1
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Marie P, Bazire M, Ladet J, Ameur LB, Chahar S, Fontrodona N, Sexton T, Auboeuf D, Bourgeois CF, Mortreux F. Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation. Nucleic Acids Res 2024; 52:1527-1543. [PMID: 38272542 PMCID: PMC10899780 DOI: 10.1093/nar/gkae015] [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: 06/10/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
The NF-κB protein p65/RelA plays a pivotal role in coordinating gene expression in response to diverse stimuli, including viral infections. At the chromatin level, p65/RelA regulates gene transcription and alternative splicing through promoter enrichment and genomic exon occupancy, respectively. The intricate ways in which p65/RelA simultaneously governs these functions across various genes remain to be fully elucidated. In this study, we employed the HTLV-1 Tax oncoprotein, a potent activator of NF-κB, to investigate its influence on the three-dimensional organization of the genome, a key factor in gene regulation. We discovered that Tax restructures the 3D genomic landscape, bringing together genes based on their regulation and splicing patterns. Notably, we found that the Tax-induced gene-gene contact between the two master genes NFKBIA and RELA is associated with their respective changes in gene expression and alternative splicing. Through dCas9-mediated approaches, we demonstrated that NFKBIA-RELA interaction is required for alternative splicing regulation and is caused by an intragenic enrichment of p65/RelA on RELA. Our findings shed light on new regulatory mechanisms upon HTLV-1 Tax and underscore the integral role of p65/RelA in coordinated regulation of NF-κB-responsive genes at both transcriptional and splicing levels in the context of the 3D genome.
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Affiliation(s)
- Paul Marie
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Matéo Bazire
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Julien Ladet
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Lamya Ben Ameur
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Sanjay Chahar
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Nicolas Fontrodona
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Cyril F Bourgeois
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Franck Mortreux
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
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2
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Zhang L, Wang Z, Liu R, Li Z, Lin J, Wojciechowicz ML, Huang J, Lee K, Ma'ayan A, He JC. Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease. Diabetes 2021; 70:589-602. [PMID: 33067313 PMCID: PMC7881868 DOI: 10.2337/db20-0580] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022]
Abstract
Diabetic kidney disease (DKD) remains the most common cause of kidney failure, and the treatment options are insufficient. Here, we used a connectivity mapping approach to first collect 15 gene expression signatures from 11 DKD-related published independent studies. Then, by querying the Library of Integrated Network-based Cellular Signatures (LINCS) L1000 data set, we identified drugs and other bioactive small molecules that are predicted to reverse these gene signatures in the diabetic kidney. Among the top consensus candidates, we selected a PLK1 inhibitor (BI-2536) for further experimental validation. We found that PLK1 expression was increased in the glomeruli of both human and mouse diabetic kidneys and localized largely in mesangial cells. We also found that BI-2536 inhibited mesangial cell proliferation and extracellular matrix in vitro and ameliorated proteinuria and kidney injury in DKD mice. Further pathway analysis of the genes predicted to be reversed by the PLK1 inhibitor was of members of the TNF-α/NF-κB, JAK/STAT, and TGF-β/Smad3 pathways. In vitro, either BI-2536 treatment or knockdown of PLK1 dampened the NF-κB and Smad3 signal transduction and transcriptional activation. Together, these results suggest that the PLK1 inhibitor BI-2536 should be further investigated as a novel therapy for DKD.
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Affiliation(s)
- Lu Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Zichen Wang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ruijie Liu
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zhengzhe Li
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jennifer Lin
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Megan L Wojciechowicz
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jiyi Huang
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Kyung Lee
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - John Cijiang He
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Renal Section, James J. Peters Veterans Affair Medical Center, Bronx, NY
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3
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Surai PF, Kochish II, Kidd MT. Redox Homeostasis in Poultry: Regulatory Roles of NF-κB. Antioxidants (Basel) 2021; 10:186. [PMID: 33525511 PMCID: PMC7912633 DOI: 10.3390/antiox10020186] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Redox biology is a very quickly developing area of modern biological sciences, and roles of redox homeostasis in health and disease have recently received tremendous attention. There are a range of redox pairs in the cells/tissues responsible for redox homeostasis maintenance/regulation. In general, all redox elements are interconnected and regulated by various means, including antioxidant and vitagene networks. The redox status is responsible for maintenance of cell signaling and cell stress adaptation. Physiological roles of redox homeostasis maintenance in avian species, including poultry, have received limited attention and are poorly characterized. However, for the last 5 years, this topic attracted much attention, and a range of publications covered some related aspects. In fact, transcription factor Nrf2 was shown to be a master regulator of antioxidant defenses via activation of various vitagenes and other protective molecules to maintain redox homeostasis in cells/tissues. It was shown that Nrf2 is closely related to another transcription factor, namely, NF-κB, responsible for control of inflammation; however, its roles in poultry have not yet been characterized. Therefore, the aim of this review is to describe a current view on NF-κB functioning in poultry with a specific emphasis to its nutritional modulation under various stress conditions. In particular, on the one hand, it has been shown that, in many stress conditions in poultry, NF-κB activation can lead to increased synthesis of proinflammatory cytokines leading to systemic inflammation. On the other hand, there are a range of nutrients/supplements that can downregulate NF-κB and decrease the negative consequences of stress-related disturbances in redox homeostasis. In general, vitagene-NF-κB interactions in relation to redox balance homeostasis, immunity, and gut health in poultry production await further research.
