DOCSLIB.ORG

Global Post-Translational Modification Profiling of HIV-1-Infected Cells Reveals

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Global Post-Translational Modification Profiling of HIV-1-Infected Cells Reveals bioRxiv preprint doi: https://doi.org/10.1101/2020.01.06.896365; this version posted January 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling Jeffrey R. Johnson1,2,3,4*, David C. Crosby5, Judd F. Hultquist1,2,3,6, Donna Li7, John Marlett8, Justine Swann8, Ruth Hüttenhain1,2,3, Erik Verschueren9, Tasha L. Johnson1,2,3, Billy W. Newton1,2,3, Michael Shales1,2,3, Pedro Beltrao10, Alan D. Frankel2, Alexander Marson11,12,13,14, Oliver I. Fregoso15, John A. T. Young16, Nevan J. Krogan6,7,8,* 1Department of Cellular and Molecular Pharmacology; University of California San Francisco; San Francisco, CA, 94158; USA 2Quantitative Biosciences Institute; University of California San Francisco; San Francisco, CA, 94158; USA 3Gladstone Institute for Data Science and Biotechnology; Gladstone Institutes; San Francisco, CA, 94158; USA 4Present address: Department of Microbiology; Icahn School of Medicine at Mount Sinai; New York, NY, 10029; USA 5Department of Biochemistry; University of California San Francisco; San Francisco, CA, 94158; USA 6Present address: Division of Infectious Diseases; Northwestern University Feinberg School of Medicine; Chicago, IL, 60611; USA 7Cancer Biology Graduate Program; University of Wisconsin School of Medicine and Public Health; Madison, WI, 53726; USA 8Viral Vector Core; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA 9Proteomics and Biological Resources; Genentech, Inc.; South San Francisco, CA, 94080; USA bioRxiv preprint doi: https://doi.org/10.1101/2020.01.06.896365; this version posted January 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. 10European Molecular Biology Laboratory, European Bioinformatics Institute; Wellcome Genome Campus; Hinxton, Cambridge, CD10 1SD; UK 11Department of Microbiology and Immunology; University of California San Francisco; San Francisco, CA, 94143; USA 12Diabetes Center; University of California San Francisco; San Francisco, CA, 94143; USA 13Innovative Genomics Institute; University of California Berkeley; Berkeley, CA, 94720; USA 14Department of Medicine; University of California San Francisco; San Francisco, CA, 94143l USA 15Deparment of Microbiology, Immunology, and Molecular Genetics; University of California Los Angeles; Los Angeles, CA, 90095; USA 16Roche Pharma Research and Early Development; Roche Innovation Center Basel; 4070 Basel; Switzerland *Correspondence: [email protected]; [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.01.06.896365; this version posted January 7, 2020. 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. SUMMARY Viruses must effectively remodel host cellular pathways to replicate and evade immune defenses, and they must do so with limited genomic coding capacity. Targeting post- translational modification (PTM) pathways provides a mechanism by which viruses can broadly and rapidly transform a hostile host environment into a hospitable one. We used quantitative proteomics to measure changes in two PTM types – phosphorylation and ubiquitination – in response to HIV-1 infection with viruses harboring targeted deletions of a subset of HIV-1 genes. PTM analysis revealed a requirement for Aurora kinase A activity in HIV-1 infection and furthermore revealed that AMP-activated kinase activity is modulated during infection via HIV-1 Vif-mediated degradation of B56-containing protein phosphatase 2A (PP2A). Finally, we demonstrated that the Cullin4A-DDB1-DCAF1 E3 ubiquitin ligase ubiquitinates histone H1 somatic variants and that HIV-1 Vpr inhibits this process, leading to defects in DNA repair. Thus, global PTM profiling of infected cells serves as an effective tool for uncovering specific mechanisms of host pathway modulation. KEYWORDS HIV-1, proteomics, phosphorylation, ubiquitination, systems biology, vpr, histone h1, vif, pp2a, b56, ampk, ampd2 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.06.896365; this version posted January 7, 2020. 