1
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Oncogenic heterogeneous nuclear ribonucleoprotein D-like modulates the growth and imatinib response of human chronic myeloid leukemia CD34 + cells via pre-B-cell leukemia homeobox 1. Oncogene 2019; 39:443-453. [PMID: 31488872 DOI: 10.1038/s41388-019-0998-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Chronic myeloid leukemia (CML) originates from normal hematopoietic stem cells acquiring BCR-ABL fusion gene, specific BCR-ABL inhibitors (e.g., imatinib mesylate, IM) have greatly improved patient management. However, some patients are still suffering from relapse and drug resistance, which urges better understanding of the growth/survival mechanisms of CML stem/progenitor cells. In the present study, the role and its underlying mechanism of heterogeneous nuclear ribonucleoprotein D-like (HNRPDL) in CML cells were investigated. Firstly, overexpression of HNRPDL promoted the growth of murine BaF3 cells in vitro and induced leukemia in vivo, which was enhanced by co-expression of BCR-ABL. Conversely, HNRPDL silencing inhibited colony-forming cell (CFC) production of CML CD34+ cells and attenuated BCR-ABL induced leukemia. In addition, HNRPDL modulated imatinib response of K562 cells and HNRPDL silencing sensitized CML CD34+ cells to imatinib treatment. Mechanistically, we found the stability of pre-B-cell leukemia homeobox 1 (PBX1) mRNA was sustained by HNRPDL through its binding to a specific motif (ACUAGC) in 3'-untranslated region (3'-UTR) of PBX1. The expression of PBX1 was significantly higher in CML CD34+ cells than that in control cells and PBX silencing inhibited the growth of CML cells and sensitized them to imatinib treatment. In contrast, overexpression of PBX1 elevated the CFC production of normal hematopoietic CD34+ cells and "rescued" HNRPDL silencing induced growth inhibition and imatinib sensitization. Taken together, our data have demonstrated that HNRPDL transforms hematopoietic cells and a novel HNRPDL/PBX1 axis plays an important role in human CML CD34+ cells.
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2
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Godet AC, David F, Hantelys F, Tatin F, Lacazette E, Garmy-Susini B, Prats AC. IRES Trans-Acting Factors, Key Actors of the Stress Response. Int J Mol Sci 2019; 20:ijms20040924. [PMID: 30791615 PMCID: PMC6412753 DOI: 10.3390/ijms20040924] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 12/16/2022] Open
Abstract
The cellular stress response corresponds to the molecular changes that a cell undergoes in response to various environmental stimuli. It induces drastic changes in the regulation of gene expression at transcriptional and posttranscriptional levels. Actually, translation is strongly affected with a blockade of the classical cap-dependent mechanism, whereas alternative mechanisms are activated to support the translation of specific mRNAs. A major mechanism involved in stress-activated translation is the internal ribosome entry site (IRES)-driven initiation. IRESs, first discovered in viral mRNAs, are present in cellular mRNAs coding for master regulators of cell responses, whose expression must be tightly controlled. IRESs allow the translation of these mRNAs in response to different stresses, including DNA damage, amino-acid starvation, hypoxia or endoplasmic reticulum stress, as well as to physiological stimuli such as cell differentiation or synapse network formation. Most IRESs are regulated by IRES trans-acting factor (ITAFs), exerting their action by at least nine different mechanisms. This review presents the history of viral and cellular IRES discovery as well as an update of the reported ITAFs regulating cellular mRNA translation and of their different mechanisms of action. The impact of ITAFs on the coordinated expression of mRNA families and consequences in cell physiology and diseases are also highlighted.