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Affiliation(s)
- Peter F. Surai
- Department of Biochemistry, Vitagene and Health Research Centre, Bristol BS4 2RS, UK
- Department of Hygiene and Poultry Sciences, Moscow State Academy of Veterinary Medicine and Biotechnology named after K. I. Skryabin, 109472 Moscow, Russia;
- Department of Biochemistry and Physiology, Saint-Petersburg State Academy of Veterinary Medicine, 196084 St. Petersburg, Russia
- Department of Microbiology and Biochemistry, Faculty of Veterinary Medicine, Trakia University, 6000 Stara Zagora, Bulgaria
- Department of Animal Nutrition, Faculty of Agricultural and Environmental Sciences, Szent Istvan University, H-2103 Gödöllo, Hungary
| | - Ivan I. Kochish
- Department of Hygiene and Poultry Sciences, Moscow State Academy of Veterinary Medicine and Biotechnology named after K. I. Skryabin, 109472 Moscow, Russia;
| | - Michael T. Kidd
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA;
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4
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An JY, Meng FR, Yan ZJ. An efficient computational method for predicting drug-target interactions using weighted extreme learning machine and speed up robot features. BioData Min 2021; 14:3. [PMID: 33472664 PMCID: PMC7816443 DOI: 10.1186/s13040-021-00242-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/10/2021] [Indexed: 01/09/2023] Open
Abstract
Background Prediction of novel Drug–Target interactions (DTIs) plays an important role in discovering new drug candidates and finding new proteins to target. In consideration of the time-consuming and expensive of experimental methods. Therefore, it is a challenging task that how to develop efficient computational approaches for the accurate predicting potential associations between drug and target. Results In the paper, we proposed a novel computational method called WELM-SURF based on drug fingerprints and protein evolutionary information for identifying DTIs. More specifically, for exploiting protein sequence feature, Position Specific Scoring Matrix (PSSM) is applied to capturing protein evolutionary information and Speed up robot features (SURF) is employed to extract sequence key feature from PSSM. For drug fingerprints, the chemical structure of molecular substructure fingerprints was used to represent drug as feature vector. Take account of the advantage that the Weighted Extreme Learning Machine (WELM) has short training time, good generalization ability, and most importantly ability to efficiently execute classification by optimizing the loss function of weight matrix. Therefore, the WELM classifier is used to carry out classification based on extracted features for predicting DTIs. The performance of the WELM-SURF model was evaluated by experimental validations on enzyme, ion channel, GPCRs and nuclear receptor datasets by using fivefold cross-validation test. The WELM-SURF obtained average accuracies of 93.54, 90.58, 85.43 and 77.45% on enzyme, ion channels, GPCRs and nuclear receptor dataset respectively. We also compared our performance with the Extreme Learning Machine (ELM), the state-of-the-art Support Vector Machine (SVM) on enzyme and ion channels dataset and other exiting methods on four datasets. By comparing with experimental results, the performance of WELM-SURF is significantly better than that of ELM, SVM and other previous methods in the domain. Conclusion The results demonstrated that the proposed WELM-SURF model is competent for predicting DTIs with high accuracy and robustness. It is anticipated that the WELM-SURF method is a useful computational tool to facilitate widely bioinformatics studies related to DTIs prediction.
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Affiliation(s)
- Ji-Yong An
- Engineering Research Center of Mine Digitalization (China University of Mining and Technology), Ministry of Education, Xuzhou, China. .,School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, 21116, Jiangsu, China.
| | - Fan-Rong Meng
- Engineering Research Center of Mine Digitalization (China University of Mining and Technology), Ministry of Education, Xuzhou, China.,School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, 21116, Jiangsu, China
| | - Zi-Ji Yan
- Engineering Research Center of Mine Digitalization (China University of Mining and Technology), Ministry of Education, Xuzhou, China.,School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, 21116, Jiangsu, China
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5
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Brasier AR. RSV Reprograms the CDK9•BRD4 Chromatin Remodeling Complex to Couple Innate Inflammation to Airway Remodeling. Viruses 2020; 12:v12040472. [PMID: 32331282 PMCID: PMC7232410 DOI: 10.3390/v12040472] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 02/06/2023] Open
Abstract
Respiratory syncytial virus infection is responsible for seasonal upper and lower respiratory tract infections worldwide, causing substantial morbidity. Self-inoculation of the virus into the nasopharynx results in epithelial replication and distal spread into the lower respiratory tract. Here, respiratory syncytial virus (RSV) activates sentinel cells important in the host inflammatory response, resulting in epithelial-derived cytokine and interferon (IFN) expression resulting in neutrophilia, whose intensity is associated with disease severity. I will synthesize key findings describing how RSV replication activates intracellular NFκB and IRF signaling cascades controlling the innate immune response (IIR). Recent studies have implicated a central role for Scg1a1+ expressing progenitor cells in IIR, a cell type uniquely primed to induce neutrophilic-, T helper 2 (Th2)-polarizing-, and fibrogenic cytokines that play distinct roles in disease pathogenesis. Molecular studies have linked the positive transcriptional elongation factor-b (P-TEFb), a pleiotrophic chromatin remodeling complex in immediate-early IIR gene expression. Through intrinsic kinase activity of cyclin dependent kinase (CDK) 9 and atypical histone acetyl transferase activity of bromodomain containing protein 4 (BRD4), P-TEFb mediates transcriptional elongation of IIR genes. Unbiased proteomic studies show that the CDK9•BRD4 complex is dynamically reconfigured by the innate response and targets TGFβ-dependent fibrogenic gene networks. Chronic activation of CDK9•BRD4 mediates chromatin remodeling fibrogenic gene networks that cause epithelial mesenchymal transition (EMT). Mesenchymal transitioned epithelial cells elaborate TGFβ and IL6 that function in a paracrine manner to expand the population of subepithelial myofibroblasts. These findings may account for the long-term reduction in pulmonary function in children with severe lower respiratory tract infection (LRTI). Modifying chromatin remodeling properties of the CDK9•BRD4 coactivators may provide a mechanism for reducing post-infectious airway remodeling that are a consequence of severe RSV LRTIs.