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. INTRODUCTION Human immunodeficiency virus type-1 (HIV-1) remains a major threat to public health worldwide. While there has been tremendous success in the development of combination antiretroviral therapies (cART) for treatment and prophylaxis, there is a need for next-generation therapies that are less toxic, have fewer side effects, and are longer-acting. Drug resistance is also a threat to existing therapies, with an estimated 10 percent of people received cART that are resistant to at least one drug in their cART formulation (Organization, 2017). The identification of new drug targets is critical to next-generation antiretroviral drug development, and as such a precise molecular understanding of HIV-1 gene functions is of critical importance. The HIV-1 genome encodes several accessory genes that are dispensable for replication in some cell lines but are required for evasion of host antiviral pathways and in vivo replication and pathogenesis. Three accessory genes, Vif, Vpr, and Vpu, bind to Cullin RING-type E3 ubiquitin ligases in order to rewire host ubiquitination systems and antagonize antiviral host pathways (Sauter and Kirchhoff, 2018). The HIV-1 Vif protein binds to the Cullin-5/Elogin-B/Elongin-C RING-type E3 ubiquitin ligases (CRL5EloB/EloC) in order to promote ubiquitination and proteasomal degradation of antiviral APOBEC3 proteins, a family of single-stranded DNA-editing enzymes with the capacity to incorporate into HIV-1 virions and inactivate the virus by hypermutation of the genome during reverse transcription (eehy et al., 2002; Harris et al., 2003). Vif also targets the PP2A-B56 subfamily of protein phosphatases for ubiquitination and degradation, and this degradation is associated with G2 cell cycle arrest (Greenwood et al., 2016; Salamango et al., 2019). The substrate(s) of PP2A-B56 affected by its degradation and the molecular mechanism underlying Vif-mediated G2 arrest remains unknown. The HIV-1 Vpu protein binds to the Cullin-1/Skp1/βTrCP ligase (SCFβTrCP) to promote bioRxiv preprint doi: https://doi.org/10.1101/2020.01.06.896365; this version posted January 7, 2020. 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. ubiquitination and removal from the cell surface of BST/tetherin, an antiviral protein that inhibits viral budding and release (Neil et al., 2008). HIV-2, an independent zoonotic transmission of simian immunodeficiency virus (SIV) from primate in humans that is distinct from HIV-1, encodes the additional Vpx protein that binds to the Cullin4/DDB1/DCAF1 (CRL4DCAF1) ligase to promote ubiquitination and degradation of the antiviral protein SAMHD1, which restricts free deoxynucleotide pools and impairs viral reverse transcription (Hrecka et al., 2011; Laguette et al., 2011). Intriguingly, HIV- 2 Vpx also utilizes CRL4DCAF1 to promote ubiquitination and degradation of the HUSH transcriptional silencing complex that otherwise acts to silence incoming proviruses in the nucleus (Chougui et al., 2018; Dahabieh et al., 2015; Lai and Pugh, 2017; Yurkovetskiy et al., 2018). It is not yet clear whether HUSH is wired to the innate immune system. The HIV-1 Vpr protein also binds to CRL4DCAF1, but it does not share SAMHD1 and HUSH inactivation functions with HIV-2 Vpx. Several Vpr-CRL4DCAF1 substrates have been identified including the uracil N-glycosylase 2 (UNG2), Mus81 (part of the SLX4 complex), helicase-like transcription factor (HLTF), exonuclease 1 (EXO1), and Tet DNA dioxygenase 2 (TET2) (Laguette et al., 2014; Lahouassa et al., 2016; Lv et al., 2018; Yan et al., 2018). However, only TET2 has been demonstrated to rescue a replication defect of Vpr-deficient viral replication in primary monocyte-derived macrophages and the rescue was only partial (Wang and Su, 2019). Furthermore, none of the Vpr-CRL4DCAF1 substrates identified thus far explain the ability of Vpr to potently activate cell cycle arrest at the G2/M-phase checkpoint. The identification of post-translational modification (PTM) enzyme-substrate relationships can be challenging due to the relatively transient nature of their physical interactions. The discoveries of APOBEC3 and BST2/tetherin proteins as ubiquitination targets of Vif-CRL5ELOB/ELOC and Vpu-SCFβTrCP, respectively, were made by comparing bioRxiv preprint doi: https://doi.org/10.1101/2020.01.06.896365; this version posted January 7, 2020. 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. gene expression patterns in closely related cell lines that were permissive or non- permissive to HIV-1 replication with Vif- and Vpu-deficient viruses. Conversely, the suite of Vpr and Vpx substrates have been identified by physical interactions with Vpr/Vpx- CRL4DCAF1, as suitable non-permissive cell lines for HIV-1 replication with Vpr- or Vpx- deficient viruses have not been established.