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Affiliation(s)
- Anne-Claire Godet
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florian David
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Fransky Hantelys
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florence Tatin
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Eric Lacazette
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Barbara Garmy-Susini
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Anne-Catherine Prats
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
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3
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hnRNPDL extensively regulates transcription and alternative splicing. Gene 2018; 687:125-134. [PMID: 30447347 DOI: 10.1016/j.gene.2018.11.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 08/30/2018] [Accepted: 11/08/2018] [Indexed: 01/31/2023]
Abstract
RNA binding proteins (RBPs) are key players of genome regulation. Here we report the transcriptome study of HnRNP D-Like protein, which belongs to the hnRNP family. We used RNA-seq to analyze the global transcript level and alternative splicing on hnRNPDL shRNA-treated cells and control. Sh-hnRNPDL extensively increased in the expression of genes involved in female pregnancy, cell apoptosis, cell proliferation and cell migration. HnRNPDL regulated alternative splicing of hundreds of genes enriched in transcription regulation and signaling pathways including NOD-like receptor signaling, Notch signaling, and TNF signaling. This study provides the first transcriptome-wide analysis of hnRNPDL regulation of gene expression, which adds to the understanding of critical hnRNPDL functions.
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4
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Zhang P, Ji D, Hu X, Ni H, Ma W, Zhang X, Liao S, Zeng Z, Zhao Y, Zhou H. Oncogenic heterogeneous nuclear ribonucleoprotein D-like promotes the growth of human colon cancer SW620 cells via its regulation of cell-cycle. Acta Biochim Biophys Sin (Shanghai) 2018; 50:880-887. [PMID: 30052712 DOI: 10.1093/abbs/gmy085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Indexed: 01/01/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins. Heterogeneous nuclear ribonucleoprotein D-like (HNRPDL) is a member of this family. Though aberrant expression of HNRPDL has been reported in a few cancers, whether HNRPDL is deregulated in colon cancer patients and what role this protein plays in these cells are not known yet. In this study, we found that HNRPDL was significantly up-regulated in colon cancer specimens than control. We also demonstrated that HNRPDL silencing inhibited the growth of SW620 cells both in vitro and in vivo. Conversely, we constructed a retroviral vector to deliver HNRPDL into non-malignant NIH-3T3 cells and injected these cells into nude mice. HNRPDL-overexpressing NIH-3T3 cells generated tumors in nude mice but not the control cells. Mechanistically, HNRPDL promoted cell-cycle progression associated with enhanced expressions of cyclin D3 and Ki-67 but decreased expressions of p53 and p21. Taken together, our data demonstrate that HNRPDL is aberrantly expressed in colon cancer cells, which promotes the growth of these cells by activating cell-cycle progression.
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Affiliation(s)
- Pengshan Zhang
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
| | - Dehuan Ji
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
| | - Xiaohui Hu
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hengli Ni
- Department of Pathology, Medical College of Soochow University, Suzhou, China
| | - Wenjuan Ma
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
| | - Xiuyan Zhang
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
| | - Shibing Liao
- Department of Oncology, The Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Zheng Zeng
- Department of Oncology, The Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Yun Zhao
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
- The Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Haixia Zhou
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
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5
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Kemmerer K, Fischer S, Weigand JE. Auto- and cross-regulation of the hnRNPs D and DL. RNA (NEW YORK, N.Y.) 2018; 24:324-331. [PMID: 29263134 PMCID: PMC5824352 DOI: 10.1261/rna.063420.117] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/18/2017] [Indexed: 05/17/2023]
Abstract
HnRNP D, better known as AUF1, is an extensively studied protein that controls a variety of cellular pathways. Consequently, its expression has to be tightly regulated to prevent the onset of pathologies. In contrast, the cellular functions and regulation of its ubiquitously expressed paralog hnRNP DL are barely explored. Here, we present an intricate crosstalk between these two proteins. Both hnRNP D and DL are able to control their own expression by alternative splicing of cassette exons in their 3'UTRs. Exon inclusion produces mRNAs degraded by nonsense-mediated decay. Moreover, hnRNP D and DL control the expression of one another by the same mechanism. Thus, we identified two novel ways of how hnRNP D expression is controlled. The tight interconnection of expression control directly links hnRNP DL to hnRNP D-related diseases and emphasizes the importance of a systematic analysis of its cellular functions.
