NF-Κb Activation by a Signaling Complex Containing TRAF2, TANK and TBK1, a Novel IKK-Related Kinase
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Compound Name DiscoveRx Gene Symbol Entrez Gene Percent Compound Symbol Control Concentration (nM) JNK-IN-8 AAK1 AAK1 69 1000 JNK-IN-8 ABL1(E255K)-phosphorylated ABL1 100 1000 JNK-IN-8 ABL1(F317I)-nonphosphorylated ABL1 87 1000 JNK-IN-8 ABL1(F317I)-phosphorylated ABL1 100 1000 JNK-IN-8 ABL1(F317L)-nonphosphorylated ABL1 65 1000 JNK-IN-8 ABL1(F317L)-phosphorylated ABL1 61 1000 JNK-IN-8 ABL1(H396P)-nonphosphorylated ABL1 42 1000 JNK-IN-8 ABL1(H396P)-phosphorylated ABL1 60 1000 JNK-IN-8 ABL1(M351T)-phosphorylated ABL1 81 1000 JNK-IN-8 ABL1(Q252H)-nonphosphorylated ABL1 100 1000 JNK-IN-8 ABL1(Q252H)-phosphorylated ABL1 56 1000 JNK-IN-8 ABL1(T315I)-nonphosphorylated ABL1 100 1000 JNK-IN-8 ABL1(T315I)-phosphorylated ABL1 92 1000 JNK-IN-8 ABL1(Y253F)-phosphorylated ABL1 71 1000 JNK-IN-8 ABL1-nonphosphorylated ABL1 97 1000 JNK-IN-8 ABL1-phosphorylated ABL1 100 1000 JNK-IN-8 ABL2 ABL2 97 1000 JNK-IN-8 ACVR1 ACVR1 100 1000 JNK-IN-8 ACVR1B ACVR1B 88 1000 JNK-IN-8 ACVR2A ACVR2A 100 1000 JNK-IN-8 ACVR2B ACVR2B 100 1000 JNK-IN-8 ACVRL1 ACVRL1 96 1000 JNK-IN-8 ADCK3 CABC1 100 1000 JNK-IN-8 ADCK4 ADCK4 93 1000 JNK-IN-8 AKT1 AKT1 100 1000 JNK-IN-8 AKT2 AKT2 100 1000 JNK-IN-8 AKT3 AKT3 100 1000 JNK-IN-8 ALK ALK 85 1000 JNK-IN-8 AMPK-alpha1 PRKAA1 100 1000 JNK-IN-8 AMPK-alpha2 PRKAA2 84 1000 JNK-IN-8 ANKK1 ANKK1 75 1000 JNK-IN-8 ARK5 NUAK1 100 1000 JNK-IN-8 ASK1 MAP3K5 100 1000 JNK-IN-8 ASK2 MAP3K6 93 1000 JNK-IN-8 AURKA AURKA 100 1000 JNK-IN-8 AURKA AURKA 84 1000 JNK-IN-8 AURKB AURKB 83 1000 JNK-IN-8 AURKB AURKB 96 1000 JNK-IN-8 AURKC AURKC 95 1000 JNK-IN-8 -
Expression and Prognostic Role of IKBKE and TBK1 in Stage I Non-Small Cell Lung Cancer
Cancer Management and Research Dovepress open access to scientific and medical research Open Access Full Text Article ORIGINAL RESEARCH Expression and prognostic role of IKBKE and TBK1 in stage I non-small cell lung cancer This article was published in the following Dove Press journal: Cancer Management and Research Xin Wang1,2 Background: The inhibitors of nuclear factor kappa-B kinase subunit epsilon (IKBKE) and Feifei Teng2 TANK-binding kinase 1 (TBK1) are important members of the nonclassical IKK family that Jie Lu3 share the kinase domain. They are important oncogenes for activation of several signaling Dianbin Mu4 pathways in several tumors. This study aims to explore the expression of IKBKE and TBK1 Jianbo Zhang4 and their prognostic role in stage I non-small cell lung cancer (NSCLC). Jinming Yu1,2 Patients and methods: A total of 142 surgically resected stage I NSCLC patients were enrolled and immunohistochemistry of IKBKE and TBK1 was performed. 1 Department of Oncology, Renmin Results: IKBKE and TBK1 were expressed in 121 (85.2%) and 114 (80.3%) of stage I Hospital of Wuhan University, Wuhan, fi Hubei 430060, People’s Republic of China; NSCLC patients respectively. IKBKE expression was signi cantly associated with TBK1 2Department of Radiation Oncology, expression (P=0.004). Furthermore, multivariate regression analyses showed there was a fi Shandong Cancer Hospital Af liated to significant relationship between patients with risk factors, the recurrence pattern of metas- Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong tasis and IKBKE+/TBK1+ co-expression (P=0.032 and P=0.022, respectively). In Kaplan– 250117, People’s Republic of China; Meier survival curve analyses, the IKBKE+/TBK1+ co-expression subgroup was signifi- 3Department of Neurosurgery, Shandong Province Qianfoshan Hospital of Shandong cantly associated with poor overall survival (P=0.014). -