Load more

Recommended publications
  • Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. 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. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. 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 Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis.
    [Show full text]
  • Mapping Influenza-Induced Posttranslational Modifications On
    viruses Article Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells Svetlana Rezinciuc 1, Zhixin Tian 2, Si Wu 2, Shawna Hengel 2, Ljiljana Pasa-Tolic 2 and Heather S. Smallwood 1,3,* 1 Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; [email protected] 2 Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; [email protected] (Z.T.); [email protected] (S.W.); [email protected] (S.H.); [email protected] (L.P.-T.) 3 Children’s Foundation Research Institute, Memphis, TN 38105, USA * Correspondence: [email protected]; Tel.: +1-(901)-448–3068 Academic Editor: Italo Tempera Received: 10 October 2020; Accepted: 2 December 2020; Published: 8 December 2020 Abstract: T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection.
    [Show full text]
  • Cytoplasmic Activation-Induced Cytidine Deaminase (AID) Exists in Stoichiometric Complex with Translation Elongation Factor 1Α (Eef1a)
    Cytoplasmic activation-induced cytidine deaminase (AID) exists in stoichiometric complex with translation elongation factor 1α (eEF1A) Julien Häsler, Cristina Rada, and Michael S. Neuberger1 Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom Edited by Frederick W. Alt, Howard Hughes Medical Institute, Harvard Medical School, Children’s Hospital Immune Disease Institute, Boston, MA, and approved October 12, 2011 (received for review April 27, 2011) Activation-induced cytidine deaminase (AID) is a B lymphocyte- results reveal that endogenous cytoplasmic AID partakes in a specific DNA deaminase that acts on the Ig loci to trigger antibody complex containing stoichiometric quantities of translation elon- gene diversification. Most AID, however, is retained in the cyto- gation factor 1α (eEF1A), with this association likely implicated in plasm and its nuclear abundance is carefully regulated because the regulation of AID’s intracellular trafficking. off-target action of AID leads to cancer. The nature of the cytosolic AID complex and the mechanisms regulating its release from the Results cytoplasm and import into the nucleus remain unknown. Here, we Flag-Tagging the Endogenous AID Locus in DT40 Cells. We generated show that cytosolic AID in DT40 B cells is part of an 11S complex derivatives of the DT40 B-cell line in which the endogenous AID and, using an endogenously tagged AID protein to avoid overex- locus was modified so as to incorporate a single Flag tag at the pression artifacts, that it is bound in good stoichiometry to the AID N terminus. To allow targeting of both alleles, one targeting translation elongation factor 1 alpha (eEF1A).
    [Show full text]
  • 35 Disorders of Purine and Pyrimidine Metabolism
    35 Disorders of Purine and Pyrimidine Metabolism Georges van den Berghe, M.- Françoise Vincent, Sandrine Marie 35.1 Inborn Errors of Purine Metabolism – 435 35.1.1 Phosphoribosyl Pyrophosphate Synthetase Superactivity – 435 35.1.2 Adenylosuccinase Deficiency – 436 35.1.3 AICA-Ribosiduria – 437 35.1.4 Muscle AMP Deaminase Deficiency – 437 35.1.5 Adenosine Deaminase Deficiency – 438 35.1.6 Adenosine Deaminase Superactivity – 439 35.1.7 Purine Nucleoside Phosphorylase Deficiency – 440 35.1.8 Xanthine Oxidase Deficiency – 440 35.1.9 Hypoxanthine-Guanine Phosphoribosyltransferase Deficiency – 441 35.1.10 Adenine Phosphoribosyltransferase Deficiency – 442 35.1.11 Deoxyguanosine Kinase Deficiency – 442 35.2 Inborn Errors of Pyrimidine Metabolism – 445 35.2.1 UMP Synthase Deficiency (Hereditary Orotic Aciduria) – 445 35.2.2 Dihydropyrimidine Dehydrogenase Deficiency – 445 35.2.3 Dihydropyrimidinase Deficiency – 446 35.2.4 Ureidopropionase Deficiency – 446 35.2.5 Pyrimidine 5’-Nucleotidase Deficiency – 446 35.2.6 Cytosolic 5’-Nucleotidase Superactivity – 447 35.2.7 Thymidine Phosphorylase Deficiency – 447 35.2.8 Thymidine Kinase Deficiency – 447 References – 447 434 Chapter 35 · Disorders of Purine and Pyrimidine Metabolism Purine Metabolism Purine nucleotides are essential cellular constituents 4 The catabolic pathway starts from GMP, IMP and which intervene in energy transfer, metabolic regula- AMP, and produces uric acid, a poorly soluble tion, and synthesis of DNA and RNA. Purine metabo- compound, which tends to crystallize once its lism can be divided into three pathways: plasma concentration surpasses 6.5–7 mg/dl (0.38– 4 The biosynthetic pathway, often termed de novo, 0.47 mmol/l). starts with the formation of phosphoribosyl pyro- 4 The salvage pathway utilizes the purine bases, gua- phosphate (PRPP) and leads to the synthesis of nine, hypoxanthine and adenine, which are pro- inosine monophosphate (IMP).