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Affiliation(s)
- Katrin Kemmerer
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Sandra Fischer
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Julia E Weigand
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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6
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Qiu W, He JH, Zuo H, Niu S, Li C, Zhang S, Weng S, He J, Xu X. Identification, characterization, and function analysis of the NF-κB repressing factor (NKRF) gene from Litopenaeus vannamei. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 76:83-92. [PMID: 28564581 DOI: 10.1016/j.dci.2017.05.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 06/07/2023]
Abstract
The NF-κB family transcription factors regulate a wide spectrum of biological processes, in particular immune responses. The studies in human suggest that the NF-κB repressing factor (NKRF) negatively regulates the activity of NF-κB through a direct protein-protein interaction. However, the function of NKRF has not been studied outside mammals up to now. The current study identified a NKRF gene (LvNKRF) from the Pacific white shrimp, Litopenaeus vannamei, which showed homology with NKRFs from insects, fishes and mammals. LvNKRF was high expressed in intestine, stomach and muscle tissues and was localized in the nucleus. LvNKRF could interact with both Dorsal and Relish, the two members of the shrimp NF-κB family. Interestingly, although sharing a similar protein structure with that of human NKRF, LvNKRF showed no inhibitory but instead enhancing effects on activities of Dorsal and Relish, which was contrary to those of mammalian NKRFs. The expression of LvNKRF could not be induced by Gram-positive and -negative bacteria and immunostimulants lipopolysaccharide (LPS) and poly (I:C) but was significantly up-regulated after white spot syndrome virus (WSSV) infection. Silencing of LvNKRF significantly decreased the mortalities of shrimp caused by WSSV infection and down-regulated the WSSV copies and the expression of WSSV structural gene in tissues. These suggested that LvNKRF could facilitate the infection of shrimp by WSSV, which may be an additional strategy for WSSV to hijack the host NF-κB pathway to favor its own replication. The current study could provide a valuable context for further investigating the evolutionary derivation of NKRFs and facilitate the study of regulatory mechanisms of invertebrate NF-κB pathways.
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Affiliation(s)
- Wei Qiu
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; School of Marine Sciences, Sun Yat-sen University, Guangzhou, PR China; School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Jian-Hui He
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Hongliang Zuo
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China; School of Marine Sciences, Sun Yat-sen University, Guangzhou, PR China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, PR China
| | - Shengwen Niu
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Chaozheng Li
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China; School of Marine Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Shuang Zhang
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Shaoping Weng
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Jianguo He
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China; School of Marine Sciences, Sun Yat-sen University, Guangzhou, PR China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, PR China.
| | - Xiaopeng Xu
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, PR China.
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7
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Ho SC, Wu SM, Feng PH, Liu WT, Chen KY, Chuang HC, Chan YF, Kuo LW, Lee KY. Noncanonical NF-κB mediates the Suppressive Effect of Neutrophil Elastase on IL-8/CXCL8 by Inducing NKRF in Human Airway Smooth Muscle. Sci Rep 2017; 7:44930. [PMID: 28322300 PMCID: PMC5359717 DOI: 10.1038/srep44930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/16/2017] [Indexed: 01/06/2023] Open
Abstract
Neutrophil elastase (NE) suppresses IL-8/CXCL8 in human airway smooth muscle cells (hASM) while stimulating its production in respiratory epithelial cells. This differential effect is mediated by the selective induction of NKRF and dysregulation in chronic inflammatory diseases. We hypothesized that the differential activation of NF-κB subunits confer the opposite effect of NKRF on IL-8/CXCL8 in primary hASM and A549 cells stimulated with NE. The events occurring at the promoters of NKRF and IL-8/CXCL8 were observed by ChIP assays, and the functional role of RelB was confirmed by knockdown and overexpression. Although p65 was stimulated in both cell types, RelB was only activated in NE-treated hASM, as confirmed by NF-κB DNA binding ELISA, Western blotting and confocal microscopy. Knockdown of RelB abolished the induction of NKRF and converted the suppression of IL-8/CXCL8 to stimulation. The forced expression of RelB induced NKRF production in hASM and A549 cells. NE activated the NIK/IKK1/RelB non-canonical NF-κB pathway in hASM but not in A549. The nuclear-translocated RelB was recruited to the NKRF promoter around the putative κB site, accompanied by p52 and RNA polymerase II. In conclusion, NFRF is a novel RelB-response gene, and NE is a stimulator of the non-canonical RelB/NF-κB pathway in hASM.
