Targeting the Transcription Factor C-Jun in Cervical Cancer Cells
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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. -
IAIS Abstracts Melbourne 2005
Book of Abstracts List of Committees Organising Committee Steering Committee Chairs Ian Adcock, UK John Hamilton, Australia Ian Ahnfelt-Ronne, Denmark Eric Morand, Australia Gareth Bowen, UK Michel Chignard, France Gary Anderson, Australia John Hamilton, Australia Gareth Bowen, UK Gordon Letts, USA Andrew Cook, Australia Lisa Marshall, USA Michael Hickey, Australia Tineke Meijers, Canada Gordon Letts, USA Tatsutoshi Nakahata, Japan Alan Lewis, USA Wim van den Berg, The Netherlands Lisa Marshall, USA Kouji Matsushima, Japan Amy Roshak, USA Glen Scholz, Australia Ross Vlahos, Australia Young Investigator Award Committee Program Committee Chair: Chair: Glen Scholz, Australia Michael Hickey, Australia Laurent Audoly, Canada Andrew Cook, Australia Susan Brain, UK John Hamilton, Australia John Schrader, Canada Lisa Marshall, USA Vincent Lagente, France Eric Morand, Australia Kouji Matsushima, Japan Glen Scholz, Australia Ross Vlahos, Australia For enquiries after the Congress please contact the Congress Secretariat: ICMS Pty Ltd Attention: 7th World Congress on Infl ammation 2005 84 Queensbridge Street Southbank Vic 3006 Australia P: +61 3 9682 0244 F: +61 3 9682 0288 E: infl [email protected] W: www.infl ammation2005.com Contents Sunday 21 August 2005 Abstract No. Page Title Morning 1001 — Plenary 1: Peter Doherty 1002 -1004 — Symposium 1: Chronic Obstructive Pulmonary Disease 1005 - 1008 S 85 Symposium 2: Arthritis Afternoon 1010 - 1013 S 85 Focus Group 1: Understanding Infl ammation through Genetics, Genomics and Proteomics 1014 - 1018 S 86 Focus Group 2: Asthma 1019 - 1022 S 88 Focus Group 3: The Immunoregulatory Response 1023 -1027 S 89 Focus Group 4; Structure-Based Drug Design 1028 - 1032 S 90 Focus Group 5: Chronic Obstructive Pulmonary Disease 1033 - 1037 S 90 Focus Group 6: Rheumatic Diseases Monday 22 August 2005 Abstract No. -
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. -
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 -
Immunological Defects in Mice with a Targeted Disruption in Bcl-3
Downloaded from genesdev.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Immunological defects in mice with a targeted disruption in Bcl-3 Edward M. Schwarz/'^ Paul Krimpenfort/'^ Anton Berns,^ and Inder M. Verma 1,4 ^Laboratory of Genetics, The Salk Institute, San Diego, California 92186-5800 USA; ^Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands The proto-oncogene bcl-3 is a member ol the IKB family. The Bcl-3 protein is known to interact specifically with the p50 and p52 subunits of NFKB. However, the function of this interaction is not well understood. To determine the in vivo role of Bcl-3, mice were generated that lack the bcl-3 gene, Bel 3(-/-). Here we report that Bel 3(-/-) mice appear developmentally normal, but exhibit severe defects in humoral immune responses and protection from in vivo pathogenic challenges. Relative to wild-type mice, Bel 3(-/-) mice are unable to clear L. monocytogenes and are more susceptible to infection with S. pneumoniae. This phenotype is similar to that observed in the p50(-/-) mice and the cross between the Bcl-3(-/-) and p50(-/-) mice generates animals with an enhanced phenotype. In accordance with the observed defects in their immune response, the Bel 3(-/-) mice have normal immunoglobulin levels before and after immunization, but fail to produce antigen-specific antibodies. Additionally, spleens from Bcl-3(-/-) mice are abnormal and void of germinal centers. In contrast, the p50(-/-) mice have normal germinal centers. We propose that in in vivo, Bcl-3 can function independently of p50. -
B-Cell Lymphomas with Concurrent MYC and BCL2 Abnormalities Other Than Translocations Behave Similarly to MYC&Sol