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Affiliation(s)
- Allan R Brasier
- Institute for Clinical and Translational Research; University of Wisconsin-Madison School of Medicine and Public Health; Madison, WI 53705, USA
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6
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de Jesús TJ, Ramakrishnan P. NF-κB c-Rel Dictates the Inflammatory Threshold by Acting as a Transcriptional Repressor. iScience 2020; 23:100876. [PMID: 32062419 PMCID: PMC7031323 DOI: 10.1016/j.isci.2020.100876] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/11/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022] Open
Abstract
NF-κB/Rel family of transcription factors plays a central role in initiation and resolution of inflammatory responses. Here, we identified a function of the NF-κB subunit c-Rel as a transcriptional repressor of inflammatory genes. Genetic deletion of c-Rel substantially potentiates the expression of several TNF-α-induced RelA-dependent mediators of inflammation. v-Rel, the viral homologue of c-Rel, but not RelB, also possesses this repressive function. Mechanistically, we found that c-Rel selectively binds to the co-repressor HDAC1 and competitively binds to the DNA mediating HDAC1 recruitment to the promoters of inflammatory genes. A specific point mutation at tyrosine25 in c-Rel's DNA-binding domain, for which a missense single nucleotide variation (Y25H) exists in humans, completely abrogated its ability to bind DNA and repress TNF-α-induced, RelA-mediated transcription. Our findings reveal that the transactivator NF-κB subunit c-Rel also plays a role as a transcriptional repressor in the maintenance of inflammatory homeostasis.
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Affiliation(s)
- Tristan James de Jesús
- Department of Pathology, School of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, 6526, Wolstein Research Building, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Parameswaran Ramakrishnan
- Department of Pathology, School of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, 6526, Wolstein Research Building, 2103 Cornell Road, Cleveland, OH 44106, USA; Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; The Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
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7
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Tian B, Liu Z, Yang J, Sun H, Zhao Y, Wakamiya M, Chen H, Rytting E, Zhou J, Brasier AR. Selective Antagonists of the Bronchiolar Epithelial NF-κB-Bromodomain-Containing Protein 4 Pathway in Viral-Induced Airway Inflammation. Cell Rep 2019; 23:1138-1151. [PMID: 29694891 DOI: 10.1016/j.celrep.2018.03.106] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 02/11/2018] [Accepted: 03/22/2018] [Indexed: 11/25/2022] Open
Abstract
The mechanisms by which the mammalian airway detects invading viral pathogens to trigger protective innate neutrophilic inflammation are incompletely understood. We observe that innate activation of nuclear factor κB (NF-κB)/RelA transcription factor indirectly activates atypical BRD4 histone acetyltransferase (HAT) activity, RNA polymerase II (Pol II) phosphorylation, and secretion of neutrophilic chemokines. To study this pathway in vivo, we developed a conditional knockout of RelA in distal airway epithelial cells; these animals have reduced mucosal BRD4/Pol II activation and neutrophilic inflammation to viral patterns. To further understand the role of BRD4 in vivo, two potent, highly selective small-molecule BRD4 inhibitors were developed. These well-tolerated inhibitors disrupt the BRD4 complex with Pol II and histones, completely blocking inducible epithelial chemokine production and neutrophilia. We conclude that RelA-BRD4 signaling in distal tracheobronchiolar epithelial cells mediates acute inflammation in response to luminal viral patterns. These potent BRD4 antagonists are versatile pharmacological tools for investigating BRD4 functions in vivo.
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Affiliation(s)
- Bing Tian
- Department of Internal Medicine, University of Texas, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas, Galveston, TX 77555, USA
| | - Zhiqing Liu
- Department of Pharmacology and Toxicology, University of Texas, Galveston, TX 77555, USA
| | - Jun Yang
- Department of Internal Medicine, University of Texas, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas, Galveston, TX 77555, USA
| | - Hong Sun
- Department of Internal Medicine, University of Texas, Galveston, TX 77555, USA
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas, Galveston, TX 77555, USA; Institute for Translational Sciences, University of Texas, Galveston, TX 77555, USA
| | - Maki Wakamiya
- Institute for Translational Sciences, University of Texas, Galveston, TX 77555, USA
| | - Haiying Chen
- Department of Pharmacology and Toxicology, University of Texas, Galveston, TX 77555, USA
| | - Erik Rytting
- Department of Obstetrics and Gynecology, University of Texas, Galveston, TX 77555, USA
| | - Jia Zhou
- Sealy Center for Molecular Medicine, University of Texas, Galveston, TX 77555, USA; Department of Pharmacology and Toxicology, University of Texas, Galveston, TX 77555, USA; Institute for Translational Sciences, University of Texas, Galveston, TX 77555, USA
| | - Allan R Brasier
- School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA.
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8
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Jiao HL, Ye YP, Yang RW, Sun HY, Wang SY, Wang YX, Xiao ZY, He LQ, Cai JJ, Wei WT, Chen YR, Gu CC, Cai YL, Hu YT, Lai QH, Qiu JF, Liang L, Cao GW, Liao WT, Ding YQ. Downregulation of SAFB Sustains the NF- κB Pathway by Targeting TAK1 during the Progression of Colorectal Cancer. Clin Cancer Res 2017; 23:7108-7118. [PMID: 28912140 DOI: 10.1158/1078-0432.ccr-17-0747] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/17/2017] [Accepted: 09/07/2017] [Indexed: 11/16/2022]
Abstract
Purpose: To investigate the role and the underlying mechanism of scaffold attachment factor B (SAFB) in the progression of colorectal cancer (CRC).Experimental Design: SAFB expression was analyzed in the Cancer Outlier Profile Analysis of Oncomine and in 175 paraffin-embedded archived CRC tissues. Gene Ontology analyses were performed to explore the mechanism of SAFB in CRC progression. Western blot, RT-PCR, luciferase assay, and chromatin immunoprecipitation (ChIP) were used to detect the regulation of transforming growth factor-β-activated kinase 1 (TAK1) and NF-κB signaling by SAFB The role of SAFB in invasion, metastasis, and angiogenesis was investigated using in vitro and in vivo assays. The relationship between SAFB and TAK1 was analyzed in CRC tissues.Results: SAFB was downregulated in CRC tissues, and low expression of SAFB was significantly associated with an aggressive phenotype and poorer survival of CRC patients. The downregulation of SAFB activated NF-κB signaling by targeting the TAK1 promoter. Ectopic expression of SAFB inhibited the development of aggressive features and metastasis of CRC cells both in vitro and in vivo The overexpression of TAK1 could rescue the aggressive features in SAFB-overexpressed cells. Furthermore, the expression of SAFB in CRC tissues was negatively correlated with the expression of TAK1- and NF-κB-related genes.Conclusions: Our results show that SAFB regulated the activity of NF-κB signaling in CRC by targeting TAK1 This novel mechanism provides a comprehensive understanding of both SAFB and the NF-κB signaling pathway in the progression of CRC and indicates that the SAFB-TAK1-NF-κB axis is a potential target for early therapeutic intervention in CRC progression. Clin Cancer Res; 23(22); 7108-18. ©2017 AACR.