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Affiliation(s)
- Shu-Chuan Ho
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Sheng-Ming Wu
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Po-Hao Feng
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wen-Te Liu
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Kuan-Yuan Chen
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Hsiao-Chi Chuang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yao-Fei Chan
- Division of Pulmonary Oncology and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang-Gung Memorial Hospital, Taoyuan, Taiwan
| | - Lu-Wei Kuo
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Kang-Yun Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
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8
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Rother S, Bartels M, Schweda AT, Resch K, Pallua N, Nourbakhsh M. NF‐κB‐repressing factor phosphorylation regulates transcription elongation
via
its interactions with 5'→3' exoribonuclease 2 and negative elongation factor. FASEB J 2015; 30:174-85. [DOI: 10.1096/fj.15-270256] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/31/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Sascha Rother
- Institute of Pharmacology, Hannover Medical SchoolHannoverGermany
| | - Myriam Bartels
- Institute of Pharmacology, Hannover Medical SchoolHannoverGermany
| | | | - Klaus Resch
- Institute of Pharmacology, Hannover Medical SchoolHannoverGermany
| | - Norbert Pallua
- Department of Plastic and Reconstructive Surgery, Hand Surgery and Burn CenterRheinisch‐Westfälische Technische Hochschule (RWTH) Aachen University HospitalAachenGermany
| | - Mahtab Nourbakhsh
- Department of Plastic and Reconstructive Surgery, Hand Surgery and Burn CenterRheinisch‐Westfälische Technische Hochschule (RWTH) Aachen University HospitalAachenGermany
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9
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Laing EE, Johnston JD, Möller-Levet CS, Bucca G, Smith CP, Dijk DJ, Archer SN. Exploiting human and mouse transcriptomic data: Identification of circadian genes and pathways influencing health. Bioessays 2015; 37:544-56. [PMID: 25772847 PMCID: PMC5031210 DOI: 10.1002/bies.201400193] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The power of the application of bioinformatics across multiple publicly available transcriptomic data sets was explored. Using 19 human and mouse circadian transcriptomic data sets, we found that NR1D1 and NR1D2 which encode heme‐responsive nuclear receptors are the most rhythmic transcripts across sleep conditions and tissues suggesting that they are at the core of circadian rhythm generation. Analyzes of human transcriptomic data show that a core set of transcripts related to processes including immune function, glucocorticoid signalling, and lipid metabolism is rhythmically expressed independently of the sleep‐wake cycle. We also identify key transcripts associated with transcription and translation that are disrupted by sleep manipulations, and through network analysis identify putative mechanisms underlying the adverse health outcomes associated with sleep disruption, such as diabetes and cancer. Comparative bioinformatics applied to existing and future data sets will be a powerful tool for the identification of core circadian‐ and sleep‐dependent molecules.
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Affiliation(s)
- Emma E Laing
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
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10
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Lenarcic EM, Ziehr BJ, Moorman NJ. An unbiased proteomics approach to identify human cytomegalovirus RNA-associated proteins. Virology 2015; 481:13-23. [PMID: 25765003 DOI: 10.1016/j.virol.2015.02.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/18/2014] [Accepted: 02/06/2015] [Indexed: 12/13/2022]
Abstract
Post-transcriptional events regulate herpesvirus gene expression, yet few herpesvirus RNA-binding proteins have been identified. We used an unbiased approach coupling oligo(dT) affinity capture with proteomics to identify viral RNA-associated proteins during infection. Using this approach, we identified and confirmed changes in the abundance or activity of two host RNA-associated proteins, DHX9 and DDX3, in cells infected with human cytomegalovirus (HCMV). We also identified and confirmed previously unreported activities for the HCMV US22 and pp71 proteins as RNA-associated viral proteins and confirmed that a known viral RNA-binding protein, pTRS1, associates with RNA in infected cells. Further, we found that HCMV pp71 co-sedimented with polysomes, associated with host and viral RNAs, and stimulated the overall rate of protein synthesis. These results demonstrate that oligo(dT) affinity capture coupled with proteomics provides a rapid and straightforward means to identify RNA-associated viral proteins during infection that may participate in the post-transcriptional control of gene expression.
