golbik RP, Behrens SE. NF90-NF45 is a selective RNA chaperone that rearranges viral and cellular riboswitches: biochemical analysis of a virus host factor activity. Nucleic Acids Res 2017; 45:12441-12454. [PMID: 29040738 PMCID: PMC5716087 DOI: 10.1093/nar/gkx931] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/10/2017] [Indexed: 01/28/2023] Open
Abstract
The heterodimer NF90-NF45 is an RNA-binding protein complex that modulates the expression of various cellular mRNAs on the post-transcriptional level. Furthermore, it acts as a host factor that supports the replication of several RNA viruses. The molecular mechanisms underlying these activities have yet to be elucidated. Recently, we showed that the RNA-binding capabilities and binding specificity of NF90 considerably improves when it forms a complex with NF45. Here, we demonstrate that NF90 has a substrate-selective RNA chaperone activity (RCA) involving RNA annealing and strand displacement activities. The mechanism of the NF90-catalyzed RNA annealing was elucidated to comprise a combination of 'matchmaking' and compensation of repulsive charges, which finally results in the population of dsRNA products. Heterodimer formation with NF45 enhances 'matchmaking' of complementary ssRNAs and substantially increases the efficiency of NF90's RCA. During investigations of the relevance of the NF90-NF45 RCA, the complex was shown to stimulate the first step in the RNA replication process of hepatitis C virus (HCV) in vitro and to stabilize a regulatory element within the mRNA of vascular endothelial growth factor (VEGF) by protein-guided changes of the RNAs' structures. Thus, our study reveals how the intrinsic properties of an RNA-binding protein determine its biological activities.
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Affiliation(s)
- Tobias Schmidt
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
- To whom correspondence should be addressed. Tel: +49 3455 5249 60; Fax: +49 3455 5273 87; . Correspondence may also be addressed to Tobias Schmidt.
| | - Susann Friedrich
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
| | - Ralph Peter Golbik
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
- To whom correspondence should be addressed. Tel: +49 3455 5249 60; Fax: +49 3455 5273 87; . Correspondence may also be addressed to Tobias Schmidt.
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Ezegbunam W, Foronjy R. Posttranscriptional control of airway inflammation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [PMID: 29071794 DOI: 10.1002/wrna.1455] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 12/18/2022]
Abstract
Acute inflammation in the lungs is a vital protective response, efficiently and swiftly eliminating inciters of tissue injury. However, in respiratory diseases characterized by chronic inflammation, such as chronic obstructive pulmonary disease and asthma, enhanced expression of inflammatory mediators leads to tissue damage and impaired lung function. Although transcription is an essential first step in the induction of proinflammatory genes, tight regulation of inflammation requires more rapid, flexible responses. Increasing evidence shows that such responses are achieved by posttranscriptional mechanisms directly affecting mRNA stability and translation initiation. RNA-binding proteins, microRNAs, and long noncoding RNAs interact with messenger RNA and each other to impact the stability and/or translation of mRNAs implicated in lung inflammation. Recent research has shown that these biological processes play a central role in the pathogenesis of several important pulmonary conditions. This review will highlight several posttranscriptional control mechanisms that influence lung inflammation and the known associations of derangements in these mechanisms with common respiratory diseases. WIREs RNA 2018, 9:e1455. doi: 10.1002/wrna.1455 This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Wendy Ezegbunam
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Robert Foronjy
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA
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32
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The properties of the RNA-binding protein NF90 are considerably modulated by complex formation with NF45. Biochem J 2016; 474:259-280. [PMID: 28062840 DOI: 10.1042/bcj20160790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/07/2016] [Accepted: 11/11/2016] [Indexed: 12/31/2022]
Abstract
Nuclear factor 90 (NF90) is an RNA-binding protein (RBP) that regulates post-transcriptionally the expression of various mRNAs. NF90 was recently shown to be capable of discriminating between different RNA substrates. This is mediated by an adaptive and co-operative interplay between three RNA-binding motifs (RBMs) in the protein's C-terminus. In many cell types, NF90 exists predominantly in a complex with NF45. Here, we compared the RNA-binding properties of the purified NF90 monomer and the NF90-NF45 heterodimer by biophysical and biochemical means, and demonstrate that the interaction with NF45 considerably affects the characteristics of NF90. Along with a thermodynamic stabilization, complex formation substantially improves the RNA-binding capacity of NF90 by modulating its binding mode and by enhancing its affinity for single- and double-stranded RNA substrates. Our data suggest that features of both the N- and C-termini of NF90 participate in the heterodimerization with NF45 and that the formation of NF90-NF45 changes the conformation of NF90's RBMs to a status in which the co-operative interplay of the RBMs is optimal. NF45 is considered to act as a conformational scaffold for NF90's RBMs, which alters the RNA-binding specificity of NF90. Accordingly, the monomeric NF90 and the NF90-NF45 heterodimer may exert different functions in the cell.