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Affiliation(s)
- Hong-Li Jiao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Ya-Ping Ye
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Run-Wei Yang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Hui-Ying Sun
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Shu-Yang Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Yong-Xia Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Zhi-Yuan Xiao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Liu-Qing He
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Juan-Juan Cai
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Wen-Ting Wei
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Yan-Ru Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Chun-Cai Gu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Yue-Long Cai
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Yun-Teng Hu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Qiu-Hua Lai
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Jun-Feng Qiu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Li Liang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Guang-Wen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Wen-Ting Liao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China. .,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Yan-Qing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China. .,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
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9
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Zhang Y, Sun H, Zhang J, Brasier AR, Zhao Y. Quantitative Assessment of the Effects of Trypsin Digestion Methods on Affinity Purification-Mass Spectrometry-based Protein-Protein Interaction Analysis. J Proteome Res 2017; 16:3068-3082. [PMID: 28726418 DOI: 10.1021/acs.jproteome.7b00432] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Affinity purification-mass spectrometry (AP-MS) has become the method of choice for discovering protein-protein interactions (PPIs) under native conditions. The success of AP-MS depends on the efficiency of trypsin digestion and the recovery of the tryptic peptides for MS analysis. Several different protocols have been used for trypsin digestion of protein complexes in AP-MS studies, but no systematic studies have been conducted on the impact of trypsin digestion conditions on the identification of PPIs. Here, we used NFκB/RelA and Bromodomain-containing protein 4 (BRD4) as baits and test five distinct trypsin digestion methods (two using "on-beads," three using "elution-digestion" protocols). Although the performance of the trypsin digestion protocols change slightly depending on the different baits, antibodies and cell lines used, we found that elution-digestion methods consistently outperformed on-beads digestion methods. The high-abundance interactors can be identified universally by all five methods, but the identification of low-abundance RelA interactors is significantly affected by the choice of trypsin digestion method. We also found that different digestion protocols influence the selected reaction monitoring (SRM)-MS quantification of PPIs, suggesting that optimization of trypsin digestion conditions may be required for robust targeted analysis of PPIs.
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Affiliation(s)
- Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Hong Sun
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Jing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
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10
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Martin M, Hua L, Wang B, Wei H, Prabhu L, Hartley AV, Jiang G, Liu Y, Lu T. Novel Serine 176 Phosphorylation of YBX1 Activates NF-κB in Colon Cancer. J Biol Chem 2017; 292:3433-3444. [PMID: 28077578 DOI: 10.1074/jbc.m116.740258] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 01/09/2017] [Indexed: 12/22/2022] Open
Abstract
Y box protein 1 (YBX1) is a well known oncoprotein that has tumor-promoting functions. YBX1 is widely considered to be an attractive therapeutic target in cancer. To develop novel therapeutics to target YBX1, it is of great importance to understand how YBX1 is finely regulated in cancer. Previously, we have shown that YBX1 could function as a tumor promoter through phosphorylation of its Ser-165 residue, leading to the activation of the NF-κB signaling pathway (1). In this study, using mass spectrometry analysis, we discovered a distinct phosphorylation site, Ser-176, on YBX1. Overexpression of the YBX1-S176A (serine-to-alanine) mutant in either HEK293 cells or colon cancer HT29 cells showed dramatically reduced NF-κB-activating ability compared with that of WT-YBX1, confirming that Ser-176 phosphorylation is critical for the activation of NF-κB by YBX1. Importantly, the mutant of Ser-176 and the previously reported Ser-165 sites regulate distinct groups of NF-κB target genes, suggesting the unique and irreplaceable function of each of these two phosphorylated serine residues. Our important findings could provide a novel cancer therapy strategy by blocking either Ser-176 or Ser-165 phosphorylation or both of YBX1 in colon cancer.
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Affiliation(s)
| | | | - Benlian Wang
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Han Wei
- Departments of Pharmacology and Toxicology
| | | | | | - Guanglong Jiang
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Yunlong Liu
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Tao Lu
- Departments of Pharmacology and Toxicology; Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202; Biochemistry and Molecular Biology.
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11
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Targeting Chromatin Remodeling in Inflammation and Fibrosis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 107:1-36. [PMID: 28215221 DOI: 10.1016/bs.apcsb.2016.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mucosal surfaces of the human body are lined by a contiguous epithelial cell surface that forms a barrier to aerosolized pathogens. Specialized pattern recognition receptors detect the presence of viral pathogens and initiate protective host responses by triggering activation of the nuclear factor κB (NFκB)/RelA transcription factor and formation of a complex with the positive transcription elongation factor (P-TEFb)/cyclin-dependent kinase (CDK)9 and Bromodomain-containing protein 4 (BRD4) epigenetic reader. The RelA·BRD4·P-TEFb complex produces acute inflammation by regulating transcriptional elongation, which produces a rapid genomic response by inactive genes maintained in an open chromatin configuration engaged with hypophosphorylated RNA polymerase II. We describe recent studies that have linked prolonged activation of the RelA-BRD4 pathway with the epithelial-mesenchymal transition (EMT) by inducing a core of EMT corepressors, stimulating secretion of growth factors promoting airway fibrosis. The mesenchymal state produces rewiring of the kinome and reprogramming of innate responses toward inflammation. In addition, the core regulator Zinc finger E-box homeodomain 1 (ZEB1) silences the expression of the interferon response factor 1 (IRF1), required for type III IFN expression. This epigenetic silencing is mediated by the Enhancer of Zeste 2 (EZH2) histone methyltransferase. Because of their potential applications in cancer and inflammation, small-molecule inhibitors of NFκB/RelA, CDK9, BRD4, and EZH2 have been the targets of medicinal chemistry efforts. We suggest that disruption of the RelA·BRD4·P-TEFb pathway and EZH2 methyltransferase has important implications for reversing fibrosis and restoring normal mucosal immunity in chronic inflammatory diseases.