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Affiliation(s)
- Erik M Lenarcic
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Benjamin J Ziehr
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Nathaniel J Moorman
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States.
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11
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Cellular STAT3 functions via PCBP2 to restrain Epstein-Barr Virus lytic activation in B lymphocytes. J Virol 2015; 89:5002-11. [PMID: 25717101 DOI: 10.1128/jvi.00121-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/13/2015] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED A major hurdle to killing Epstein-Barr virus (EBV)-infected tumor cells using oncolytic therapy is the presence of a substantial fraction of EBV-infected cells that does not support the lytic phase of EBV despite exposure to lytic cycle-promoting agents. To determine the mechanism(s) underlying this refractory state, we developed a strategy to separate lytic from refractory EBV-positive (EBV(+)) cells. By examining the cellular transcriptome in separated cells, we previously discovered that high levels of host STAT3 (signal transducer and activator of transcription 3) curtail the susceptibility of latently infected cells to lytic cycle activation signals. The goals of the present study were 2-fold: (i) to determine the mechanism of STAT3-mediated resistance to lytic activation and (ii) to exploit our findings to enhance susceptibility to lytic activation. We therefore analyzed our microarray data set, cellular proteomes of separated lytic and refractory cells, and a publically available STAT3 chromatin immunoprecipitation sequencing (ChIP-Seq) data set to identify cellular PCBP2 [poly(C)-binding protein 2], an RNA-binding protein, as a transcriptional target of STAT3 in refractory cells. Using Burkitt lymphoma cells and EBV(+) cell lines from patients with hypomorphic STAT3 mutations, we demonstrate that single cells expressing high levels of PCBP2 are refractory to spontaneous and induced EBV lytic activation, STAT3 functions via cellular PCBP2 to regulate lytic susceptibility, and suppression of PCBP2 levels is sufficient to increase the number of EBV lytic cells. We expect that these findings and the genome-wide resources that they provide will accelerate our understanding of a longstanding mystery in EBV biology and guide efforts to improve oncolytic therapy for EBV-associated cancers. IMPORTANCE Most humans are infected with Epstein-Barr virus (EBV), a cancer-causing virus. While EBV generally persists silently in B lymphocytes, periodic lytic (re)activation of latent virus is central to its life cycle and to most EBV-related diseases. However, a substantial fraction of EBV-infected B cells and tumor cells in a population is refractory to lytic activation. This resistance to lytic activation directly and profoundly impacts viral persistence and the effectiveness of oncolytic therapy for EBV(+) cancers. To identify the mechanisms that underlie susceptibility to EBV lytic activation, we used host gene and protein expression profiling of separated lytic and refractory cells. We find that STAT3, a transcription factor overactive in many cancers, regulates PCBP2, a protein important in RNA biogenesis, to regulate susceptibility to lytic cycle activation signals. These findings advance our understanding of EBV persistence and provide important leads on devising methods to improve viral oncolytic therapies.