    [Show full text]
  • Exogenous Hydrogen Sulfide Plays an Important Role by Regulating
    International Journal of Molecular Sciences Review Exogenous Hydrogen Sulfide Plays an Important Role by Regulating Autophagy in Diabetic-Related Diseases Shuangyu Lv , Huiyang Liu and Honggang Wang * Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng 475000, China; [email protected] (S.L.); [email protected] (H.L.) * Correspondence: [email protected] Abstract: Autophagy is a vital cell mechanism which plays an important role in many physiological processes including clearing long-lived, accumulated and misfolded proteins, removing damaged organelles and regulating growth and aging. Autophagy also participates in a variety of biological functions, such as development, cell differentiation, resistance to pathogens and nutritional hunger. Recently, autophagy has been reported to be involved in diabetes, but the mechanism is not fully understood. Hydrogen sulfide (H2S) is a colorless, water-soluble, flammable gas with the typical odor of rotten eggs, which has been known as a highly toxic gas for many years. However, it has been reported recently that H2S, together with nitric oxide and carbon monoxide, is an important gas signal transduction molecule. H2S has been reported to play a protective role in many diabetes- related diseases, but the mechanism is not fully clear. Recent studies indicate that H2S plays an important role by regulating autophagy in many diseases including cancer, tissue fibrosis diseases and glycometabolic diseases; however, the related mechanism has not been fully studied. In this review, we summarize recent research on the role of H2S in regulating autophagy in diabetic-related diseases to provide references for future related research.
    [Show full text]
  • Metabolism of Purines and Pyrimidines in Health and Disease
    39th Meeting of the Polish Biochemical Society Gdañsk 16–20 September 2003 SESSION 6 Metabolism of purines and pyrimidines in health and disease Organized by A. C. Sk³adanowski, A. Guranowski 182 Session 6. Metabolism of purines and pyrimidines in health and disease 2003 323 Lecture The role of DNA methylation in cytotoxicity mechanism of adenosine analogues in treatment of leukemia Krystyna Fabianowska-Majewska Zak³ad Chemii Medycznej IFiB, Uniwersytet Medyczny, ul. Mazowiecka 6/8, 92 215 £ódŸ Changes in DNA methylation have been recognized tory effects of cladribine and fludarabine on DNA as one of the most common molecular alterations in hu- methylation, after 48 hr growth of K562 cells with the man neoplastic diseases and hypermethylation of drugs, are non-random and affect mainly CpG rich is- gene-promoter regions is one of the most frequent lands or CCGG sequences but do not affect sepa- mechanisms of the loss of gene functions. For this rea- rately-located CpG sequences. The analysis showed son, DNA methylation may be a tool for detection of that cladribine (0.1 mM) reduced the methylated early cell transformations as well as predisposition to cytosines in CpG islands and CCGG sequences to a sim- metastasis process. Moreover, DNA methylation seems ilar degree. The inhibition of cytosine methylation by to be a promissing target for new preventive and thera- fludarabine (3 mM) was observed mainly in CCGG se- peutic strategies. quences, sensitive to HpaII, but the decline in the meth- Our studies on DNA methylation and cytotoxicity ylated cytosine, located in CpG island was 2-fold lower mechanism of antileukemic drugs, cladribine and than that with cladribine.