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12
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Kędzierska H, Popławski P, Hoser G, Rybicka B, Rodzik K, Sokół E, Bogusławska J, Tański Z, Fogtman A, Koblowska M, Piekiełko-Witkowska A. Decreased Expression of SRSF2 Splicing Factor Inhibits Apoptotic Pathways in Renal Cancer. Int J Mol Sci 2016; 17:ijms17101598. [PMID: 27690003 PMCID: PMC5085631 DOI: 10.3390/ijms17101598] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/31/2016] [Accepted: 09/05/2016] [Indexed: 12/14/2022] Open
Abstract
Serine and arginine rich splicing factor 2(SRSF2) belongs to the serine/arginine (SR)-rich family of proteins that regulate alternative splicing. Previous studies suggested that SRSF2 can contribute to carcinogenic processes. Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer, highly aggressive and difficult to treat, mainly due to resistance to apoptosis. In this study we hypothesized that SRSF2 contributes to the regulation of apoptosis in ccRCC. Using tissue samples obtained from ccRCC patients, as well as independent validation on The Cancer Genome Atlas (TCGA) data, we demonstrate for the first time that expression of SRSF2 is decreased in ccRCC tumours when compared to non-tumorous control tissues. Furthermore, by employing a panel of ccRCC-derived cell lines with silenced SRSF2 expression and qPCR arrays we show that SRSF2 contributes not only to splicing patterns but also to expression of multiple apoptotic genes, including new SRSF2 targets: DIABLO, BIRC5/survivin, TRAIL, BIM, MCL1, TNFRSF9, TNFRSF1B, CRADD, BCL2L2, BCL2A1, and TP53. We also identified a new splice variant of CFLAR, an inhibitor of caspase activity. These changes culminate in diminished caspase-9 activity and inhibition of apoptosis. In summary, we show for the first time that decreased expression of SRSF2 in ccRCC contributes to protection of cancer cells viability.
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Affiliation(s)
- Hanna Kędzierska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Piotr Popławski
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Grażyna Hoser
- Laboratory of Flow Cytometry, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Beata Rybicka
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Katarzyna Rodzik
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Elżbieta Sokół
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Joanna Bogusławska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Zbigniew Tański
- Department of Urology, Regional Hospital, 07-410 Ostrołęka, Poland.
| | - Anna Fogtman
- Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.
| | - Marta Koblowska
- Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland.
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13
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Ramos-Marquès E, Zambrano S, Tiérrez A, Bianchi ME, Agresti A, García-Del Portillo F. Single-cell analyses reveal an attenuated NF-κB response in the Salmonella-infected fibroblast. Virulence 2016; 8:719-740. [PMID: 27575017 DOI: 10.1080/21505594.2016.1229727] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The eukaryotic transcriptional regulator Nuclear Factor kappa B (NF-κB) plays a central role in the defense to pathogens. Despite this, few studies have analyzed NF-κB activity in single cells during infection. Here, we investigated at the single cell level how NF-κB nuclear localization - a proxy for NF-κB activity - oscillates in infected and uninfected fibroblasts co-existing in cultures exposed to Salmonella enterica serovar Typhimurium. Fibroblasts were used due to the capacity of S. Typhimurium to persist in this cell type. Real-time dynamics of NF-κB was examined in microfluidics, which prevents cytokine accumulation. In this condition, infected (ST+) cells translocate NF-κB to the nucleus at higher rate than the uninfected (ST-) cells. Surprisingly, in non-flow (static) culture conditions, ST- fibroblasts exhibited higher NF-κB nuclear translocation than the ST+ population, with these latter cells turning refractory to external stimuli such as TNF-α or a second infection. Sorting of ST+ and ST- cell populations confirmed enhanced expression of NF-κB target genes such as IL1B, NFKBIA, TNFAIP3, and TRAF1 in uninfected (ST-) fibroblasts. These observations proved that S. Typhimurium dampens the NF-κB response in the infected fibroblast. Higher expression of SOCS3, encoding a "suppressor of cytokine signaling," was also observed in the ST+ population. Intracellular S. Typhimurium subverts NF-κB activity using protein effectors translocated by the secretion systems encoded by pathogenicity islands 1 (T1) and 2 (T2). T1 is required for regulating expression of SOCS3 and all NF-κB target genes analyzed whereas T2 displayed no role in the control of SOCS3 and IL1B expression. Collectively, these data demonstrate that S. Typhimurium attenuates NF-κB signaling in fibroblasts, an effect only perceptible when ST+ and ST- populations are analyzed separately. This tune-down in a central host defense might be instrumental for S. Typhimurium to establish intracellular persistent infections.