Supplementary Table 7. Characterization of Human Proteins Involved in the Prostate Cancer Pathway
Supplementary Table 7. Characterization of human proteins involved in the prostate cancer pathway f Protein UniProt Protein PONDR-FIT MobiDB Location (length) Location (length) Nint ID length (%)b consensus of long disordered of AIBSse a c d (NAIBS) (%) regions BAD, Bcl2-associated Q92934 168 100.00 84.54 1-105 (105) 1-53 (53) 66 agonist of cell death (4/70.8) 122-147 (27) 57-80 (24) 158-168 (11) 100-129 (30) 146-157 (12) CREB5; cyclic AMP- Q02930 508 85.24 75.39 46-59 (14) 66-86 (21) 65 responsive element (7/67.9) 86-393 (308) 99-183 (85) binding protein 5 447-470 (24) 188-358 (171) 479-508 (31) 362-370 (9) 378-406 (29) 421-444 (24) 503-508 (6) CREB1, cyclic AMP- P16220 341 79.47 40.47 1-32 (32) 32-44 (13) 169 responsive element- (7/29.3) 40-50 (11) 89-104 (16) binding protein 1 102-132 (33) 128-145 (18) 138-171 (34) 166-191 (26) 271-285 (15) 265-270 (6) 307-314 (8) 329-341 (13) FOXO1, Forkhead box Q12778 655 78.63 72.82 1-69 (69) 1-32 (32) 68 protein O1 (19/56.9) 74-101 (28) 54-82 (29) 105-160 (56) 88-118 (31) 199-210 (12) 160-172 (13) 229-336 (107) 182-196 (15) 385-450 (66) 216-226 (11) 463-488 (26) 258-280 (23) 498-569 (72) 289-297 (9) 644-655 (12) 306-314 (9) 323-365 (43) 371-388 (18) 301-409 (8) 447-469 (23) 483-517 (35) 528-545 (18) 550-565 (16) 570-592 (23) 605-612 (8) TCF7L1, transcription Q9HCS4 588 77.04 61.90 1-104 (104) 1-46 (46) 4 factor 7 like 1 (16/54.5) 161-183 (23) 53-74 (22) 192-238 (47) 94-135 (42) 316-344 (29) 146-159 (14) 406-512 (107) 191-201 (11) 524-546 (21) 234-252 (19) 274-288 (15) 349-371 (23) 373-383 (11) -
Molecular Classification of Patients with Unexplained Hamartomatous and Hyperplastic Polyposis
ORIGINAL CONTRIBUTION Molecular Classification of Patients With Unexplained Hamartomatous and Hyperplastic Polyposis Kevin Sweet, MS, CGC Context Significant proportions of patients with hamartomatous polyposis or with Joseph Willis, MD hyperplastic/mixed polyposis remain without specific clinical and molecular diagnosis Xiao-Ping Zhou, MD, PhD or present atypically. Assigning a syndromic diagnosis is important because it guides management, especially surveillance and prophylactic surgery. Carol Gallione, PhD Objective To systematically classify patients with unexplained hamartomatous or hy- Takeshi Sawada, MD, PhD perplastic/mixed polyposis by extensive molecular analysis in the context of central Pia Alhopuro, MD rereview of histopathology results. Sok Kean Khoo, PhD Design, Setting, and Patients Prospective, referral-based study of 49 unrelated patients from outside institutions (n=28) and at a comprehensive cancer center (n=21), Attila Patocs, MD, PhD conducted from May 2, 2002, until December 15, 2004. Germline analysis of PTEN, Cossette Martin, PhD BMPR1A, STK11 (sequence, deletion), SMAD4, and ENG (sequence), specific exon screen- Scott Bridgeman, BSc ing of BRAF, MYH, and BHD, and rereview of polyp histology results were performed. John Heinz, PhD Main Outcome Measures Molecular, clinical, and histopathological findings in pa- tients with unexplained polyposis. Robert Pilarski, MS, CGC Results Of the 49 patients, 11 (22%) had germline mutations. Of 14 patients with Rainer Lehtonen, BSc juvenile polyposis, 2 with early-onset disease had mutations in ENG, encoding endo- Thomas W. Prior, PhD glin, previously only associated with hereditary hemorrhagic telangiectasia; 1 had hemi- zygous deletion encompassing PTEN and BMPR1A; and 1 had an SMAD4 mutation. Thierry Frebourg, MD, PhD One individual previously classified with Peutz-Jeghers syndrome had a PTEN dele- Bin Tean Teh, MD, PhD tion. -
