NFKB1 and Cancer: Friend Or Foe?
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Activated Peripheral-Blood-Derived Mononuclear Cells
Transcription factor expression in lipopolysaccharide- activated peripheral-blood-derived mononuclear cells Jared C. Roach*†, Kelly D. Smith*‡, Katie L. Strobe*, Stephanie M. Nissen*, Christian D. Haudenschild§, Daixing Zhou§, Thomas J. Vasicek¶, G. A. Heldʈ, Gustavo A. Stolovitzkyʈ, Leroy E. Hood*†, and Alan Aderem* *Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103; ‡Department of Pathology, University of Washington, Seattle, WA 98195; §Illumina, 25861 Industrial Boulevard, Hayward, CA 94545; ¶Medtronic, 710 Medtronic Parkway, Minneapolis, MN 55432; and ʈIBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598 Contributed by Leroy E. Hood, August 21, 2007 (sent for review January 7, 2007) Transcription factors play a key role in integrating and modulating system. In this model system, we activated peripheral-blood-derived biological information. In this study, we comprehensively measured mononuclear cells, which can be loosely termed ‘‘macrophages,’’ the changing abundances of mRNAs over a time course of activation with lipopolysaccharide (LPS). We focused on the precise mea- of human peripheral-blood-derived mononuclear cells (‘‘macro- surement of mRNA concentrations. There is currently no high- phages’’) with lipopolysaccharide. Global and dynamic analysis of throughput technology that can precisely and sensitively measure all transcription factors in response to a physiological stimulus has yet to mRNAs in a system, although such technologies are likely to be be achieved in a human system, and our efforts significantly available in the near future. To demonstrate the potential utility of advanced this goal. We used multiple global high-throughput tech- such technologies, and to motivate their development and encour- nologies for measuring mRNA levels, including massively parallel age their use, we produced data from a combination of two distinct signature sequencing and GeneChip microarrays. -
Regulation of DNA Binding by Rel/NF-Kb Transcription Factors: Structural Views
Oncogene (1999) 18, 6845 ± 6852 ã 1999 Stockton Press All rights reserved 0950 ± 9232/99 $15.00 http://www.stockton-press.co.uk/onc Regulation of DNA binding by Rel/NF-kB transcription factors: structural views Frances E Chen1 and Gourisankar Ghosh*,2 1Department of Biology, University of California ± San Diego, 9500 Gilman Drive, MC 0359, La Jolla, California, CA 92093-0359, USA; 2Department of Chemistry and Biochemistry, University of California ± San Diego, 9500 Gilman Drive, MC 0359, La Jolla, California, CA 92093-0359, USA Rel/NF-kB transcription factors form homo- and nuclear localization and IkB binding. Additional Rel/ heterodimers with dierent DNA binding site speci®cities NF-kB family members include the v-Rel oncoprotein and DNA binding anities. Several intracellular path- of the avian Rev-T retrovirus, and the Drosophila ways evoked by a wide range of biological factors and Dorsal, Dif and Relish proteins. Rel/NF-kB proteins environmental conditions can lead to the activation of bind to DNA segments with a consensus sequence of Rel/NF-kB dimers by signaling degradation of the 5'-GGGRNYYYCC-3' collectively referred to as kB inhibitory IkB protein. In the nucleus Rel/NF-kB dimers elements or kB sites. For the NF-kB p50/RelA modulate the expression of a variety of genes including heterodimer alone, there are a large number of those encoding cytokines, growth factors, acute phase dierent kB sites that display varying degrees of response proteins, immunoreceptors, other transcription consensus (Figure 1). factors, cell adhesion molecules, viral proteins and Rel/NF-kB regulation can occur at multiple levels: regulators of apoptosis. -
Rela, P50 and Inhibitor of Kappa B Alpha Are Elevated in Human Metastatic Melanoma Cells and Respond Aberrantly to Ultraviolet Light B
