Vascular Inflammatory Response Deneddylase-1/SENP8 in Fine
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Vascular Inflammatory Response Deneddylase-1/SENP8 in Fine
Central Role for Endothelial Human Deneddylase-1/SENP8 in Fine-Tuning the Vascular Inflammatory Response This information is current as Stefan F. Ehrentraut, Douglas J. Kominsky, Louise E. of September 30, 2021. Glover, Eric L. Campbell, Caleb J. Kelly, Brittelle E. Bowers, Amanda J. Bayless and Sean P. Colgan J Immunol 2013; 190:392-400; Prepublished online 3 December 2012; doi: 10.4049/jimmunol.1202041 Downloaded from http://www.jimmunol.org/content/190/1/392 Supplementary http://www.jimmunol.org/content/suppl/2012/12/03/jimmunol.120204 Material 1.DC1 http://www.jimmunol.org/ References This article cites 53 articles, 15 of which you can access for free at: http://www.jimmunol.org/content/190/1/392.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 30, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2012 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Central Role for Endothelial Human Deneddylase-1/SENP8 in Fine-Tuning the Vascular Inflammatory Response Stefan F. -
Genome-Wide CRISPR Screens Reveal Genetic Mediators of Cereblon Modulator Toxicity in Primary Effusion Lymphoma
bioRxiv preprint doi: https://doi.org/10.1101/619312; this version posted April 25, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Genome-wide CRISPR Screens Reveal Genetic Mediators of Cereblon Modulator Toxicity in Primary Effusion Lymphoma Ajinkya Patil1, Mark Manzano1, and Eva Gottwein1 1Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611 USA. Short Title: Cereblon Modulator Resistance Screens in PEL Corresponding Author: Eva Gottwein Department of Microbiology-Immunology Northwestern University Feinberg School of Medicine 320 E Superior St., Tarry Bldg., Room 6-735 Chicago, Illinois 60611 USA e-mail address: [email protected] Phone: +1-312-503-3075 Fax: +1-312-503-5101 Word Count Text: 3986 Word Count Abstract: 250 Figure Count: 7 main figures, 8 supplementary figures Table Count: 0 main manuscript, 8 supplementary tables Reference Count: 43 Scientific Category: Lymphoid Neoplasia 1 bioRxiv preprint doi: https://doi.org/10.1101/619312; this version posted April 25, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Genome-wide CRISPR/Cas9 screens represent a powerful approach to study mechanisms of drug action and resistance. Cereblon modulating agents (CMs) have recently emerged as candidates for therapeutic intervention in primary effusion lymphoma (PEL), a highly aggressive cancer caused by Kaposi’s sarcoma-associated herpesvirus. CMs bind to cereblon (CRBN), the substrate receptor of the cullin-RING type E3 ubiquitin ligase CRL4CRBN, and thereby trigger the acquisition and proteasomal degradation of neosubstrates. -
Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ...................................................... -
Ed with LMP1 Gene in Nasopharyngeal Carcinoma
bioRxiv preprint doi: https://doi.org/10.1101/615237; this version posted April 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Integrated analysis of the miRNA-mRNA network associat- 2 ed with LMP1 gene in nasopharyngeal carcinoma 3 Short title: A co-analysis of EBV-associated genes in NPC 4 5 Autho list:Yang Yanga, Wen Liua, Yan Zhanga,b, Shuo Wua, Bing Luoa* 6 7 Affilation: 8 a: Department of Pathogenic Biology, Qingdao University Medical College, 38 Dengzhou Road, 9 Qingdao, 266071, China 10 b: Department of Clinical Laboratory, Central Hospital of Zibo, 54 Gongqingtuan Road, ZiBo, 11 255036, China 12 13 *Corresponding author: Bing Luo 14 Affilation: Department of Pathogenic Biology, Qingdao University Medical College, 38 Dengzhou 15 Road, Qingdao, 266071, China. Tel: 86-532-8299108. 16 17 Abstract: Epstein-Barr virus oncogenic latent membrane protein 1 (LMP1) has been known to 18 play important roles in nasopharyngeal carcinoma (NPC). LMP1 gene also induced a variety of 19 microRNAs (miRNAs) which bear pivotal roles in regulation of mRNAs expression. However, 20 little was known about the global change of mRNAs and miRNAs induced by LMP1 gene in NPC. 21 In our study, one NPC tissue microarray profile and two LMP1-associated microarray expression 22 profiles data were downloaded from the Gene Expression Omnibus database. A protein-protein 23 interaction network was constructed by using bioinformatics platform Gene-Cloud of Biotech- 24 nology Information (GCBI). -
Genome-Wide CRISPR Screens Reveal Genetic Mediators of Cereblon Modulator Toxicity in Primary Effusion Lymphoma