    [Show full text]
  • Determining HDAC8 Substrate Specificity by Noah Ariel Wolfson A
    Determining HDAC8 substrate specificity by Noah Ariel Wolfson A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biological Chemistry) in the University of Michigan 2014 Doctoral Committee: Professor Carol A. Fierke, Chair Professor Robert S. Fuller Professor Anna K. Mapp Associate Professor Patrick J. O’Brien Associate Professor Raymond C. Trievel Dedication My thesis is dedicated to all my family, mentors, and friends who made getting to this point possible. ii Table of Contents Dedication ....................................................................................................................................... ii List of Figures .............................................................................................................................. viii List of Tables .................................................................................................................................. x List of Appendices ......................................................................................................................... xi Abstract ......................................................................................................................................... xii Chapter 1 HDAC8 substrates: Histones and beyond ...................................................................... 1 Overview ..................................................................................................................................... 1 HDAC introduction
    [Show full text]
  • Tissue-Specific Pathways and Networks Underlying Sexual
    Kurt et al. Biology of Sex Differences (2018) 9:46 https://doi.org/10.1186/s13293-018-0205-7 RESEARCH Open Access Tissue-specific pathways and networks underlying sexual dimorphism in non- alcoholic fatty liver disease Zeyneb Kurt1, Rio Barrere-Cain1, Jonnby LaGuardia1, Margarete Mehrabian2, Calvin Pan2, Simon T Hui2, Frode Norheim2, Zhiqiang Zhou2, Yehudit Hasin2, Aldons J Lusis2* and Xia Yang1* Abstract Background: Non-alcoholic fatty liver disease (NAFLD) encompasses benign steatosis and more severe conditions such as non-alcoholic steatohepatitis (NASH), cirrhosis, and liver cancer. This chronic liver disease has a poorly understood etiology and demonstrates sexual dimorphisms. We aim to examine the molecular mechanisms underlying sexual dimorphisms in NAFLD pathogenesis through a comprehensive multi-omics study. We integrated genomics (DNA variations), transcriptomics of liver and adipose tissue, and phenotypic data of NAFLD derived from female mice of ~ 100 strains included in the hybrid mouse diversity panel (HMDP) and compared the NAFLD molecular pathways and gene networks between sexes. Results: We identified both shared and sex-specific biological processes for NAFLD. Adaptive immunity, branched chain amino acid metabolism, oxidative phosphorylation, and cell cycle/apoptosis were shared between sexes. Among the sex-specific pathways were vitamins and cofactors metabolism and ion channel transport for females, and phospholipid, lysophospholipid, and phosphatidylinositol metabolism and insulin signaling for males. Additionally, numerous lipid and insulin-related pathways and inflammatory processes in the adipose and liver tissue appeared to show more prominent association with NAFLD in male HMDP. Using data-driven network modeling, we identified plausible sex-specific and tissue-specific regulatory genes as well as those that are shared between sexes.
    [Show full text]
  • Functional Genomics Atlas of Synovial Fibroblasts Defining Rheumatoid Arthritis
    medRxiv preprint doi: https://doi.org/10.1101/2020.12.16.20248230; this version posted December 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability Xiangyu Ge1*, Mojca Frank-Bertoncelj2*, Kerstin Klein2, Amanda Mcgovern1, Tadeja Kuret2,3, Miranda Houtman2, Blaž Burja2,3, Raphael Micheroli2, Miriam Marks4, Andrew Filer5,6, Christopher D. Buckley5,6,7, Gisela Orozco1, Oliver Distler2, Andrew P Morris1, Paul Martin1, Stephen Eyre1* & Caroline Ospelt2*,# 1Versus Arthritis Centre for Genetics and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK 2Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland 3Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia 4Schulthess Klinik, Zurich, Switzerland 5Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK 6NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, Birmingham, UK 7Kennedy Institute of Rheumatology, University of Oxford Roosevelt Drive Headington Oxford UK *These authors contributed equally #corresponding author: [email protected] NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. 1 medRxiv preprint doi: https://doi.org/10.1101/2020.12.16.20248230; this version posted December 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • Supplementary Data