PIGMENT CELL RES 14: 456–465. 2001 Copyright © Pigment Cell Res 2001 Printed in Ireland—all rights reser6ed ISSN 0893-5785 Original Research Article RelA, p50 and Inhibitor of kappa B alpha are Elevated in Human Metastatic Melanoma Cells and Respond Aberrantly to Ultraviolet Light B SUSAN E. McNULTY, NILOUFAR B. TOHIDIAN and FRANK L. MEYSKENS Jr. Department of Medicine and Chao Family Comprehensi6e Cancer Center, Uni6ersity of California Ir6ine Medical Center, 101 City Dri6e South, Orange, California 92868 *Address reprint requests to Prof. Frank L. Meyskins, Chao Family Comprehensi6e Cancer Center, Building 23, Rte 81, Uni6ersity of California Ir6ine Medical Center, 101 City Dri6e South, Orange, California 92868. E-mail: fl[email protected] Received 20 April 2001; in final form 15 August 2001 Metastatic melanomas are typically resistant to radiation and melanocytes. We also found that melanoma cells expressed chemotherapy. The underlying basis for this phenomenon may higher cytoplasmic levels of RelA, p105/p50 and the inhibitory result in part from defects in apoptotic pathways. Nuclear protein, inhibitor of kappa B alpha (IkBa) than melanocytes. factor kappa B (NFkB) has been shown to control apoptosis in To directly test whether RelA expression has an impact on many cell types and normally functions as an immediate stress melanoma cell survival, we used antisense RelA phosphoroth- response mechanism that is rigorously controlled by multiple ioate oligonucleotides and found that melanoma cell viability inhibitory complexes. We have previously shown that NFkB was significantly decreased compared with untreated or con- binding is elevated in metastatic melanoma cells relative to trol cultures. The constitutive activation of NFkBin normal melanocytes. -
Product Name: NFKB1 (Ser893) Polyclonal Antibody, ALEXA FLUOR® 594 Conjugated Catalog No
Product Name: NFKB1 (Ser893) Polyclonal Antibody, ALEXA FLUOR® 594 Conjugated Catalog No. : TAP01-94487R-A594 Intended Use: For Research Use Only. Not for used in diagnostic procedures. Size 100ul Concentration 1ug/ul Gene ID 4790 ISO Type Rabbit IgG Clone N/A Immunogen Range 880-900/968 Conjugation ALEXA FLUOR® 594 Subcellular Locations Cytoplasm, Nucleus Applications IF(IHC-P) Cross Reactive Species Human Source KLH conjugated synthetic phosphopeptide derived from human NF KappaB p105 around the phosphorylation site of Ser893 Applications with IF(IHC-P)(1:50-200) Dilutions Purification Purified by Protein A. Background NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52 and the heterodimeric p65-p50 complexappears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Differentdimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF-kappa-B inhibitor (I-kappa-B) family. -
REV-Erbα Regulates CYP7A1 Through Repression of Liver
Supplemental material to this article can be found at: http://dmd.aspetjournals.org/content/suppl/2017/12/13/dmd.117.078105.DC1 1521-009X/46/3/248–258$35.00 https://doi.org/10.1124/dmd.117.078105 DRUG METABOLISM AND DISPOSITION Drug Metab Dispos 46:248–258, March 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics REV-ERBa Regulates CYP7A1 Through Repression of Liver Receptor Homolog-1 s Tianpeng Zhang,1 Mengjing Zhao,1 Danyi Lu, Shuai Wang, Fangjun Yu, Lianxia Guo, Shijun Wen, and Baojian Wu Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy (T.Z., M.Z., D.L., S.W., F.Y., L.G., B.W.), and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research (T.Z., B.W.), Jinan University, Guangzhou, China; and School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (S.W.) Received August 15, 2017; accepted December 6, 2017 ABSTRACT a Nuclear heme receptor reverse erythroblastosis virus (REV-ERB) reduced plasma and liver cholesterol and enhanced production of Downloaded from (a transcriptional repressor) is known to regulate cholesterol 7a- bile acids. Increased levels of Cyp7a1/CYP7A1 were also found in hydroxylase (CYP7A1) and bile acid synthesis. However, the mech- mouse and human primary hepatocytes after GSK2945 treatment. anism for REV-ERBa regulation of CYP7A1 remains elusive. Here, In these experiments, we observed parallel increases in Lrh-1/LRH- we investigate the role of LRH-1 in REV-ERBa regulation of CYP7A1 1 (a known hepatic activator of Cyp7a1/CYP7A1) mRNA and protein. -