bioRxiv preprint doi: https://doi.org/10.1101/619312; this version posted April 25, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Genome-wide CRISPR Screens Reveal Genetic Mediators of Cereblon Modulator Toxicity in Primary Effusion Lymphoma Ajinkya Patil1, Mark Manzano1, and Eva Gottwein1 1Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611 USA. Short Title: Cereblon Modulator Resistance Screens in PEL Corresponding Author: Eva Gottwein Department of Microbiology-Immunology Northwestern University Feinberg School of Medicine 320 E Superior St., Tarry Bldg., Room 6-735 Chicago, Illinois 60611 USA e-mail address: [email protected] Phone: +1-312-503-3075 Fax: +1-312-503-5101 Word Count Text: 3986 Word Count Abstract: 250 Figure Count: 7 main figures, 8 supplementary figures Table Count: 0 main manuscript, 8 supplementary tables Reference Count: 43 Scientific Category: Lymphoid Neoplasia 1 bioRxiv preprint doi: https://doi.org/10.1101/619312; this version posted April 25, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Genome-wide CRISPR/Cas9 screens represent a powerful approach to study mechanisms of drug action and resistance. Cereblon modulating agents (CMs) have recently emerged as candidates for therapeutic intervention in primary effusion lymphoma (PEL), a highly aggressive cancer caused by Kaposi’s sarcoma-associated herpesvirus. CMs bind to cereblon (CRBN), the substrate receptor of the cullin-RING type E3 ubiquitin ligase CRL4CRBN, and thereby trigger the acquisition and proteasomal degradation of neosubstrates. -
NEDD8 Conjugation in Schistosoma Mansoni: Genome Analysis and Expression Profiles
Parasitology International 62 (2013) 199–207 Contents lists available at SciVerse ScienceDirect Parasitology International journal homepage: www.elsevier.com/locate/parint NEDD8 conjugation in Schistosoma mansoni: Genome analysis and expression profiles Roberta V. Pereira a, Matheus de S. Gomes b, Roenick P. Olmo a, Daniel M. Souza a, Liana K. Jannotti-Passos c, Elio H. Baba c, William Castro-Borges a, Renata Guerra-Sá a,⁎ a Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Morro do Cruzeiro, Ouro Preto, MG, Brazil b Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia Campus Avançado Patos de Minas, MG, Brazil c Centro de Pesquisas René Rachou, Fiocruz, Belo Horizonte, MG, Brazil article info abstract Article history: NEDD8 is an ubiquitin-like molecule that covalently binds to target proteins through an enzymatic cascade Received 27 June 2012 analogous to ubiquitylation. This modifier is known to bind to p53 and p73, as well as all Cullin family pro- Received in revised form 18 December 2012 teins, which are essential components of Skp1/Cul-1/F-box protein (SCF)-like Ub ligase complexes. Here, Accepted 22 December 2012 we focused on a genomic analysis of the genes involved in the NEDD8 conjugation pathway in Schistosoma Available online 8 January 2013 mansoni. The results revealed seven genes related to NEDD8 conjugation that are conserved in Schistosoma Keywords: japonicum, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. We performed quantitative fi NEDD8 RT-PCR (qRT-PCR), which showed differential pro les for Smnedd8, Smapp1, Smuba3, Smube2f, Smdcn1, Smrbx NEDDylation and Smsenp8 throughout the life cycle of S. -
UI Health Care Letterhead Template
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Brownstein, Catherine A. et al. "An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge." Genome Biology 15:.3 (2014). p.1-18. As Published http://dx.doi.org/10.1186/gb-2014-15-3-r53 Publisher BioMed Central Ltd. Version Final published version Citable link http://hdl.handle.net/1721.1/88017 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/2.0 University of Iowa Hospitals and Clinics Department of Otolaryngology – Head & Neck Surgery 200 Hawkins Drive, 21151-PFP Iowa City, IA 52242-1078 319-356-3612 Tel 319-356-4108 Fax www.uihealthcare.com September 24, 2012 Katherine Flannery Program Manager Harvard Medical School Center for Biomedical Informatics Email: [email protected] RE: CLARITY Challenge Dear Katherine, Accompanying this letter is our CLARITY Challenge reports. As stipulated in the protocol and instructions, our reports are not focused on identifying unrelated findings associated with other health issues or diseases. Pursuant to these specific aims and objectives, we have completed the following: 1. Analysis of whole genome and whole exome sequence data on three families; 2. Identification of potential alterations associated with the phenotype in the proband; 3. Determination and identification of key components for reporting these results; 4. -