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33
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Li T, Li X, Zhu W, Wang H, Mei L, Wu S, Lin X, Han X. NF90 is a novel influenza A virus NS1-interacting protein that antagonizes the inhibitory role of NS1 on PKR phosphorylation. FEBS Lett 2016; 590:2797-810. [PMID: 27423063 DOI: 10.1002/1873-3468.12311] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 12/24/2022]
Abstract
NF90 is a novel host antiviral factor that regulates PKR activation and stress granule formation in influenza A virus (IAV)-infected cells, but the precise mechanisms by which it operates remain unclear. We identified NF90 as a novel interacting protein of IAV nonstructural protein 1 (NS1). The interaction was dependent on the RNA-binding properties of NS1. NS1 associated with NF90 and PKR simultaneously; however, the interaction between NF90 and PKR was restricted by NS1. Knockdown of NF90 promoted inhibition of PKR phosphorylation induced by NS1, while coexpression of NF90 impeded reduction of PKR phosphorylation and stress granule formation triggered by NS1. In summary, NF90 exerts its antiviral activity by antagonizing the inhibitory role of NS1 on PKR phosphorylation.
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Affiliation(s)
- Ting Li
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - Xi Li
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - WenFei Zhu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, China
| | - HuiYu Wang
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - Lin Mei
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - ShaoQiang Wu
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - XiangMei Lin
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
| | - XueQing Han
- Chinese Academy of Inspection and Quarantine, Institute of Animal Quarantine, Chaoyang District, Beijing, China
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34
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Guo C, Xue Y, Yang G, Yin S, Shi W, Cheng Y, Yan X, Fan S, Zhang H, Zeng F. Nanog RNA-binding proteins YBX1 and ILF3 affect pluripotency of embryonic stem cells. Cell Biol Int 2016; 40:847-60. [PMID: 26289635 DOI: 10.1002/cbin.10539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/15/2015] [Indexed: 02/05/2023]
Abstract
Nanog is a well-known transcription factor that plays a fundamental role in stem cell self-renewal and the maintenance of their pluripotent cell identity. There remains a large data gap with respect to the spectrum of the key pluripotency transcription factors' interaction partners. Limited information is available concerning Nanog-associated RNA-binding proteins (RBPs), and the intrinsic protein-RNA interactions characteristic of the regulatory activities of Nanog. Herein, we used an improved affinity protocol to purify Nanog-interacting RBPs from mouse embryonic stem cells (ESCs), and 49 RBPs of Nanog were identified. Among them, the interaction of YBX1 and ILF3 with Nanog mRNA was further confirmed by in vitro assays, such as Western blot, RNA immunoprecipitation (RIP), and ex vivo methods, such as immunofluorescence staining and fluorescent in situ hybridization (FISH), MS2 in vivo biotin-tagged RNA affinity purification (MS2-BioTRAP). Interestingly, RNAi studies revealed that YBX1 and ILF3 positively affected the expression of Nanog and other pluripotency-related genes. Particularly, downregulation of YBX1 or ILF3 resulted in high expression of mesoderm markers. Thus, a reduction in the expression of YBX1 and ILF3 controls the expression of pluripotency-related genes in ESCs, suggesting their roles in further regulation of the pluripotent state of ESCs.