Ten Commandments for a Good Scientist
Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds Ana María Sotoca Covaleda Wageningen 2010 Thesis committee Thesis supervisors Prof. dr. ir. Ivonne M.C.M. Rietjens Professor of Toxicology Wageningen University Prof. dr. Albertinka J. Murk Personal chair at the sub-department of Toxicology Wageningen University Thesis co-supervisor Dr. ir. Jacques J.M. Vervoort Associate professor at the Laboratory of Biochemistry Wageningen University Other members Prof. dr. Michael R. Muller, Wageningen University Prof. dr. ir. Huub F.J. Savelkoul, Wageningen University Prof. dr. Everardus J. van Zoelen, Radboud University Nijmegen Dr. ir. Toine F.H. Bovee, RIKILT, Wageningen This research was conducted under the auspices of the Graduate School VLAG Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds Ana María Sotoca Covaleda Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Tuesday 14 September 2010 at 4 p.m. in the Aula Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds. Ana María Sotoca Covaleda Thesis Wageningen University, Wageningen, The Netherlands, 2010, With references, and with summary in Dutch. ISBN: 978-90-8585-707-5 “Caminante no hay camino, se hace camino al andar. Al andar se hace camino, y al volver la vista atrás se ve la senda que nunca se ha de volver a pisar” - Antonio Machado – A mi madre. -
Cell Stress and MEKK1-Mediated C-Jun Activation Modulate NF B
Molecular Biology of the Cell Vol. 13, 2933–2945, August 2002 Cell Stress and MEKK1-mediated c-Jun Activation Modulate NFB Activity and Cell Viability Isabel Sa´nchez-Pe´rez, Salvador Aznar Benitah, Montserrat Martı´nez-Gomariz, Juan Carlos Lacal, and Rosario Perona* Instituto de Investigaciones Biome´dicas Consejo Superior de Investigaciones Cientificas-Universidad Auto´noma de Madrid, 28029 Madrid, Spain Submitted January 15, 2002; Revised April 29, 2002; Accepted May 31, 2002 Monitoring Editor: Carl-Henrik Heldin Chemotherapeutic agents such as cisplatin induce persistent activation of N-terminal c-Jun Kinase, which in turn mediates induction of apoptosis. By using a common MAPK Kinase, MEKK1, cisplatin also activates the survival transcription factor NFB. We have found a cross-talk between c-Jun expression and NFB transcriptional activation in response to cisplatin. Fibroblast derived from c-jun knock out mice are more resistant to cisplatin-induced cell death, and this survival advantage is mediated by upregulation of NFB-dependent transcription and expression of MIAP3. This process can be reverted by ectopic expression of c-Jun in c-junϪ/Ϫ fibroblasts, which decreases p65 transcriptional activity back to normal levels. Negative regulation of NFB- dependent transcription by c-jun contributes to cisplatin-induced cell death, which suggests that inhibition of NFB may potentiate the antineoplastic effect of conventional chemotherapeutic agents. INTRODUCTION cis-Diaminedichloroplatinum (c-DDP, cisplatin) is a DNA- reactive agent commonly used in chemotherapy protocols in Induction of apoptosis is the primary mechanism of tumor the treatment of several kinds of human cancers. Lesions of cell killing by radiation and chemotherapeutic agents. -
Genome-Scale Identification of Transcription Factors That Mediate An
ARTICLE DOI: 10.1038/s41467-018-04406-2 OPEN Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation Zhe Ji 1,2,4, Lizhi He1, Asaf Rotem1,2,5, Andreas Janzer1,6, Christine S. Cheng2,7, Aviv Regev2,3 & Kevin Struhl 1 Transient activation of Src oncoprotein in non-transformed, breast epithelial cells can initiate an epigenetic switch to the stably transformed state via a positive feedback loop that involves 1234567890():,; the inflammatory transcription factors STAT3 and NF-κB. Here, we develop an experimental and computational pipeline that includes 1) a Bayesian network model (AccessTF) that accurately predicts protein-bound DNA