Inhibition of Mitochondrial Complex II in Neuronal Cells Triggers Unique
www.nature.com/scientificreports OPEN Inhibition of mitochondrial complex II in neuronal cells triggers unique pathways culminating in autophagy with implications for neurodegeneration Sathyanarayanan Ranganayaki1, Neema Jamshidi2, Mohamad Aiyaz3, Santhosh‑Kumar Rashmi4, Narayanappa Gayathri4, Pulleri Kandi Harsha5, Balasundaram Padmanabhan6 & Muchukunte Mukunda Srinivas Bharath7* Mitochondrial dysfunction and neurodegeneration underlie movement disorders such as Parkinson’s disease, Huntington’s disease and Manganism among others. As a corollary, inhibition of mitochondrial complex I (CI) and complex II (CII) by toxins 1‑methyl‑4‑phenylpyridinium (MPP+) and 3‑nitropropionic acid (3‑NPA) respectively, induced degenerative changes noted in such neurodegenerative diseases. We aimed to unravel the down‑stream pathways associated with CII inhibition and compared with CI inhibition and the Manganese (Mn) neurotoxicity. Genome‑wide transcriptomics of N27 neuronal cells exposed to 3‑NPA, compared with MPP+ and Mn revealed varied transcriptomic profle. Along with mitochondrial and synaptic pathways, Autophagy was the predominant pathway diferentially regulated in the 3‑NPA model with implications for neuronal survival. This pathway was unique to 3‑NPA, as substantiated by in silico modelling of the three toxins. Morphological and biochemical validation of autophagy markers in the cell model of 3‑NPA revealed incomplete autophagy mediated by mechanistic Target of Rapamycin Complex 2 (mTORC2) pathway. Interestingly, Brain Derived Neurotrophic Factor -
Workflows for Rapid Functional Annotation of Diverse
insects Article Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes Surya Saha 1,2 , Amanda M. Cooksey 2,3, Anna K. Childers 4 , Monica F. Poelchau 5 and Fiona M. McCarthy 2,* 1 Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA; [email protected] 2 School of Animal and Comparative Biomedical Sciences, University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA; [email protected] 3 CyVerse, BioScience Research Laboratories, University of Arizona, 1230 N. Cherry Ave., Tucson, AZ 85721, USA 4 Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, 10300 Baltimore Ave., Beltsville, MD 20705, USA; [email protected] 5 National Agricultural Library, Agricultural Research Service, USDA, 10301 Baltimore Ave., Beltsville, MD 20705, USA; [email protected] * Correspondence: fi[email protected] Simple Summary: Genomic technologies are accumulating information about genes faster than ever before, and sequencing initiatives, such as the Earth BioGenome Project, i5k, and Ag100Pest Initiative, are expected to increase this rate of acquisition. However, if genomic sequencing is to be used for the improvement of human health, agriculture, and our understanding of biological systems, it is necessary to identify genes and understand how they contribute to biological outcomes. While there