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Affiliation(s)
- Chuanliang Guo
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Yan Xue
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Guanheng Yang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Shang Yin
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wansheng Shi
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Cheng
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoshuang Yan
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Shuyue Fan
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huijun Zhang
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fanyi Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China.,Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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35
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Murphy J, Hall WW, Ratner L, Sheehy N. Novel interactions between the HTLV antisense proteins HBZ and APH-2 and the NFAR protein family: Implications for the HTLV lifecycles. Virology 2016; 494:129-42. [PMID: 27110706 DOI: 10.1016/j.virol.2016.04.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 01/17/2023]
Abstract
The human T-cell leukaemia virus type 1 and type 2 (HTLV-1/HTLV-2) antisense proteins HBZ and APH-2 play key roles in the HTLV lifecycles and persistence in the host. Nuclear Factors Associated with double-stranded RNA (NFAR) proteins NF90/110 function in the lifecycles of several viruses and participate in host innate immunity against infection and oncogenesis. Using GST pulldown and co-immunoprecipitation assays we demonstrate specific novel interactions between HBZ/APH-2 and NF90/110 and characterised the protein domains involved. Moreover we show that NF90/110 significantly enhance Tax mediated LTR activation, an effect that was abolished by HBZ but enhanced by APH-2. Additionally we found that HBZ and APH-2 modulate the promoter activity of survivin and are capable of antagonising NF110-mediated survivin activation. Thus interactions between HTLV antisense proteins and the NFAR protein family have an overall positive impact on HTLV infection. Hence NFARs may represent potential therapeutic targets in HTLV infected cells.
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Affiliation(s)
- Jane Murphy
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - William W Hall
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Lee Ratner
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Noreen Sheehy
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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36
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Schmidt T, Knick P, Lilie H, Friedrich S, Golbik RP, Behrens SE. Coordinated Action of Two Double-Stranded RNA Binding Motifs and an RGG Motif Enables Nuclear Factor 90 To Flexibly Target Different RNA Substrates. Biochemistry 2016; 55:948-59. [PMID: 26795062 DOI: 10.1021/acs.biochem.5b01072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanisms of how RNA binding proteins (RBP) bind to and distinguish different RNA molecules are yet uncertain. Here, we performed a comprehensive analysis of the RNA binding properties of multidomain RBP nuclear factor 90 (NF90) by investigating specifically the functional activities of two double-stranded RNA binding motifs (dsRBM) and an RGG motif in the protein's unstructured C-terminus. By comparison of the RNA binding affinities of several NF90 variants and their modes of binding to a set of defined RNA molecules, the activities of the motifs turned out to be very different. While dsRBM1 contributes little to RNA binding, dsRBM2 is essential for effective binding of double-stranded RNA. The protein's immediate C-terminus, including the RGG motif, is indispensable for interactions of the protein with single-stranded RNA, and the RGG motif decisively contributes to NF90's overall RNA binding properties. Conformational studies, which compared wild-type NF90 with a variant that contains a pseudophosphorylated residue in the RGG motif, suggest that the NF90 C-terminus is involved in conformational changes in the protein after RNA binding, with the RGG motif acting as a central regulatory element. In summary, our data propose a concerted action of all RNA binding motifs within the frame of the full-length protein, which may be controlled by regulation of the activity of the RGG motif, e.g., by phosphorylation. This multidomain interplay enables the RBP NF90 to discriminate RNA features by dynamic and adaptable interactions.