    SUPPLEMENTARY DATA A cyclin D1-dependent transcriptional program predicts clinical outcome in mantle cell lymphoma Santiago Demajo et al. 1 SUPPLEMENTARY DATA INDEX Supplementary Methods p. 3 Supplementary References p. 8 Supplementary Tables (S1 to S5) p. 9 Supplementary Figures (S1 to S15) p. 17 2 SUPPLEMENTARY METHODS Western blot, immunoprecipitation, and qRT-PCR Western blot (WB) analysis was performed as previously described (1), using cyclin D1 (Santa Cruz Biotechnology, sc-753, RRID:AB_2070433) and tubulin (Sigma-Aldrich, T5168, RRID:AB_477579) antibodies. Co-immunoprecipitation assays were performed as described before (2), using cyclin D1 antibody (Santa Cruz Biotechnology, sc-8396, RRID:AB_627344) or control IgG (Santa Cruz Biotechnology, sc-2025, RRID:AB_737182) followed by protein G- magnetic beads (Invitrogen) incubation and elution with Glycine 100mM pH=2.5. Co-IP experiments were performed within five weeks after cell thawing. Cyclin D1 (Santa Cruz Biotechnology, sc-753), E2F4 (Bethyl, A302-134A, RRID:AB_1720353), FOXM1 (Santa Cruz Biotechnology, sc-502, RRID:AB_631523), and CBP (Santa Cruz Biotechnology, sc-7300, RRID:AB_626817) antibodies were used for WB detection. In figure 1A and supplementary figure S2A, the same blot was probed with cyclin D1 and tubulin antibodies by cutting the membrane. In figure 2H, cyclin D1 and CBP blots correspond to the same membrane while E2F4 and FOXM1 blots correspond to an independent membrane. Image acquisition was performed with ImageQuant LAS 4000 mini (GE Healthcare). Image processing and quantification were performed with Multi Gauge software (Fujifilm). For qRT-PCR analysis, cDNA was generated from 1 µg RNA with qScript cDNA Synthesis kit (Quantabio). qRT–PCR reaction was performed using SYBR green (Roche).
    [Show full text]
  • DNA Topoisomerase 1 and 2A Function As Oncogenes in Liver Cancer and May Be Direct Targets of Nitidine Chloride
    INTERNATIONAL JOURNAL OF ONCOLOGY 53: 1897-1912, 2018 DNA topoisomerase 1 and 2A function as oncogenes in liver cancer and may be direct targets of nitidine chloride LI-MIN LIU1*, DAN-DAN XIONG2*, PENG LIN3, HONG YANG3, YI-WU DANG2 and GANG CHEN2 1Department of Toxicology, College of Pharmacy, Guangxi Medical University; 2Department of Pathology; 3Ultrasonics Division, Radiology Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China Received March 16, 2018; Accepted July 31, 2018 DOI: 10.3892/ijo.2018.4531 Abstract. The aim of the present study was to determine the role of patients with LC and for identification of high-risk cases, of topoisomerase 1 (TOP1) and topoisomerase 2A (TOP2A) thereby optimizing individual treatment management. More in liver cancer (LC), and to investigate the inhibitory effect importantly, the findings support TOP1 and TOP2A as poten- of nitidine chloride (NC) on these two topoisomerases. tial drug targets of NC for the treatment of LC. Immunohistochemistry (IHC) staining and microarray or RNA sequencing data mining showed markedly higher expression Introduction of TOP1 and TOP2A at the protein and mRNA levels in LC tissues compared with that in control non-tumor tissues. The Liver cancer (LC) is the second main cause of cancer-associated prognostic values of TOP1 and TOP2A expression were also mortality threatening global public health, with hepatocellular estimated based on data from The Cancer Genome Atlas. The carcinoma (HCC) being the main histopathological subtype (1,2). elevated expression levels of TOP1 and TOP2A were closely In the United States, the American Cancer Society projects that associated with poorer overall survival and disease-free >30,000 patients will succumb to LC in 2018 (3).
    [Show full text]
  • Α Regulation of Antiviral APOBEC3G By
    STAT1-Independent Cell Type-Specific Regulation of Antiviral APOBEC3G by IFN- α This information is current as Phuong Thi Nguyen Sarkis, Songcheng Ying, Rongzhen Xu of October 2, 2021. and Xiao-Fang Yu J Immunol 2006; 177:4530-4540; ; doi: 10.4049/jimmunol.177.7.4530 http://www.jimmunol.org/content/177/7/4530 Downloaded from References This article cites 50 articles, 19 of which you can access for free at: http://www.jimmunol.org/content/177/7/4530.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average by guest on October 2, 2021 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 © 2006 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology STAT1-Independent Cell Type-Specific Regulation of Antiviral APOBEC3G by IFN-␣1 Phuong Thi Nguyen Sarkis,* Songcheng Ying,† Rongzhen Xu,† and Xiao-Fang Yu2*† APOBEC3G (A3G) has broad antiviral activity against retroviruses and hepatitis B virus. However, the role of IFNs in regulating A3G during innate immunity has not been established.
    [Show full text]