are several well-established workflows for assembling genomic sequences and identifying genes, understanding gene function is essential to create actionable knowledge. Moreover, this functional annotation process must be easily accessible and provide information at a genomic scale to keep up Citation: Saha, S.; Cooksey, A.M.; with new sequence data. We report a well-defined workflow for rapid functional annotation of whole Childers, A.K.; Poelchau, M.F.; proteomes to produce Gene Ontology and pathways information. -
Molecular Basis of Tank-Binding Kinase 1 Activation by Transautophosphorylation
Molecular basis of Tank-binding kinase 1 activation by transautophosphorylation Xiaolei Maa,1, Elizabeth Helgasonb,1, Qui T. Phungc, Clifford L. Quanb, Rekha S. Iyera, Michelle W. Leec, Krista K. Bowmana, Melissa A. Starovasnika, and Erin C. Dueberb,2 Departments of aStructural Biology, bEarly Discovery Biochemistry, and cProtein Chemistry, Genentech, South San Francisco, CA 94080 Edited by Tony Hunter, Salk Institute for Biological Studies, La Jolla, CA, and approved April 25, 2012 (received for review December 30, 2011) Tank-binding kinase (TBK)1 plays a central role in innate immunity: it the C-terminal scaffolding/dimerization domain (SDD), a do- serves as an integrator of multiple signals induced by receptor- main arrangement that appears to be shared among the IKK mediated pathogen detection and as a modulator of IFN levels. family of kinases (3). Deletion or mutation of the ULD in TBK1 Efforts to better understand the biology of this key immunological or IKKε severely impairs kinase activation and substrate phos- factor have intensified recently as growing evidence implicates phorylation in cells (22, 23). Furthermore, the integrity of the aberrant TBK1 activity in a variety of autoimmune diseases and ULD in IKKβ is not only required for kinase activity (24) but was fi cancers. Nevertheless, key molecular details of TBK1 regulation and shown also to confer substrate speci city in conjunction with the β substrate selection remain unanswered. Here, structures of phos- adjacent SDD (25). Recent crystal structures of the IKK phorylated and unphosphorylated human TBK1 kinase and ubiq- homodimer demonstrate that the ULD and SDD form a joint, uitin-like domains, combined with biochemical studies, indicate three-way interface with the KD within each protomer of the a molecular mechanism of activation via transautophosphorylation. -
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cells Article Transcriptome and Methylome Analysis Reveal Complex Cross-Talks between Thyroid Hormone and Glucocorticoid Signaling at Xenopus Metamorphosis Nicolas Buisine 1,† , Alexis Grimaldi 1,†, Vincent Jonchere 1,† , Muriel Rigolet 1, Corinne Blugeon 2 , Juliette Hamroune 2 and Laurent Marc Sachs 1,* 1 UMR7221 Molecular Physiology and Adaption, CNRS, Museum National d’Histoire Naturelle, 57 Rue Cuvier, CEDEX 05, 75231 Paris, France; [email protected] (N.B.); [email protected] (A.G.); [email protected] (V.J.); [email protected] (M.R.) 2 Genomics Core Facility, Département de Biologie, Institut de Biologie de l’ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France; [email protected] (C.B.); [email protected] (J.H.) * Correspondence: [email protected] † Co-first authors, alphabetic order. Abstract: Background: Most work in endocrinology focus on the action of a single hormone, and very little on the cross-talks between