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Affiliation(s)
- Tobias Schmidt
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Paul Knick
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Susann Friedrich
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Ralph Peter Golbik
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
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37
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Nakadai T, Fukuda A, Shimada M, Nishimura K, Hisatake K. The RNA binding complexes NF45-NF90 and NF45-NF110 associate dynamically with the c-fos gene and function as transcriptional coactivators. J Biol Chem 2015; 290:26832-45. [PMID: 26381409 DOI: 10.1074/jbc.m115.688317] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 12/13/2022] Open
Abstract
The c-fos gene is rapidly induced to high levels by various extracellular stimuli. We used a defined in vitro transcription system that utilizes the c-fos promoter to purify a coactivator activity in an unbiased manner. We report here that NF45-NF90 and NF45-NF110, which possess archetypical double-stranded RNA binding motifs, have a direct function as transcriptional coactivators. The transcriptional activities of the nuclear factor (NF) complexes (NF45-NF90 and NF45-NF110) are mediated by both the upstream enhancer and core promoter regions of the c-fos gene and do not require their double-stranded RNA binding activities. The NF complexes cooperate with general coactivators, PC4 and Mediator, to elicit a high level of transcription and display multiple interactions with activators and the components of the general transcriptional machinery. Knockdown of the endogenous NF90/NF110 in mouse cells shows an important role for the NF complexes in inducing c-fos transcription. Chromatin immunoprecipitation assays demonstrate that the NF complexes occupy the c-fos enhancer/promoter region before and after serum induction and that their occupancies within the coding region of the c-fos gene increase in parallel to that of RNAPII upon serum induction. In light of their dynamic occupancy on the c-fos gene as well as direct functions in both transcription and posttranscriptional processes, the NF complexes appear to serve as multifunctional coactivators that coordinate different steps of gene expression to facilitate rapid response of inducible genes.
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Affiliation(s)
- Tomoyoshi Nakadai
- From the Department of Molecular Biology, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Iruma-gun, Saitama 350-0495, Japan and
| | - Aya Fukuda
- Department of Biochemistry, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Miho Shimada
- From the Department of Molecular Biology, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Iruma-gun, Saitama 350-0495, Japan and
| | - Ken Nishimura
- Department of Biochemistry, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Koji Hisatake
- Department of Biochemistry, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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38
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The NF45/NF90 Heterodimer Contributes to the Biogenesis of 60S Ribosomal Subunits and Influences Nucleolar Morphology. Mol Cell Biol 2015; 35:3491-503. [PMID: 26240280 DOI: 10.1128/mcb.00306-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/21/2015] [Indexed: 01/06/2023] Open
Abstract
The interleukin enhancer binding factors ILF2 (NF45) and ILF3 (NF90/NF110) have been implicated in various cellular pathways, such as transcription, microRNA (miRNA) processing, DNA repair, and translation, in mammalian cells. Using tandem affinity purification, we identified human NF45 and NF90 as components of precursors to 60S (pre-60S) ribosomal subunits. NF45 and NF90 are enriched in nucleoli and cosediment with pre-60S ribosomal particles in density gradient analysis. We show that association of the NF45/NF90 heterodimer with pre-60S ribosomal particles requires the double-stranded RNA binding domains of NF90, while depletion of NF45 and NF90 by RNA interference leads to a defect in 60S biogenesis. Nucleoli of cells depleted of NF45 and NF90 have altered morphology and display a characteristic spherical shape. These effects are not due to impaired rRNA transcription or processing of the precursors to 28S rRNA. Consistent with a role of the NF45/NF90 heterodimer in nucleolar steps of 60S subunit biogenesis, downregulation of NF45 and NF90 leads to a p53 response, accompanied by induction of the cyclin-dependent kinase inhibitor p21/CIP1, which can be counteracted by depletion of RPL11. Together, these data indicate that NF45 and NF90 are novel higher-eukaryote-specific factors required for the maturation of 60S ribosomal subunits.
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39
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Panganiban RP, Vonakis BM, Ishmael FT, Stellato C. Coordinated post-transcriptional regulation of the chemokine system: messages from CCL2. J Interferon Cytokine Res 2015; 34:255-66. [PMID: 24697203 DOI: 10.1089/jir.2013.0149] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The molecular cross-talk between epithelium and immune cells in the airway mucosa is a key regulator of homeostatic immune surveillance and is crucially involved in the development of chronic lung inflammatory diseases. The patterns of gene expression that follow the sensitization process occurring in allergic asthma and chronic rhinosinusitis and those present in the neutrophilic response of other chronic inflammatory lung diseases such as chronic obstructive pulmonary disease (COPD) are tightly regulated in their specificity. Studies exploring the global transcript profiles associated with determinants of post-transcriptional gene regulation (PTR) such as RNA-binding proteins (RBP) and microRNAs identified several of these factors as being crucially involved in controlling the expression of chemokines upon airway epithelial cell stimulation with cytokines prototypic of Th1- or Th2-driven responses. These studies also uncovered the participation of these pathways to glucocorticoids' inhibitory effect on the epithelial chemokine network. Unmasking the molecular mechanisms of chemokine PTR may likely uncover novel therapeutic strategies for the blockade of proinflammatory pathways that are pathogenetic for asthma, COPD, and other lung inflammatory diseases.