sequence motifs based on chromatin accessibility, and 2) a scoring system (TFScore) that rank-orders transcription factors as candidates for being important for a biological process. Genetic experiments validate TFScore and suggest that more than 40 transcription factors contribute to the oncogenic state in this model. Interestingly, individual depletion of several of these factors results in similar transcriptional profiles, indicating that a complex and interconnected transcriptional network promotes a stable oncogenic state. The combined experimental and computational pipeline represents a general approach to comprehensively identify transcriptional regulators important for a biological process. 1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. 2 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. 3 Department of Biology, Howard Hughes Medical Institute and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 20140, USA. 4Present address: Department of Pharmacology and Biomedical Engineering, Northwestern University, Evanston 60611 IL, USA. -
Retinoblastoma-Related P107 and Prb2/P130 Proteins in Malignant Lymphomas: Distinct Mechanisms of Cell Growth Control1
Vol. 5, 4065–4072, December 1999 Clinical Cancer Research 4065 Retinoblastoma-related p107 and pRb2/p130 Proteins in Malignant Lymphomas: Distinct Mechanisms of Cell Growth Control1 Lorenzo Leoncini, Cristiana Bellan, ated according to the Kaplan-Meier method and the log- Antonio Cossu, Pier Paolo Claudio, Stefano Lazzi, rank test. We found a positive correlation between the per- Caterina Cinti, Gabriele Cevenini, centages of cells positive for p107 and proliferative features such as mitotic index and percentage of Ki-67(1) and cyclin Tiziana Megha, Lorella Laurini, Pietro Luzi, A(1) cells, whereas such correlation could not be demon- Giulio Fraternali Orcioni, Milena Piccioli, strated for the percentages of pRb2/p130 positive cells. Low Stefano Pileri, Costantino Giardino, Piero Tosi, immunohistochemical levels of pRb2/p130 detected in un- and Antonio Giordano2 treated patients with NHLs of various histiotypes inversely Institute of Pathologic Anatomy and Histology, University of Sassari, correlated with a large fraction of cells expressing high Sassari, Italy [L. L., A. C.]; Institute of Pathologic Anatomy and levels of p107 and proliferation-associated proteins. Such a Histology [C. B., S. L., T. M., L. L., P. L., P. T.] and Institute of pattern of protein expression is normally observed in con- Thoracic and Cardiovascular Surgery and Biomedical Technology tinuously cycling cells. Interestingly, such cases showed the [G. C.], University of Siena, Siena, Italy; Departments of Pathology, highest survival percentage (82.5%) after the observation Anatomy, and Cell Biology, Jefferson Medical College, and Sbarro Institute for Cancer Research and Molecular Medicine, Philadelphia, period of 10 years. Thus, down-regulation of the RB-related Pennsylvania 19107 [P. -
Revealing Transcription Factor and Histone Modification Co-Localization and Dynamics Across Cell Lines by Integrating Chip-Seq A
Zhang et al. BMC Genomics 2018, 19(Suppl 10):914 https://doi.org/10.1186/s12864-018-5278-5 RESEARCH Open Access Revealing transcription factor and histone modification co-localization and dynamics across cell lines by integrating ChIP-seq and RNA-seq data Lirong Zhang1*, Gaogao Xue1, Junjie Liu1, Qianzhong Li1* and Yong Wang2,3,4* From 29th International Conference on Genome Informatics Yunnan, China. 