two hormones. Here we characterize the nature of interactions between thyroid hormone and glucocorticoid signaling during Xenopus tropicalis metamorphosis. Methods: We used functional genomics to derive genome wide profiles of methylated DNA and measured changes of gene expression after hormonal treatments of a highly responsive tissue, tailfin. Clustering classified the data into four types of biological responses, and biological networks were Citation: Buisine, N.; Grimaldi, A.; modeled by system biology. Results: We found that gene expression is mostly regulated by either Jonchere, V.; Rigolet, M.; Blugeon, C.; T or CORT, or their additive effect when they both regulate the same genes. A small but non- Hamroune, J.; Sachs, L.M. -
Mechanisms of IKBKE Activation in Cancer Sridevi Challa University of South Florida, [email protected]
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 1-29-2017 Mechanisms of IKBKE Activation in Cancer Sridevi Challa University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the Biochemistry Commons, Biology Commons, and the Cell Biology Commons Scholar Commons Citation Challa, Sridevi, "Mechanisms of IKBKE Activation in Cancer" (2017). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/6617 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Mechanisms of IKBKE Activation in Cancer by Sridevi Challa A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Cell Biology, Microbiology, and Molecular Biology College of Arts and Sciences University of South Florida Major Professor: Mokenge P. Malafa, M.D. Gary Reuther, Ph.D. Eric Lau, Ph.D. Domenico Coppola, M.D. Date of Approval: January 12, 2017 Keywords: EGFR, Olaparib, resistance Copyright © 2017, Sridevi Challa DEDICATION This dissertation is dedicated to my kind and courageous mother. ACKNOWLEDGMENTS I would like to acknowledge Dr. Cheng for trusting me with completion of the projects. I would like to thank him for giving me the freedom to explore any aspect of research and always willing to provide the necessary resources and guidance for my projects. I want to also acknowledge Ted and the Cheng lab personnel for their support. -
(12) United States Patent (10) Patent No.: US 7,863,289 B2 Spevak Et Al
US00786.3289B2 (12) United States Patent (10) Patent No.: US 7,863,289 B2 Spevak et al. (45) Date of Patent: *Jan. 4, 2011 (54) COMPOUNDS AND METHODS FOR KINASE 5,658,775 A 8, 1997 Gilboa MODULATION, AND INDICATIONS 5,681,959 A 10/1997 Bishop et al. THEREFOR 5,700,637 A 12/1997 Southern (75) Inventors: Wayne Spevak, Berkeley, CA (US); 5,700.809 A 12/1997 Leeson et al. Hanna Cho, Oakland, CA (US); Prabha 5,712,285 A 1/1998 Curtis et al. N. Ibrahim, Mountain View, CA (US); 5,721,118 A 2, 1998 Scheffler Shenghua Shi, San Diego, CA (US); 5,744,305 A 4/1998 Fodor et al. Shumeye Mamo, Oakland, CA (US); 5,747,276 A 5/1998 Hoch et al. Samuel J. Gillette, Oakland, CA (US); 5,763,198 A 6/1998 Hirth et al. Hongyao Zhu, Berkeley, CA (US) 5,770.456 A 6/1998 Holmes (73) Assignee: Plexxikon, Inc., Berkeley, CA (US) 5,800,992 A 9, 1998 Fodor et al. 5,807,522 A 9, 1998 Brown et al. (*) Notice: Subject to any disclaimer, the term of this 5,830,645 A 11/1998 Pinkel et al. patent is extended or adjusted under 35 5,840,485 A 11/1998 Leblet al. U.S.C. 154(b) by 356 days. 5,856,174 A 1/1999 Lipshutz et al. 5,877,007 A 3/1999 Housey This patent is Subject to a terminal dis claimer. 5,959,098 A 9/1999 Goldberg et al. 5,965,452 A 10, 1999 Kovacs (21) Appl. -