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Affiliation(s)
- Ronaldo P Panganiban
- 1 Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine , Hershey, Pennsylvania
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40
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Bridging topological and functional information in protein interaction networks by short loops profiling. Sci Rep 2015; 5:8540. [PMID: 25703051 PMCID: PMC5224520 DOI: 10.1038/srep08540] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/23/2015] [Indexed: 11/09/2022] Open
Abstract
Protein-protein interaction networks (PPINs) have been employed to identify potential novel interconnections between proteins as well as crucial cellular functions. In this study we identify fundamental principles of PPIN topologies by analysing network motifs of short loops, which are small cyclic interactions of between 3 and 6 proteins. We compared 30 PPINs with corresponding randomised null models and examined the occurrence of common biological functions in loops extracted from a cross-validated high-confidence dataset of 622 human protein complexes. We demonstrate that loops are an intrinsic feature of PPINs and that specific cell functions are predominantly performed by loops of different lengths. Topologically, we find that loops are strongly related to the accuracy of PPINs and define a core of interactions with high resilience. The identification of this core and the analysis of loop composition are promising tools to assess PPIN quality and to uncover possible biases from experimental detection methods. More than 96% of loops share at least one biological function, with enrichment of cellular functions related to mRNA metabolic processing and the cell cycle. Our analyses suggest that these motifs can be used in the design of targeted experiments for functional phenotype detection.
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41
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Castella S, Bernard R, Corno M, Fradin A, Larcher JC. Ilf3 and NF90 functions in RNA biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:243-56. [PMID: 25327818 DOI: 10.1002/wrna.1270] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/09/2014] [Accepted: 09/17/2014] [Indexed: 12/24/2022]
Abstract
Double-stranded RNA-binding proteins (DRBPs) are known to regulate many processes of RNA metabolism due, among others, to the presence of double-stranded RNA (dsRNA)-binding motifs (dsRBMs). Among these DRBPs, Interleukin enhancer-binding factor 3 (Ilf3) and Nuclear Factor 90 (NF90) are two ubiquitous proteins generated by mutually exclusive and alternative splicings of the Ilf3 gene. They share common N-terminal and central sequences but display specific C-terminal regions. They present a large heterogeneity generated by several post-transcriptional and post-translational modifications involved in their subcellular localization and biological functions. While Ilf3 and NF90 were first identified as activators of gene expression, they are also implicated in cellular processes unrelated to RNA metabolism such as regulation of the cell cycle or of enzymatic activites. The implication of Ilf3 and NF90 in RNA biology will be discussed with a focus on eukaryote transcription and translation regulation, on viral replication and translation as well as on noncoding RNA field.
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Affiliation(s)
- Sandrine Castella
- Laboratoire de Biologie du développement, Institut de Biologie Paris-Seine, Sorbonne Universités, UPMC Univ Paris 06, Paris, France; Laboratoire de Biologie du développement, Institut de Biologie Paris-Seine, CNRS, UMR 7622, Paris, France
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42
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The structure, function and evolution of proteins that bind DNA and RNA. Nat Rev Mol Cell Biol 2014; 15:749-60. [PMID: 25269475 DOI: 10.1038/nrm3884] [Citation(s) in RCA: 280] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteins that bind both DNA and RNA typify the ability of a single gene product to perform multiple functions. Such DNA- and RNA-binding proteins (DRBPs) have unique functional characteristics that stem from their specific structural features; these developed early in evolution and are widely conserved. Proteins that bind RNA have typically been considered as functionally distinct from proteins that bind DNA and studied independently. This practice is becoming outdated, in partly owing to the discovery of long non-coding RNAs (lncRNAs) that target DNA-binding proteins. Consequently, DRBPs were found to regulate many cellular processes, including transcription, translation, gene silencing, microRNA biogenesis and telomere maintenance.