Modern Pathology (2015) 28, 208–217 208 & 2015 USCAP, Inc All rights reserved 0893-3952/15 $32.00 B-cell lymphomas with concurrent MYC and BCL2 abnormalities other than translocations behave similarly to MYC/BCL2 double-hit lymphomas Shaoying Li1, Adam C Seegmiller1, Pei Lin2, Xuan J Wang1, Roberto N Miranda2, Sharathkumar Bhagavathi3 and L Jeffrey Medeiros2 1Division of Hematopathology, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Vanderbilt University School of Medicine, Nashville, TN, USA; 2Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA and 3Department of Pathology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA Large B-cell lymphomas with IGH@BCL2 and MYC rearrangement, known as double-hit lymphoma (DHL), are clinically aggressive neoplasms with a poor prognosis. Some large B-cell lymphomas have concurrent abnormalities of MYC and BCL2 other than coexistent translocations. Little is known about patients with these lymphomas designated here as atypical DHL. We studied 40 patients of atypical DHL including 21 men and 19 women, with a median age of 60 years. Nine (23%) patients had a history of B-cell non-Hodgkin lymphoma. There were 30 diffuse large B-cell lymphoma (DLBCL), 7 B-cell lymphoma, unclassifiable, with features intermediate between DLBCL and Burkitt lymphoma, and 3 DLBCL with coexistent follicular lymphoma. CD10, BCL2, and MYC were expressed in 28/39 (72%), 33/35 (94%), and 14/20 (70%) cases, respectively. Patients were treated with standard (n ¼ 14) or more aggressive chemotherapy regimens (n ¼ 17). We compared the atypical DHL group with 76 patients with DHLand 35 patients with DLBCL lacking MYC and BCL2 abnormalities. -
NFKB1 and Cancer: Friend Or Foe?
cells Review NFKB1 and Cancer: Friend or Foe? Julia Concetti and Caroline L. Wilson * Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, Tyne and Wear NE2 4HH, UK; [email protected] * Correspondence: [email protected]; Tel.: +44-191-208-8590 Received: 15 August 2018; Accepted: 4 September 2018; Published: 7 September 2018 Abstract: Current evidence strongly suggests that aberrant activation of the NF-κB signalling pathway is associated with carcinogenesis. A number of key cellular processes are governed by the effectors of this pathway, including immune responses and apoptosis, both crucial in the development of cancer. Therefore, it is not surprising that dysregulated and chronic NF-κB signalling can have a profound impact on cellular homeostasis. Here we discuss NFKB1 (p105/p50), one of the five subunits of NF-κB, widely implicated in carcinogenesis, in some cases driving cancer progression and in others acting as a tumour-suppressor. The complexity of the role of this subunit lies in the multiple dimeric combination possibilities as well as the different interacting co-factors, which dictate whether gene transcription is activated or repressed, in a cell and organ-specific manner. This review highlights the multiple roles of NFKB1 in the development and progression of different cancers, and the considerations to make when attempting to manipulate NF-κB as a potential cancer therapy. Keywords: NF-κB; NFKB1; p105/p50; Bcl-3; cancer; inflammation; apoptosis 1. Introduction One of the emerging questions in cancer biology is: “How are inflammation and dysregulated immune responses linked to cancer?” It is now widely accepted that chronic inflammation and infection represent major risk factors for certain cancers. -
Deoxyribozymes As Catalytic Nanotherapeutic Agents Levon M