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12
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Li LF, Lai YT, Chang CH, Lin MC, Liu YY, Kao KC, Tsai YH. Neutrophil elastase inhibitor reduces ventilation-induced lung injury via nuclear factor-κB and NF-κB repressing factor in mice. Exp Biol Med (Maywood) 2014; 239:1045-1057. [PMID: 24728725 DOI: 10.1177/1535370214529393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Mechanical ventilation used in patients with acute lung injury can damage pulmonary epithelial cells through production of inflammatory cytokines, oxygen radicals, and neutrophil infiltration, termed ventilator-induced lung injury. Neutrophil elastase, nuclear factor-κB (NF-κB), and NF-κB repressing factor (NRF) have previously been shown to participate in the regulation of macrophage inflammatory protein-2 (MIP-2) during airway inflammation. However, the mechanisms regulating interactions among mechanical ventilation, neutrophil influx, and NF-κB/NRF remain unclear. Thus, we hypothesized that neutrophil elastase inhibitor attenuated ventilation-induced neutrophil recruitment and MIP-2 production through inhibition of the NF-κB/NRF pathway. Male C57BL/6 mice were exposed to low-tidal-volume (6 mL/kg) or high-tidal-volume (30 mL/kg) mechanical ventilation using room air with or without 2 µg/g NF-κB inhibitor SN50 or 6 µg/g NRF short interfering RNA or 100 µg/g neutrophil elastase inhibitor administration. Nonventilated mice served as a control group. Evan blue dye, lung wet-to-dry weight ratio, free radicals, myeloperoxidase, histopathologic grading of lung tissue, inflammatory cytokines, Western blot of NF-κB and NRF, and gene expression of NRF were measured to establish the extent of lung injury. Neutrophil elastase inhibitor ameliorated high-tidal-volume ventilation-induced lung injury, neutrophil influx, production of MIP-2 and malondialdehyde, activation of NF-κB and NRF, apoptotic epithelial cell death, and disruption of bronchial microstructure in mice. Mechanical stretch-augmented acute lung injury was also attenuated through pharmacological inhibition of NF-κB activity by SN50 and NRF expression by NRF short interfering RNA. Our data suggest that neutrophil elastase inhibitor attenuates high-tidal-volume mechanical ventilation-induced neutrophil influx, oxidative stress, and production of MIP-2, at least partly, through inhibition of NF-κB/NRF pathway. Understanding the protective effects of neutrophil elastase inhibitor associated with the reduction of MIP-2 allow clarification of the pathophysiological mechanisms regulating severe lung inflammation and development of possible therapeutic strategies involved in acute lung injury.
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Affiliation(s)
- Li-Fu Li
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan 333, Taiwan Department of Respiratory Therapy, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Yi-Ting Lai
- Department of Respiratory Therapy, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan Graduate Institute of Clinical Medical Sciences and Department of Respiratory Care, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Chih-Hao Chang
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan 333, Taiwan
| | - Meng-Chih Lin
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Yung-Yang Liu
- Chest Department, Taipei Veterans General Hospital, Taipei 112, Taiwan Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan
| | - Kuo-Chin Kao
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan 333, Taiwan Department of Respiratory Therapy, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Ying-Huang Tsai
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan 333, Taiwan Department of Respiratory Therapy, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
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13
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Bhoj E, Halbach S, McDonald-McGinn D, Tan C, Lande R, Waggoner D, Zackai E. Expanding the spectrum of microdeletion 4q21 syndrome: A partial phenotype with incomplete deletion of the minimal critical region and a new association with cleft palate and pierre robin sequence. Am J Med Genet A 2013; 161A:2327-33. [DOI: 10.1002/ajmg.a.36061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/03/2012] [Accepted: 04/25/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Elizabeth Bhoj
- Division of Genetics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Sara Halbach
- Department of Human Genetics; University of Chicago; Chicago Illinois
| | - Donna McDonald-McGinn
- Division of Genetics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Christopher Tan
- Department of Human Genetics; University of Chicago; Chicago Illinois
| | - Rachel Lande
- Division of Genetics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Darrel Waggoner
- Department of Human Genetics; University of Chicago; Chicago Illinois
| | - Elaine Zackai
- Division of Genetics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
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14
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Thiouracil cross-linking mass spectrometry: a cell-based method to identify host factors involved in viral amplification. J Virol 2013; 87:8697-712. [PMID: 23740976 DOI: 10.1128/jvi.00950-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic RNA viruses are known to utilize host factors; however, the identity of these factors and their role in the virus life cycle remain largely undefined. Here, we report a method to identify proteins bound to the viral RNA during amplification in cell culture: thiouracil cross-linking mass spectrometry (TUX-MS). TUX-MS relies on incorporation of a zero-distance cross-linker into the viral RNA during infection. Proteins bound to viral RNA are cross-linked prior to cell lysis, purified, and identified using mass spectrometry. Using the TUX-MS method, an unbiased screen for poliovirus (PV) host factors was conducted. All host and viral proteins that are known to interact with the poliovirus RNA were identified. In addition, TUX-MS identified an additional 66 host proteins that have not been previously described in poliovirus amplification. From these candidates, eight were selected and validated. Furthermore, we demonstrate that small interfering RNA (siRNA)-mediated knockdown of two of these uncharacterized host factors results in either a decrease in copy number of positive-stranded RNA or a decrease in PV translation. These data demonstrate that TUX-MS is a robust, unbiased method to identify previously unknown host cell factors that influence virus growth. This method is broadly applicable to a range of RNA viruses, such as flaviviruses, alphaviruses, picornaviruses, bunyaviruses, and coronaviruses.