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43
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Kafasla P, Skliris A, Kontoyiannis DL. Post-transcriptional coordination of immunological responses by RNA-binding proteins. Nat Immunol 2014; 15:492-502. [PMID: 24840980 DOI: 10.1038/ni.2884] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/01/2014] [Indexed: 12/22/2022]
Abstract
Immunological reactions are propelled by ever-changing signals that alter the translational ability of the RNA in the cells involved. Such alterations are considered to be consequential modifications in the transcriptomic decoding of the genetic blueprint. The identification of RNA-binding protein (RBP) assemblies engaged in the coordinative regulation of state-specific RNAs indicates alternative and exclusive means for determining the activation, plasticity and tolerance of cells of the immune system. Here we review current knowledge about RBP-regulated post-transcriptional events involved in the reactivity of cells of the immune system and the importance of their alteration during chronic inflammatory pathology and autoimmunity.
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Affiliation(s)
- Panagiota Kafasla
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Antonis Skliris
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Dimitris L Kontoyiannis
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
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44
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Wen X, Huang X, Mok BWY, Chen Y, Zheng M, Lau SY, Wang P, Song W, Jin DY, Yuen KY, Chen H. NF90 Exerts Antiviral Activity through Regulation of PKR Phosphorylation and Stress Granules in Infected Cells. THE JOURNAL OF IMMUNOLOGY 2014; 192:3753-64. [DOI: 10.4049/jimmunol.1302813] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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45
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Waysbort N, Russ D, Chain BM, Friedman N. Coupled IL-2-dependent extracellular feedbacks govern two distinct consecutive phases of CD4 T cell activation. THE JOURNAL OF IMMUNOLOGY 2013; 191:5822-30. [PMID: 24244020 DOI: 10.4049/jimmunol.1301575] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
T cells integrate cell-specific Ag receptor signaling with shared signals mediated by secreted cytokines, which often involve regulatory feedback loops. IL-2 signaling, for example, reduces the synthesis of IL-2 and increases the synthesis of IL-2Rα-chain, whereas both genes require TCR signaling for their activation. The ways by which T cells dynamically integrate these private and public signals during activation are not well understood. We combined robotics, multiparameter flow cytometry, and real-time quantitative PCR to analyze T cell activation at high temporal resolution over several days. Two distinct temporal phases of T cell activation were evident. First, Ag-dependent signals activated low IL-2Rα and high IL-2 production, independent of IL-2 signaling. Subsequently, secreted IL-2 acted as a shared resource driving high IL-2Rα expression, reduced IL-2 synthesis, and cell proliferation. This transition was independent of continued TCR signaling. Our data allowed the determination of the parameters of the IL-2-mediated extracellular positive and negative feedback circuits and demonstrated that the two loops are coupled and become activated at a similar level of IL-2 signaling. We propose that temporal separation of private and shared signals allows T cells to first integrate Ag-specific responses and subsequently share information leading to collective decision making.
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Affiliation(s)
- Nir Waysbort
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
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Abstract
Post-transcriptional mechanisms that modulate global and/or transcript-specific mRNA stability and translation contribute to the rapid and flexible control of gene expression in immune effector cells. These mechanisms rely on RNA-binding proteins (RBPs) that direct regulatory complexes (e.g. exosomes, deadenylases, decapping complexes, RNA-induced silencing complexes) to the 3'-untranslated regions of specific immune transcripts. Here, we review the surprising variety of post-transcriptional control mechanisms that contribute to gene expression in the immune system and discuss how defects in these pathways can contribute to autoimmune disease.
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Affiliation(s)
- Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA.