3-5 December 2018 Abstract Background: Interactions among transcription factors (TFs) and histone modifications (HMs) play an important role in the precise regulation of gene expression. The context specificity of those interactions and further its dynamics in normal and disease remains largely unknown. Recent development in genomics technology enables transcription profiling by RNA-seq and protein’s binding profiling by ChIP-seq. Integrative analysis of the two types of data allows us to investigate TFs and HMs interactions both from the genome co-localization and downstream target gene expression. Results: We propose a integrative pipeline to explore the co-localization of 55 TFs and 11 HMs and its dynamics in human GM12878 and K562 by matched ChIP-seq and RNA-seq data from ENCODE. We classify TFs and HMs into three types based on their binding enrichment around transcription start site (TSS). Then a set of statistical indexes are proposed to characterize the TF-TF and TF-HM co-localizations. We found that Rad21, SMC3, and CTCF co-localized across five cell lines. High resolution Hi-C data in GM12878 shows that they associate most of the Hi-C peak loci with a specific CTCF-motif “anchor” and supports that CTCF, SMC3, and RAD2 co-localization serves important role in 3D chromatin structure. -
Functional Genomics Analysis of Vitamin D Effects on CD4+ T Cells In
Functional genomics analysis of vitamin D effects PNAS PLUS on CD4+ T cells in vivo in experimental autoimmune encephalomyelitis Manuel Zeitelhofera,b, Milena Z. Adzemovica, David Gomez-Cabreroc,d,e, Petra Bergmana, Sonja Hochmeisterf, Marie N’diayea, Atul Paulsona, Sabrina Ruhrmanna, Malin Almgrena, Jesper N. Tegnérc,d,g, Tomas J. Ekströma, André Ortlieb Guerreiro-Cacaisa, and Maja Jagodica,1 aDepartment of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden; bVascular Biology Unit, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden; cUnit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden; dScience for Life Laboratory, 171 21 Solna, Sweden; eMucosal and Salivary Biology Division, King’s College London Dental Institute, London SE1 9RT, United Kingdom; fDepartment of General Neurology, Medical University of Graz, 8036 Graz, Austria; and gBiological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, 23955 Thuwal, Kingdom of Saudi Arabia Edited by Tomas G. M. Hokfelt, Karolinska Institutet, Stockholm, Sweden, and approved January 19, 2017 (received for review September 24, 2016) Vitamin D exerts multiple immunomodulatory functions and has autoimmune destruction of myelin, axonal loss, and brain atro- been implicated in the etiology and treatment of several autoim- phy (6). Increased risk of developing MS has been described in mune diseases, including multiple sclerosis (MS). We have previously carriers of rare and common variants of the CYP27B gene (7, 8), reported that in juvenile/adolescent rats, vitamin D supplementation which encodes the enzyme that catalyzes the last step in con- protects from experimental autoimmune encephalomyelitis (EAE), a verting vitamin D to its active form, from 25(OH)D3 to 1,25 model of MS. -
UC San Diego Electronic Theses and Dissertations
UC San Diego UC San Diego Electronic Theses and Dissertations Title Bcl3 and REG-gamma are the Regulators of NF-kappaB p50 and p52 Permalink https://escholarship.org/uc/item/2293k9sk Author Du, Qian Publication Date 2017 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERISTY OF CALIFORNIA, SAN DIEGO Bcl3 and REG-gamma are the Regulators of NF-kappaB p50 and p52 A thesis submitted in partial satisfaction of the requirements for the degree Master of Science in Chemistry by Qian Du Committee in Charge: Professor Gourisankar Ghosh, Chair Professor Simpson Joseph Professor Emmanuel Theodorakis Professor Wei Wang 2017 ii The Thesis of Qian Du is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2017 iii DEDICATION This thesis is dedicated to my beloved parents, for their endless love, caring and under- standing throughout my life. This thesis is also dedicated to my beloved grandparents, for their kindness and devo- tion. Their selflessness will always be remembered. iv TABLE OF CONTENTS Signature Page……………………………………………………………………………ⅲ Dedication.......................................................................................................................…ⅳ Table of Contents…………………………………………………………………………ⅴ List of Figures…………………………………………………………………………….ⅵ Preface……………………………………………………….....………………………...ⅷ Acknowledgemnts………………………………………….……...……………………...ⅸ Abstract of the Thesis……………………………………...…………………...………....ⅺ