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15
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Reboll MR, Ritter B, Sasse F, Niggemann J, Frank R, Nourbakhsh M. The myxobacterial compounds spirangien a and spirangien M522 are potent inhibitors of IL-8 expression. Chembiochem 2012; 13:409-15. [PMID: 22271561 DOI: 10.1002/cbic.201100635] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Indexed: 11/07/2022]
Abstract
Elevated expression of interleukin-8 (IL-8) has been implicated in inflammatory diseases, in tumor growth, and in angiogenesis. The aim of this study was to identify natural or synthetic compounds that suppress IL-8 production in response to interleukin-1 (IL-1), the natural inflammatory stimulus of the IL-8 gene. We therefore developed an IL-1-inducible cell-based screening assay by stable integration of an IL-8 reporter gene into HeLa S3 cells. The screening of heterogeneous compound libraries revealed several compounds that displayed an inhibitory effect on the reporter gene expression. Following hit validation, we focused on the most efficient compound, spirangien A, and its chemical derivate spirangien M522. Detailed analysis shows that both compounds are potent inhibitors of the endogenous IL-8 gene transcription. Furthermore, both compounds decelerate the phosphorylation and degradation of IκBα, the key regulator of the IL-1-stimulated NF-κB signaling pathway. Our study has identified the two spirangiens A and M522 as potent inhibitors of IL-1/NF-κB-mediated IL-8 gene expression.
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Affiliation(s)
- Marc René Reboll
- Department of Chemical Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
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16
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Reboll MR, Schweda AT, Bartels M, Franke R, Frank R, Nourbakhsh M. Mapping of NRF binding motifs of NF-kappaB p65 subunit. J Biochem 2011; 150:553-62. [PMID: 21821668 DOI: 10.1093/jb/mvr099] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
NF-kappaB repressing factor (NRF) is a nuclear transcription factor that binds to a specific DNA sequence in NF-kappaB target promoters. Previous reports suggested that NRF interferes with the transcriptional activity of NF-kappaB binding sites through a direct interaction with NF-kappaB subunits. The aim of this study was to map specific NRF binding domains in the NF-kappaB proteins, p65 and p50. Our data demonstrate that NRF is able to interact with the p65 subunit and inhibit its transcription enhancing activity in reporter gene experiments. Using tandem affinity purifications (TAP), we show that NRF protein significantly binds to the endogenous p65, subunit but not to the p50 subunit. The selective binding activity of the NRF protein is consistently mediated by the N-terminal domain of NRF (Amino acids 1-380). Moreover, the Rel homology domain (RHD) of p65 is sufficient for binding to the N-terminal domain of NRF. Using detailed peptide mapping studies, we finally identify three peptide motifs in p65 RHD showing distinctive binding specificities for the NRF protein. According to the predicted structure of p65, all three peptide motifs align within an exposed region of p65 and might hint at promising targets for inhibitors.
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Affiliation(s)
- Marc R Reboll
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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