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Yao P, Potdar AA, Ray PS, Eswarappa SM, Flagg AC, Willard B, Fox PL. The HILDA complex coordinates a conditional switch in the 3'-untranslated region of the VEGFA mRNA. PLoS Biol 2013; 11:e1001635. [PMID: 23976881 PMCID: PMC3747992 DOI: 10.1371/journal.pbio.1001635] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 07/12/2013] [Indexed: 11/19/2022] Open
Abstract
Cell regulatory circuits integrate diverse, and sometimes conflicting, environmental cues to generate appropriate, condition-dependent responses. Here, we elucidate the components and mechanisms driving a protein-directed RNA switch in the 3'UTR of vascular endothelial growth factor (VEGF)-A. We describe a novel HILDA (hypoxia-inducible hnRNP L-DRBP76-hnRNP A2/B1) complex that coordinates a three-element RNA switch, enabling VEGFA mRNA translation during combined hypoxia and inflammation. In addition to binding the CA-rich element (CARE), heterogeneous nuclear ribonucleoprotein (hnRNP) L regulates switch assembly and function. hnRNP L undergoes two previously unrecognized, condition-dependent posttranslational modifications: IFN-γ induces prolyl hydroxylation and von Hippel-Lindau (VHL)-mediated proteasomal degradation, whereas hypoxia stimulates hnRNP L phosphorylation at Tyr(359), inducing binding to hnRNP A2/B1, which stabilizes the protein. Also, phospho-hnRNP L recruits DRBP76 (double-stranded RNA binding protein 76) to the 3'UTR, where it binds an adjacent AU-rich stem-loop (AUSL) element, "flipping" the RNA switch by disrupting the GAIT (interferon-gamma-activated inhibitor of translation) element, preventing GAIT complex binding, and driving robust VEGFA mRNA translation. The signal-dependent, HILDA complex coordinates the function of a trio of neighboring RNA elements, thereby regulating translation of VEGFA and potentially other mRNA targets. The VEGFA RNA switch might function to ensure appropriate angiogenesis and tissue oxygenation during conflicting signals from combined inflammation and hypoxia. We propose the VEGFA RNA switch as an archetype for signal-activated, protein-directed, multi-element RNA switches that regulate posttranscriptional gene expression in complex environments.
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Affiliation(s)
- Peng Yao
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Alka A. Potdar
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Partho Sarothi Ray
- Department of Biology, Indian Institute of Science Education and Research, Kolkata, India
| | - Sandeepa M. Eswarappa
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Andrew C. Flagg
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Belinda Willard
- Mass Spectrometry Laboratory for Protein Sequencing, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Paul L. Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- * E-mail:
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48
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Pisapia L, Cicatiello V, Barba P, Malanga D, Maffei A, Hamilton RS, Del Pozzo G. Co-regulated expression of alpha and beta mRNAs encoding HLA-DR surface heterodimers is mediated by the MHCII RNA operon. Nucleic Acids Res 2013; 41:3772-86. [PMID: 23393186 PMCID: PMC3616700 DOI: 10.1093/nar/gkt059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Major histocompatibility complex class II (MHCII) molecules are heterodimeric surface proteins involved in the presentation of exogenous antigens during the adaptive immune response. We demonstrate the existence of a fine level of regulation, coupling the transcription and processing of mRNAs encoding α and β chains of MHCII molecules, mediated through binding of their Untraslated Regions (UTRs) to the same ribonucleoproteic complex (RNP). We propose a dynamic model, in the context of the 'MHCII RNA operon' in which the increasing levels of DRA and DRB mRNAs are docked by the RNP acting as a bridge between 5'- and 3'-UTR of the same messenger, building a loop structure and, at the same time, joining the two chains, thanks to shared common predicted secondary structure motifs. According to cell needs, as during immune surveillance, this RNP machinery guarantees a balanced synthesis of DRA and DRB mRNAs and a consequent balanced surface expression of the heterodimer.