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Affiliation(s)
- Estel Ramos-Marquès
- a Laboratory of Intracellular Bacterial Pathogens , Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC) , Madrid , Spain
| | | | - Alberto Tiérrez
- a Laboratory of Intracellular Bacterial Pathogens , Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC) , Madrid , Spain
| | - Marco E Bianchi
- c Genetics and Cell Biology Division , San Raffaele Scientific Institute , Milan , Italy
| | - Alessandra Agresti
- c Genetics and Cell Biology Division , San Raffaele Scientific Institute , Milan , Italy
| | - Francisco García-Del Portillo
- a Laboratory of Intracellular Bacterial Pathogens , Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC) , Madrid , Spain
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14
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Zhang L, Shao L, Creighton CJ, Zhang Y, Xin L, Ittmann M, Wang J. Function of phosphorylation of NF-kB p65 ser536 in prostate cancer oncogenesis. Oncotarget 2016; 6:6281-94. [PMID: 25749044 PMCID: PMC4467437 DOI: 10.18632/oncotarget.3366] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/12/2015] [Indexed: 01/11/2023] Open
Abstract
Majority of prostate cancer (PCa) patients carry TMPRSS2/ERG (T/E) fusion genes and there has been tremendous interest in understanding how the T/E fusion may promote progression of PCa. We showed that T/E fusion can activate NF-kB pathway by increasing phosphorylation of NF-kB p65 Ser536 (p536), but the function of p536 has never been studied in PCa. We report here that active p536 can significantly increase cell motility and transform PNT1a cells (an immortalized normal cell line), suggesting p536 plays a critical role in promoting PCa tumorigenesis. We have discovered a set of p536 regulated genes, among which we validated the regulation of CCL2 by p536. Based on all evidence, we favor that T/E fusion, NF-kB p536 and CCL2 form a signaling chain. Finally, PNT1a cells (not tumorigenic) can form tumors in SCID mice when overexpressing of either wild type or active p65 in the presence of activated AKT, demonstrating synergistic activities of NF-kB and AKT signals in promoting PCa tumorigenesis. These findings indicate that combination therapies targeting T/E fusion, NF-kB, CCL2 and/or AKT pathways may have efficacy in T/E fusion gene expressing PCa. If successful, such targeted therapy will benefit more than half of PCa patients who carry T/E fusions.
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Affiliation(s)
- Li Zhang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China.,Department of Pathology and Immunology, Baylor College of Medicine and Michael E. DeBakey Deptartment of Veterans Affairs Medical Center, Houston, Texas, USA
| | - Longjiang Shao
- Department of Pathology and Immunology, Baylor College of Medicine and Michael E. DeBakey Deptartment of Veterans Affairs Medical Center, Houston, Texas, USA
| | - Chad J Creighton
- Duncan Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, Texas, USA.,Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Yiqun Zhang
- Duncan Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, Texas, USA
| | - Li Xin
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Michael Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine and Michael E. DeBakey Deptartment of Veterans Affairs Medical Center, Houston, Texas, USA
| | - Jianghua Wang
- Department of Pathology and Immunology, Baylor College of Medicine and Michael E. DeBakey Deptartment of Veterans Affairs Medical Center, Houston, Texas, USA
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15
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Wu XB, Liu Y, Wang GH, Xu X, Cai Y, Wang HY, Li YQ, Meng HF, Dai F, Jin JD. Mesenchymal stem cells promote colorectal cancer progression through AMPK/mTOR-mediated NF-κB activation. Sci Rep 2016; 6:21420. [PMID: 26892992 PMCID: PMC4759824 DOI: 10.1038/srep21420] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/22/2016] [Indexed: 12/12/2022] Open
Abstract
Mesenchymal stem cells (MSCs) exert a tumor-promoting effect in a variety of human cancers. This study was designed to identify the molecular mechanisms related to the tumor-promoting effect of MSCs in colorectal cancer. In vitro analysis of colorectal cancer cell lines cultured in MSC conditioned media (MSC-CM) showed that MSC-CM significantly promoted the progression of the cancer cells by enhancing cell proliferation, migration and colony formation. The tumorigenic effect of MSC-CM was attributed to altered expression of cell cycle regulatory proteins and inhibition of apoptosis. Furthermore, MSC-CM induced high level expression of a number of pluripotency factors in the cancer cells. ELISAs revealed MSC-CM contained higher levels of IL-6 and IL-8, which are associated with the progression of cancer. Moreover, MSC-CM downregulated AMPK mRNA and protein phosphorylation, but upregulated mTOR mRNA and protein phosphorylation. The NF-κB pathway was activated after addition of MSC-CM. An in vivo model in Balb/C mice confirmed the ability of MSC-CM to promote the invasion and proliferation of colorectal cancer cells. This study indicates that MSCs promote the progression of colorectal cancer via AMPK/mTOR-mediated NF-κB activation.
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Affiliation(s)
- Xiao-Bing Wu
- Department of Gastroenterology, the Third Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230061, P. R. China.,Institute of Radiation Medicine, Academy Military Medical Sciences, Beijing 100850, P. R. China
| | - Yang Liu
- The First Hospital Attached to Guiyang College of Traditional Chinese Medicine. Department of Clinical Laboratory, The First Hospital Attached to Guiyang College of Traditional Chinese Medicine, NO.71, Bao Shan North Road, Yunyan District, Guiyang City
| | - Gui-Hua Wang
- Institute of Radiation Medicine, Academy Military Medical Sciences, Beijing 100850, P. R. China
| | - Xiao Xu
- The General Hospital of Chinese Armed Force Police, Beijing 100039, P. R. China
| | - Yang Cai
- Institute of Radiation Medicine, Academy Military Medical Sciences, Beijing 100850, P. R. China
| | - Hong-Yi Wang
- Institute of Radiation Medicine, Academy Military Medical Sciences, Beijing 100850, P. R. China
| | - Yan-Qi Li
- Institute of Radiation Medicine, Academy Military Medical Sciences, Beijing 100850, P. R. China
| | - Hong-Fang Meng
- Institute of Radiation Medicine, Academy Military Medical Sciences, Beijing 100850, P. R. China
| | - Fu Dai
- Department of Gastroenterology, the Third Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230061, P. R. China
| | - Ji-De Jin
- Institute of Radiation Medicine, Academy Military Medical Sciences, Beijing 100850, P. R. China
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16
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Zambrano S, De Toma I, Piffer A, Bianchi ME, Agresti A. NF-κB oscillations translate into functionally related patterns of gene expression. eLife 2016; 5:e09100. [PMID: 26765569 PMCID: PMC4798970 DOI: 10.7554/elife.09100] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 01/13/2016] [Indexed: 12/18/2022] Open
Abstract
Several transcription factors (TFs) oscillate, periodically relocating between the cytoplasm and the nucleus. NF-κB, which plays key roles in inflammation and cancer, displays oscillations whose biological advantage remains unclear. Recent work indicated that NF-κB displays sustained oscillations that can be entrained, that is, reach a persistent synchronized state through small periodic perturbations. We show here that for our GFP-p65 knock-in cells NF-κB behaves as a damped oscillator able to synchronize to a variety of periodic external perturbations with no memory. We imposed synchronous dynamics to prove that transcription of NF-κB-controlled genes also oscillates, but mature transcript levels follow three distinct patterns. Two sets of transcripts accumulate fast or slowly, respectively. Another set, comprising chemokine and chemokine receptor mRNAs, oscillates and resets at each new stimulus, with no memory of the past. We propose that TF oscillatory dynamics is a means of segmenting time to provide renewing opportunity windows for decision.