Inhibiting Neddylation with MLN4924 Suppresses Growth and Delays Multicellular Development in Dictyostelium Discoideum
biomolecules Article Inhibiting Neddylation with MLN4924 Suppresses Growth and Delays Multicellular Development in Dictyostelium discoideum Robert J. Huber 1,* , William D. Kim 2 and Sabateeshan Mathavarajah 3 1 Department of Biology, Trent University, Peterborough, ON K9L 0G2, Canada 2 Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9L 0G2, Canada; [email protected] 3 Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-705-748-1011 (ext. 7316) Abstract: Neddylation is a post-translational modification that is essential for a variety of cellular processes and is linked to many human diseases including cancer, neurodegeneration, and au- toimmune disorders. Neddylation involves the conjugation of the ubiquitin-like modifier neural precursor cell expressed developmentally downregulated protein 8 (NEDD8) to target proteins, and has been studied extensively in various eukaryotes including fungi, plants, and metazoans. Here, we examine the biological processes influenced by neddylation in the social amoeba, Dictyostelium discoideum, using a well-established inhibitor of neddylation, MLN4924 (pevonedistat). NEDD8, and the target of MLN4924 inhibition, NEDD8-activating enzyme E1 (NAE1), are highly conserved in D. discoideum (Nedd8 and Nae1, respectively). Treatment of D. discoideum cells with MLN4924 increased the amount of free Nedd8, suggesting that MLN4924 inhibited neddylation. During growth, MLN4924 suppressed cell proliferation and folic acid-mediated chemotaxis. During multicellular Citation: Huber, R.J.; Kim, W.D.; development, MLN4924 inhibited cyclic adenosine monophosphate (cAMP)-mediated chemotaxis, Mathavarajah, S. Inhibiting delayed aggregation, and suppressed fruiting body formation. Together, these findings indicate that Neddylation with MLN4924 neddylation plays an important role in regulating cellular and developmental events during the D. -
The Molecular Determinants of NEDD8 Specific Recognition by Human SENP8
The Molecular Determinants of NEDD8 Specific Recognition by Human SENP8 Yung-Cheng Shin, Siao-Jing Tang, Jou-Han Chen, Pei-Han Liao, Shih-Chung Chang* Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan Abstract Although neuronal-precursor-cell-expressed developmentally downregulated protein-8 (NEDD8) and ubiquitin share the highest level of sequence identity and structural similarity among several known ubiquitin-like proteins, their conjugation to a protein leads to distinct biological consequences. In the study, we first identified the NEDD8 protein of Chlamydomonas reinhardtii (CrNEDD8) and discovered that CrNEDD8 is fused at the C-terminus of a ubiquitin moiety (CrUb) in a head-to-tail arrangement. This CrUb-CrNEDD8 protein was termed CrRUB1 (related to ubiquitin 1) by analogy with a similar protein in Arabidopsis thaliana (AtRUB1). Since there is high sequence identity in comparison to the corresponding human proteins (97% for ubiquitin and 84% for NEDD8), a His-CrRUB1-glutathione S-transferase (GST) fusion construct was adopted as the alternative substrate to characterize the specificity of NEDD8-specific peptidase SENP8 for CrNEDD8. The data showed that SENP8 only cleaved the peptide bond beyond the di-glycine motif of CrNEDD8 and His-RUB1 was subsequently generated, confirming that SENP8 has exquisite specificity for CrNEDD8 but not CrUb. To further determine the basis of this specificity, site-directed mutagenesis at earlier reported putative molecular determinants of NEDD8 specific recognition by SENP8 was performed. We found that a single N51E mutation of CrNEDD8 completely inhibited its hydrolysis by SENP8. Conversely, a single E51N mutation of CrUb enabled this ubiquitin mutant to undergo hydrolysis by SENP8, revealing that a single residue difference at the position 51 contributes substantially to the substrate selectivity of SENP8. -
Mitochondrial Trna Methylation in Alzheimer’S Disease and Progressive Supranuclear Palsy Talisa K