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Affiliation(s)
- Laura Pisapia
- Institute of Genetics and Biophysics Adriano Buzzati Traverso-CNR, Naples, 80131, Italy
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49
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Chaumet A, Castella S, Gasmi L, Fradin A, Clodic G, Bolbach G, Poulhe R, Denoulet P, Larcher JC. Proteomic analysis of interleukin enhancer binding factor 3 (Ilf3) and nuclear factor 90 (NF90) interactome. Biochimie 2013; 95:1146-57. [PMID: 23321469 DOI: 10.1016/j.biochi.2013.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 01/04/2013] [Indexed: 11/17/2022]
Abstract
Interleukin enhancer binding factor 3 (Ilf3) and Nuclear Factor 90 (NF90) are two ubiquitous proteins generated by alternative splicing from the ILF3 gene that provides each protein with a long and identical N-terminal domain of 701 amino acids and a specific C-terminal domain of 210 and 15 amino acids, respectively. They exhibit a high polymorphism due to their posttranscriptional and posttranslational modifications. Ilf3 and NF90 functions remain unclear although they have been described as RNA binding proteins but have been implicated in a large scale of cellular phenomena depending on the nature of their interacting partners, the composition of their protein complexes and their subcellular localization. In order to better understand the functions of Ilf3 and NF90, we have investigated their protein partners by an affinity chromatography approach. In this report, we have identified six partners of Ilf3 and NF90 that interact with their double-stranded RNA binding motifs: hnRNP A/B, hnRNP A2/B1, hnRNP A3, hnRNP D, hnRNP Q and PSF. These hnRNP are known to be implicated in mRNA stabilization, transport and/or translation regulation whereas PSF is a splicing factor. Furthermore, Ilf3, NF90 and most of their identified partners have been shown to be present in large complexes. Altogether, these data suggest an implication of Ilf3 and NF90 in mRNA metabolism. This work allows to establish a link between Ilf3 and NF90 functions, as RNA binding proteins, and their interacting partners implicated in these functions.
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Affiliation(s)
- Alexandre Chaumet
- Laboratoire de Biologie du Développement, UMR 7622 CNRS, UPMC Univ Paris 06, 9 quai Saint Bernard, 75252 Paris Cedex 05, France
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50
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Shamanna RA, Hoque M, Pe'ery T, Mathews MB. Induction of p53, p21 and apoptosis by silencing the NF90/NF45 complex in human papilloma virus-transformed cervical carcinoma cells. Oncogene 2012. [PMID: 23208500 PMCID: PMC4032571 DOI: 10.1038/onc.2012.533] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The heterodimeric nuclear factor 90/nuclear factor 45 complex (NF90/NF45) binds nucleic acids and is a multifunctional regulator of gene expression. Here we report that depletion of NF90/NF45 restores the expression of the p53 and p21 proteins in cervical carcinoma cells infected with high-risk human papillomaviruses (HPV). Knockdown of either NF90 or NF45 by RNA interference led to greatly elevated levels of p53 and p21 proteins in HPV-derived HeLa and SiHa cells, but not in other cancerous or normal cell lines. In HeLa cells, p21 mRNA increased concomitantly but the level of p53 mRNA was unaffected. RNA interference directed against p53 prevented the induction of both proteins. These results indicated that the up-regulation of p21 is due to p53-dependent transcription, whereas p53 is regulated post-transcriptionally. Proteasome-mediated turnover of p53 is accelerated by the HPV E6 and cellular E6AP proteins. We therefore examined the hypothesis that this pathway is regulated by NF90/NF45. Indeed, depletion of NF90 attenuated the expression of E6 RNA and inhibited transcription from the HPV early promoter, revealing a new role for NF90/NF45 in HPV gene expression. The transcription inhibition was largely independent of the reduction of P-TEFb levels caused by NF90 depletion. Consistent with p53 derepression, NF90/NF45-depleted HeLa cells displayed elevated PARP cleavage and susceptibility to camptothecin-induced apoptosis. We conclude that high-risk strains of HPV utilize the cellular NF90/NF45 complex for viral E6 expression in infected cervical carcinoma cell lines. Interference with NF90/NF45 function could assist in controlling cervical carcinoma.
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Affiliation(s)
- R A Shamanna
- 1] Department of Biochemistry and Molecular Biology, New Jersey Medical School, UMDNJ, Newark, NJ, USA [2] Graduate School of Biomedical Sciences, UMDNJ, Newark, NJ, USA
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