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Affiliation(s)
- Samuel Zambrano
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
- San Raffaele University, Milan, Italy
| | | | | | - Marco E Bianchi
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
- San Raffaele University, Milan, Italy
| | - Alessandra Agresti
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
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17
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Li X, Zhu M, Brasier AR, Kudlicki AS. Inferring genome-wide functional modulatory network: a case study on NF-κB/RelA transcription factor. J Comput Biol 2016; 22:300-12. [PMID: 25844669 DOI: 10.1089/cmb.2014.0299] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
How different pathways lead to the activation of a specific transcription factor (TF) with specific effects is not fully understood. We model context-specific transcriptional regulation as a modulatory network: triplets composed of a TF, target gene, and modulator. Modulators usually affect the activity of a specific TF at the posttranscriptional level in a target gene-specific action mode. This action may be classified as enhancement, attenuation, or inversion of either activation or inhibition. As a case study, we inferred, from a large collection of expression profiles, all potential modulations of NF-κB/RelA. The predicted modulators include many proteins previously not reported as physically binding to RelA but with relevant functions, such as RNA processing, cell cycle, mitochondrion, ubiquitin-dependent proteolysis, and chromatin modification. Modulators from different processes exert specific prevalent action modes on distinct pathways. Modulators from noncoding RNA, RNA-binding proteins, TFs, and kinases modulate the NF-κB/RelA activity with specific action modes consistent with their molecular functions and modulation level. The modulatory networks of NF-κB/RelA in the context epithelial-mesenchymal transition (EMT) and burn injury have different modulators, including those involved in extracellular matrix (FBN1), cytoskeletal regulation (ACTN1), and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long intergenic nonprotein coding RNA, and tumor suppression (FOXP1) for EMT, and TXNIP, GAPDH, PKM2, IFIT5, LDHA, NID1, and TPP1 for burn injury.
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Affiliation(s)
- Xueling Li
- 1 Department of Biochemistry and Molecular Biology, University of Texas Medical Branch , Galveston, Texas
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18
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Yang J, Zhao Y, Kalita M, Li X, Jamaluddin M, Tian B, Edeh CB, Wiktorowicz JE, Kudlicki A, Brasier AR. Systematic Determination of Human Cyclin Dependent Kinase (CDK)-9 Interactome Identifies Novel Functions in RNA Splicing Mediated by the DEAD Box (DDX)-5/17 RNA Helicases. Mol Cell Proteomics 2015. [PMID: 26209609 DOI: 10.1074/mcp.m115.049221] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Inducible transcriptional elongation is a rapid, stereotypic mechanism for activating immediate early immune defense genes by the epithelium in response to viral pathogens. Here, the recruitment of a multifunctional complex containing the cyclin dependent kinase 9 (CDK9) triggers the process of transcriptional elongation activating resting RNA polymerase engaged with innate immune response (IIR) genes. To identify additional functional activity of the CDK9 complex, we conducted immunoprecipitation (IP) enrichment-stable isotope labeling LC-MS/MS of the CDK9 complex in unstimulated cells and from cells activated by a synthetic dsRNA, polyinosinic/polycytidylic acid [poly (I:C)]. 245 CDK9 interacting proteins were identified with high confidence in the basal state and 20 proteins in four functional classes were validated by IP-SRM-MS. These data identified that CDK9 interacts with DDX 5/17, a family of ATP-dependent RNA helicases, important in alternative RNA splicing of NFAT5, and mH2A1 mRNA two proteins controlling redox signaling. A direct comparison of the basal versus activated state was performed using stable isotope labeling and validated by IP-SRM-MS. Recruited into the CDK9 interactome in response to poly(I:C) stimulation are HSPB1, DNA dependent kinases, and cytoskeletal myosin proteins that exchange with 60S ribosomal structural proteins. An integrated human CDK9 interactome map was developed containing all known human CDK9- interacting proteins. These data were used to develop a probabilistic global map of CDK9-dependent target genes that predicted two functional states controlling distinct cellular functions, one important in immune and stress responses. The CDK9-DDX5/17 complex was shown to be functionally important by shRNA-mediated knockdown, where differential accumulation of alternatively spliced NFAT5 and mH2A1 transcripts and alterations in downstream redox signaling were seen. The requirement of CDK9 for DDX5 recruitment to NFAT5 and mH2A1 chromatin target was further demonstrated using chromatin immunoprecipitation (ChIP). These data indicate that CDK9 is a dynamic multifunctional enzyme complex mediating not only transcriptional elongation, but also alternative RNA splicing and potentially translational control.