Supp Material.Pdf
Supplemental Material STRESS-INDUCED H3S28 PHOSPHORYLATION MODULATES LOCAL HISTONE ACETYLATION LEVELS Anna Sawicka, Dominik Hartl, Malgorzata Goiser, Oliver Pusch, Roman R Stocsits, Ido M Tamir, Karl Mechtler, Christian Seiser Supplemental Methods Supplemental Figure Legends Supplemental Tables (SUPPL. TABLES 1-2, 4-5) Supplemental Tables (SUPPL. TABLES 3, 6-9, provided as txt files) References Supplemental Figures (SUPPL. FIGURES 1-21) Supplemental Methods Histone peptides used for the pull-down assay and mass spectrometry analysis: H3unmodified (3-20): H2N-TKQTARKSTGGKAPRKQLC-CONH2 H3S10phK14ac (3-20): H2N-TKQTARKS(ph)TGGK(Ac)APRKQLC -CONH2 H3unmodified (19-36): H2N-QLATKAARKSAPATGGVKKC-CONH2 H3S28ph (19-36): H2N-QLATKAARKS(ph)APATGGVKKC-CONH2 Histone peptide pull-down assay For histone peptide pull down assays, 0.1 mg of synthetic peptides (peptide sequences are given above), corresponding to amino acids 3-20 and 19-36 of histone H3 (numbered from N-terminus of histone H3) with a C-terminal cysteine added were coupled to 40 µl (bed volume) of SulfoLink Coupling Resin (Thermo Scientific) according to the manufacturerʼs instructions. Peptide-coupled resin was incubated overnight at 4oC on a roller with 500 µg of nuclear extract (isolated from proliferating HeLa cells treated with 188.5 nM Anisomycin for 1 hour) diluted to 0.5 µg/µl in the binding buffer (20 mM Tris-HCl pH 8.0, 135 mM NaCl, 0.5% NP40, 10% glycerol). The beads were washed 3 times 20 mM Tris-HCl pH 8.0, 135 mM NaCl, 0.5% NP40, 10% glycerol, followed by two washes with 200 mM NaCl, 50 mM Tris-HCl pH 8.0, 0.1 % SDS, 0.1% NP40, 0.5% sodium deoxycholate. -
The Human Gene Connectome As a Map of Short Cuts for Morbid Allele Discovery
The human gene connectome as a map of short cuts for morbid allele discovery Yuval Itana,1, Shen-Ying Zhanga,b, Guillaume Vogta,b, Avinash Abhyankara, Melina Hermana, Patrick Nitschkec, Dror Friedd, Lluis Quintana-Murcie, Laurent Abela,b, and Jean-Laurent Casanovaa,b,f aSt. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065; bLaboratory of Human Genetics of Infectious Diseases, Necker Branch, Paris Descartes University, Institut National de la Santé et de la Recherche Médicale U980, Necker Medical School, 75015 Paris, France; cPlateforme Bioinformatique, Université Paris Descartes, 75116 Paris, France; dDepartment of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; eUnit of Human Evolutionary Genetics, Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Institut Pasteur, F-75015 Paris, France; and fPediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, 75015 Paris, France Edited* by Bruce Beutler, University of Texas Southwestern Medical Center, Dallas, TX, and approved February 15, 2013 (received for review October 19, 2012) High-throughput genomic data reveal thousands of gene variants to detect a single mutated gene, with the other polymorphic genes per patient, and it is often difficult to determine which of these being of less interest. This goes some way to explaining why, variants underlies disease in a given individual. However, at the despite the abundance of NGS data, the discovery of disease- population level, there may be some degree of phenotypic homo- causing alleles from such data remains somewhat limited. geneity, with alterations of specific physiological pathways under- We developed the human gene connectome (HGC) to over- come this problem.