Published OnlineFirst February 13, 2019; DOI: 10.1158/0008-5472.CAN-18-2474 Cancer Review Research Deoxyribozymes as Catalytic Nanotherapeutic Agents Levon M. Khachigian Abstract RNA-cleaving deoxyribozymes (DNAzymes) are synthet- and nanosponges, and the emerging role of adaptive ic single-stranded DNA-based catalytic molecules that can immunity underlying DNAzyme inhibition of cancer be engineered to bind to and cleave target mRNA at growth. DNAzymes represent a promising new class of predetermined sites. These have been used as therapeutic nucleic acid–based therapeutics in cancer. This article dis- agents in a range of preclinical cancer models and have cusses mechanistic and therapeutic insights brought about entered clinical trials in Europe, China, and Australia. This by DNAzyme use as nanotools and reagents in a range of review surveys regulatory insights into mechanisms of basic science, experimental therapeutic and clinical appli- disease brought about by use of catalytic DNA in vitro and cations. Current limitations and future perspectives are also in vivo, including recent uses as nanosensors, nanoflowers, discussed. DNAzyme Catalysts: Mechanistic and transfected with commercial delivery agents or electroporated Design Considerations into cells. DNAzyme use in experimental animal models can be hampered by delivery issues, especially in regard to systemic DNAzymes are synthetic single-stranded enzymatic DNA mole- administration (10). This has motivated local delivery meth- cules that bind to their target mRNA via Watson–Crick base odologies in animals, such as intracardiac, intratumoral, and pairing and cleave a specific interbase junction in the mRNA by intraarticular injection, or tissue immersion. Novel biodegrad- a deesterification reaction (1–3). This involves metal-assisted able template-based DNAzymes have recently been developed 0 deprotonation of 2 -hydroxyl in the RNA, producing RNA frag- that facilitate cancer cell recognition and internalization (11). -
Mouse Bcl3 Conditional Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Bcl3 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Bcl3 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Bcl3 gene (NCBI Reference Sequence: NM_033601 ; Ensembl: ENSMUSG00000053175 ) is located on Mouse chromosome 7. 9 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 9 (Transcript: ENSMUST00000120537). Exon 3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Bcl3 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-33H23 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Mice lacking functional copies of this gene exhibit defects of the immune system including disruption of the humoral immune response and abnormal spleen and Peyer's patch organogenesis. Mutant mice show increased susceptibility to pathogens. Exon 3 starts from about 29.46% of the coding region. The knockout of Exon 3 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 7533 bp, and the size of intron 3 for 3'-loxP site insertion: 705 bp. The size of effective cKO region: ~609 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 3 4 5 6 9 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Bcl3 Homology arm cKO region loxP site Page 2 of 7 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. -
Effect of EBV LMP1 Targeted Dnazymes on Cell Proliferation And
Cancer Gene Therapy (2005) 12, 647–654 r 2005 Nature Publishing Group All rights reserved 0929-1903/05 $30.00 www.nature.com/cgt Effect of EBV LMP1 targeted DNAzymes on cell proliferation and apoptosis Zhong-Xin Lu,1 Mao Ye,1 Guang-Rong Yan,1 Qun Li,1 Min Tang,1 Leo M Lee,2 Lun-Quan Sun,3 and Ya Cao1 1Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China; 2Laboratory of Molecular Technology SAIC-Frederick, National Cancer Institute, Frederick, Maryland, USA; and 3St Vincent’s Clinical School, Faculty of Medicine, The University of New South Wales, Sydney, Australia. The latent membrane protein (LMP1) encoded by Epstein–Barr virus (EBV) has been suggested to be one of the major oncogenic factors in EBV-mediated carcinogenesis. RNA-cleaving DNA enzymes are catalytic nucleic acids that bind and cleave a target RNA in a highly sequence-specific manner. In this study, we explore the potential of using DNAzymes as a therapeutic approach to EBV- associated carcinomas by targeting the LMP1 gene. In all, 13 different phosphorothioate-modified ‘‘10–23’’ deoxyribozymes (DNAzymes) were designed and synthesized against the LMP1 mRNA and transfected into B95-8 cells, which constitutively express the LMP1. Fluorescence microscopy was used to examine the cellular uptake and distribution in B95-8 cells. As demonstrated in Western blots, three out of 13 deoxyribozymes significantly downregulated the expression of LMP1 in B95-8 cells. These DNAzymes were shown to markedly inhibit B95-8 cell growth compared with a disabled DNAzyme and untreated controls, as determined by an alamarBlue Assay. -