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Affiliation(s)
- Jun Yang
- From the ‡Department of Internal Medicine; §Sealy Center for Molecular Medicine; ¶Institute for Translational Sciences
| | - Yingxin Zhao
- From the ‡Department of Internal Medicine; §Sealy Center for Molecular Medicine; ¶Institute for Translational Sciences
| | - Mridul Kalita
- §Sealy Center for Molecular Medicine; ¶Institute for Translational Sciences
| | - Xueling Li
- ¶Institute for Translational Sciences; ‖Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - Mohammad Jamaluddin
- From the ‡Department of Internal Medicine; ¶Institute for Translational Sciences
| | - Bing Tian
- From the ‡Department of Internal Medicine; §Sealy Center for Molecular Medicine; ¶Institute for Translational Sciences
| | | | - John E Wiktorowicz
- §Sealy Center for Molecular Medicine; ¶Institute for Translational Sciences; ‖Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - Andrzej Kudlicki
- §Sealy Center for Molecular Medicine; ¶Institute for Translational Sciences; ‖Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - Allan R Brasier
- From the ‡Department of Internal Medicine; §Sealy Center for Molecular Medicine; ¶Institute for Translational Sciences;
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19
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Tian B, Li X, Kalita M, Widen SG, Yang J, Bhavnani SK, Dang B, Kudlicki A, Sinha M, Kong F, Wood TG, Luxon BA, Brasier AR. Analysis of the TGFβ-induced program in primary airway epithelial cells shows essential role of NF-κB/RelA signaling network in type II epithelial mesenchymal transition. BMC Genomics 2015; 16:529. [PMID: 26187636 PMCID: PMC4506436 DOI: 10.1186/s12864-015-1707-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 06/17/2015] [Indexed: 12/21/2022] Open
Abstract
Background The airway epithelial cell plays a central role in coordinating the pulmonary response to injury and inflammation. Here, transforming growth factor-β (TGFβ) activates gene expression programs to induce stem cell-like properties, inhibit expression of differentiated epithelial adhesion proteins and express mesenchymal contractile proteins. This process is known as epithelial mesenchymal transition (EMT); although much is known about the role of EMT in cellular metastasis in an oncogene-transformed cell, less is known about Type II EMT, that occurring in normal epithelial cells. In this study, we applied next generation sequencing (RNA-Seq) in primary human airway epithelial cells to understand the gene program controlling Type II EMT and how cytokine-induced inflammation modifies it. Results Generalized linear modeling was performed on a two-factor RNA-Seq experiment of 6 treatments of telomerase immortalized human small airway epithelial cells (3 replicates). Using a stringent cut-off, we identified 3,478 differentially expressed genes (DEGs) in response to EMT. Unbiased transcription factor enrichment analysis identified three clusters of EMT regulators, one including SMADs/TP63 and another NF-κB/RelA. Surprisingly, we also observed 527 of the EMT DEGs were also regulated by the TNF-NF-κB/RelA pathway. This Type II EMT program was compared to Type III EMT in TGFβ stimulated A549 alveolar lung cancer cells, revealing significant functional differences. Moreover, we observe that Type II EMT modifies the outcome of the TNF program, reducing IFN signaling and enhancing integrin signaling. We confirmed experimentally that TGFβ-induced the NF-κB/RelA pathway by observing a 2-fold change in NF-κB/RelA nuclear translocation. A small molecule IKK inhibitor blocked TGFβ-induced core transcription factor (SNAIL1, ZEB1 and Twist1) and mesenchymal gene (FN1 and VIM) expression. Conclusions These data indicate that NF-κB/RelA controls a SMAD-independent gene network whose regulation is required for initiation of Type II EMT. Type II EMT dramatically affects the induction and kinetics of TNF-dependent gene networks. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1707-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bing Tian
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA. .,Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA.
| | - Xueling Li
- Institute for Translational Sciences, UTMB, Galveston, TX, USA. .,Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA.
| | - Mridul Kalita
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA.
| | - Steven G Widen
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA.
| | - Jun Yang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA.
| | - Suresh K Bhavnani
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA. .,Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. .,Institute for Translational Sciences, UTMB, Galveston, TX, USA.
| | - Bryant Dang
- Institute for Translational Sciences, UTMB, Galveston, TX, USA.
| | - Andrzej Kudlicki
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. .,Institute for Translational Sciences, UTMB, Galveston, TX, USA. .,Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA.
| | - Mala Sinha
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. .,Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA. .,Bioinformatics Program, UTMB, Galveston, TX, USA.
| | - Fanping Kong
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. .,Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA. .,Bioinformatics Program, UTMB, Galveston, TX, USA.
| | - Thomas G Wood
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. .,Institute for Translational Sciences, UTMB, Galveston, TX, USA. .,Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA.
| | - Bruce A Luxon
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. .,Institute for Translational Sciences, UTMB, Galveston, TX, USA. .,Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA. .,Bioinformatics Program, UTMB, Galveston, TX, USA.
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA. .,Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. .,Institute for Translational Sciences, UTMB, Galveston, TX, USA.
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Homouz D, Chen G, Kudlicki AS. Correcting positional correlations in Affymetrix® genome chips. Sci Rep 2015; 5:9078. [PMID: 25767049 PMCID: PMC4649851 DOI: 10.1038/srep09078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/16/2015] [Indexed: 12/03/2022] Open
Abstract
We report and model a previously undescribed systematic error causing spurious excess correlations that depend on the distance between probes on Affymetrix® microarrays. The phenomenon affects pairs of features with large chip separations, up to over 100 probes apart. The effect may have a significant impact on analysis of correlations in large collections of expression data, where the systematic experimental errors are repeated in many data sets. Examples of such studies include analysis of functions and interactions in groups of genes, as well as global properties of genomes. We find that the average correlations between probes on Affymetrix microarrays are larger for smaller chip distances, which points out to a previously undescribed positional artifact. The magnitude of the artifact depends on the design of the chip, and we find it to be especially high for the yeast S98 microarray, where spurious excess correlations reach 0.1 at a distance of 50 probes. We have designed an algorithm to correct this bias and provide new data sets with the corrected expression values. This algorithm was successfully implemented to remove the positional artifact from the S98 chip data while preserving the integrity of the data.
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Affiliation(s)
- Dirar Homouz
- Khalifa University of Science, Technology and Research, Abu Dhabi, UAE
| | | | - Andrzej S Kudlicki
- 1] Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA [2] Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA [3] Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
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