Silzer et al. BMC Medical Genomics (2020) 13:71 https://doi.org/10.1186/s12920-020-0727-9 RESEARCH ARTICLE Open Access Mitochondrial tRNA methylation in Alzheimer’s disease and progressive supranuclear palsy Talisa K. Silzer, Gita A. Pathak and Nicole R. Phillips* Abstract Background: Methylation of mitochondrial tRNAs (mt-tRNA) at the 9th position (“p9 site”) is known to impact translational efficiency and downstream mitochondrial function; however, direct assessment of mt-RNA methylation is challenging. Recent RNA sequence-based methods have been developed to reliably identify post-transcriptional methylation. Though p9 methylation has been studied in healthy human populations and in the context of cancer, it has not yet been analyzed in neurodegenerative disease, where mitochondrial dysfunction is a prominent and early hallmark of disease progression. Methods: Mitochondrial p9 methylation was inferred from multi-allelic calls in RNA-seq data. Gene-based association studies were performed in FUMA. Correlations between nuclear gene expression and p9 methylation were tested using Spearman’s rho. Fisher’s Exact test was used in PANTHER and IPA to test for overrepresentation and enrichment of biological processes and pathways in the top nuclear genes correlated with p9 methylation. Results: Variable methylation was observed at 11 p9 sites in post-mortem cerebellar tissue of elderly subjects who were either healthy or diagnosed with Alzheimer’s disease (AD), progressive supranuclear palsy (PSP) or pathological aging (PA). Similarities in degree of methylation were observed between AD and PSP. Certain nuclear encoded genes were identified as significantly associated with p9 methylation. Expression of 5300 nuclear encoded genes was significantly correlated with p9 methylation, with AD and PSP subjects exhibiting similar expression profiles. -
Mitochondrial Trna Methylation in Alzheimer's
Mitochondrial tRNA methylation in Alzheimer’s disease and progressive supranuclear palsy Talisa K. Silzer University of North Texas Health Science Center Gita A. Pathak Yale School of Medicine Nicole Phillips ( [email protected] ) University of North Texas Health Science Center Research article Keywords: Mitochondria, methylation, neurodegenerative disease, tRNA Posted Date: March 10th, 2020 DOI: https://doi.org/10.21203/rs.2.20546/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at BMC Medical Genomics on May 19th, 2020. See the published version at https://doi.org/10.1186/s12920-020-0727-9. Page 1/20 Abstract Background Methylation of mitochondrial tRNAs (mt-tRNA) at the 9 th position (“p9 site”) is known to impact translational eciency and downstream mitochondrial function; however, direct assessment of mt-RNA methylation is challenging. Recent RNA sequence-based methods have been developed to reliably identify post-transcriptional methylation. Though p9 methylation has been studied in healthy human populations and in the context of cancer, it has not yet been analyzed in neurodegenerative disease, where mitochondrial dysfunction is a prominent and early hallmark of disease progression. Results Here we show variable methylation at 11 p9 sites in post-mortem cerebellar tissue of elderly subjects who were either healthy or diagnosed with Alzheimer’s disease (AD), progressive supranuclear palsy (PSP) or pathological aging (PA). Similarities in degree of methylation were observed between AD and PSP. Expression of 5300 genes was signicantly correlated with p9 methylation, with AD and PSP subjects exhibiting similar expression proles. -
Gene Trap Cassettes for Random and Targeted
(19) & (11) EP 1 815 001 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 15/90 (2006.01) A01K 67/027 (2006.01) 02.02.2011 Bulletin 2011/05 C12N 5/10 (2006.01) (21) Application number: 05813398.4 (86) International application number: PCT/EP2005/056282 (22) Date of filing: 28.11.2005 (87) International publication number: WO 2006/056617 (01.06.2006 Gazette 2006/22) (54) GENE TRAP CASSETTES FOR RANDOM AND TARGE TED CONDITIONAL GENE INACTIVATION GEN-FALLEN-KASSETTE FÜR EINE GERICHTETE UND UNGERICHTETE KONDITIONELLE GENINAKTIVIERUNG CASSETTES DE PIEGE A GENES POUR L’INACTIVATION GENETIQUE CONDITIONNELLE ALEATOIRE ET CIBLEE (84) Designated Contracting States: • FLOSS, Thomas AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 85406 Oberappersdorf (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • HANSEN, Jens SK TR 85551 Kirchheim (DE) (30) Priority: 26.11.2004 EP 04028194 (74) Representative: von Kreisler Selting Werner 18.04.2005 EP 05103092 Deichmannhaus am Dom Bahnhofsvorplatz 1 (43) Date of publication of application: 50667 Köln (DE) 08.08.2007 Bulletin 2007/32 (56) References cited: (73) Proprietors: WO-A-02/40685 WO-A-02/088353 • FrankGen Biotechnologie AG 61476 Kronberg/Taunus (DE) • SCHNUETGEN FRANK ET AL: "A directional • Helmholtz Zentrum München Deutsches strategy for monitoring Cre-mediated Forschungszentrum für Gesundheit recombination at the cellular level in the mouse." und Umwelt (GmbH) NATURE BIOTECHNOLOGY, vol. 21, no. 5, May 85764 Neuherberg (DE) 2003 (2003-05), pages 562-565, XP001206846 •MPGMax- Planck-Gesellschaft zur Förderung der ISSN: 1087-0156 Wissenschaften e.V.