SUPPLEMENTARY MATERIAL Supplementary Fig. S1. LD Mice Used in This Study Accumulate Polyglucosan Inclusions (Lafora Bodies) in the Brain
1 SUPPLEMENTARY MATERIAL Supplementary Fig. S1. LD mice used in this study accumulate polyglucosan inclusions (Lafora bodies) in the brain. Samples from the hippocampus of five months old control, Epm2a-/- (lacking laforin) and Epm2b-/- mice (lacking malin) were stained with periodic acid Schiff reagent (PAS staining), which colors polysaccharide granules in red. Bar: 50 m. Supplementary Fig. S2. Principal component analysis (PCA) representing the first two components with the biggest level of phenotypic variability. Samples 1_S1 to 4_S4 corresponded to control, 5_S5, 6_S6 and 8_S8 to Epm2a-/- and 9_S9 to 12_S12 to Epm2b- /- samples, of animals of 16 months of age respectively. Supplementary Table S1. Primers used in this work to validate the expression of the corresponding genes by RT-qPCR. Supplementary Table S2: Genes downregulated more than 0.5 fold in Epm2a-/- and Epm2b-/- mice of 16 months of age. The gene name, false discovery rate (FDR), fold change (FC), description and MGI Id (mouse genome informatics) are indicated. Genes are arranged according to FC. Supplementary Table S3: Genes upregulated more than 1.5 fold in Epm2a-/- mice of 16 months of age. The gene name, false discovery rate (FDR), fold change (FC), description and MGI Id (mouse genome informatics) are indicated. Genes are arranged according to FC. Supplementary Table S4: Genes upregulated more than 1.5 fold in Epm2b-/- mice of 16 months of age. The gene name, false discovery rate (FDR), fold change (FC), description and MGI Id (mouse genome informatics) are indicated. Genes are arranged according to FC. 2 Supplementary Table S5: Genes upregulated in both Epm2a-/- and Epm2b-/- mice of 16 months of age. -
The Landscape and Driver Potential of Site-Specific Hotspots Across Cancer
www.nature.com/npjgenmed ARTICLE OPEN The landscape and driver potential of site-specific hotspots across cancer genomes ✉ ✉ Randi Istrup Juul 1 , Morten Muhlig Nielsen1, Malene Juul1, Lars Feuerbach2 and Jakob Skou Pedersen 1,3 Large sets of whole cancer genomes make it possible to study mutation hotspots genome-wide. Here we detect, categorize, and characterize site-specific hotspots using 2279 whole cancer genomes from the Pan-Cancer Analysis of Whole Genomes project and provide a resource of annotated hotspots genome-wide. We investigate the excess of hotspots in both protein-coding and gene regulatory regions and develop measures of positive selection and functional impact for individual hotspots. Using cancer allele fractions, expression aberrations, mutational signatures, and a variety of genomic features, such as potential gain or loss of transcription factor binding sites, we annotate and prioritize all highly mutated hotspots. Genome-wide we find more high- frequency SNV and indel hotspots than expected given mutational background models. Protein-coding regions are generally enriched for SNV hotspots compared to other regions. Gene regulatory hotspots show enrichment of potential same-patient second-hit missense mutations, consistent with enrichment of hotspot driver mutations compared to singletons. For protein-coding regions, splice-sites, promoters, and enhancers, we see an excess of hotspots associated with cancer genes. Interestingly, missense hotspot mutations in tumor suppressors are associated with elevated expression, suggesting localized amino-acid changes with functional impact. For individual non-coding hotspots, only a small number show clear signs of positive selection, including known sites in the TERT promoter and the 5’ UTR of TP53.