Inactivation of the Putative Ubiquitin-E3 Ligase PDLIM2 in Classical Hodgkin and Anaplastic Large Cell Lymphoma

Total Page:16

File Type:pdf, Size:1020Kb

Inactivation of the Putative Ubiquitin-E3 Ligase PDLIM2 in Classical Hodgkin and Anaplastic Large Cell Lymphoma OPEN Leukemia (2016), 1–12 www.nature.com/leu ORIGINAL ARTICLE Inactivation of the putative ubiquitin-E3 ligase PDLIM2 in classical Hodgkin and anaplastic large cell lymphoma KD Wurster1,2, F Hummel1,2, J Richter3, M Giefing3,4, S Hartmann5, M-L Hansmann5, S Kreher2, K Köchert1,2, D Krappmann6, W Klapper7, M Hummel8, S-S Wenzel2, G Lenz9, M Janz1,2, B Dörken1,2,10, R Siebert3,11 and S Mathas1,2,10 Apart from its unique histopathological appearance with rare tumor cells embedded in an inflammatory background of bystander cells, classical Hodgkin lymphoma (cHL) is characterized by an unusual activation of a broad range of signaling pathways involved in cellular activation. This includes constitutive high-level activity of nuclear factor-κB (NF-κB), Janus kinase/signal transducer and activator of transcription (JAK/STAT), activator protein-1 (AP-1) and interferon regulatory factor (IRF) transcription factors (TFs) that are physiologically only transiently activated. Here, we demonstrate that inactivation of the putative ubiquitin E3-ligase PDLIM2 contributes to this TF activation. PDLIM2 expression is lost at the mRNA and protein levels in the majority of cHL cell lines and Hodgkin and Reed–Sternberg (HRS) cells of nearly all cHL primary samples. This loss is associated with PDLIM2 genomic alterations, promoter methylation and altered splicing. Reconstitution of PDLIM2 in HRS cell lines inhibits proliferation, blocks NF-κB transcriptional activity and contributes to cHL-specific gene expression. In non-Hodgkin B-cell lines, small interfering RNA-mediated PDLIM2 knockdown results in superactivation of TFs NF-κB and AP-1 following phorbol 12-myristate 13-acetate (PMA) stimulation. Furthermore, expression of PDLIM2 is lost in anaplastic large cell lymphoma (ALCL) that shares key biological aspects with cHL. We conclude that inactivation of PDLIM2 is a recurrent finding in cHL and ALCL, promotes activation of inflammatory signaling pathways and thereby contributes to their pathogenesis. Leukemia advance online publication, 14 October 2016; doi:10.1038/leu.2016.238 INTRODUCTION of negative regulators of more downstream located signaling Classical Hodgkin lymphoma (cHL) is characterized by a unique components (for example, inhibitor of NF-κB(IκB)α mutations in 10,11 12,13 histopathological appearance in the affected lymph nodes the NF-κB pathway), genomic alterations of respective TFs 14 demonstrating only a minority of tumor cells, the so-called and the constitutive activation of upstream kinases. The strength Hodgkin and Reed–Sternberg (HRS) cells, that are embedded in an and plethora of pathway activation in HRS cells is exceptional abundant inflammatory microenvironment.1 It is assumed that among lymphoid malignancies. Interestingly, despite their com- HRS cells attract these inflammatory bystander cells by high-level plex transcriptional alterations including long-terminal repeat activation,15,16 HRS cells demonstrate a surprisingly constant production of cytokines and chemokines, and that the interaction phenotype. Our recent data on the pivotal role of IRF5 together between HRS cells and their surrounding cells supports their 1–3 with NF-κB regarding the orchestration of the HL-specific gene growth, survival and immune escape. The abundant production 7 fl fl expression program suggest that only a limited number of of in ammatory mediators by HRS cells re ects their highly pathogenic events coordinate the cHL phenotype. activated phenotype. In line with such a phenotype, HRS cells Given the number of high-level activated TFs in HRS cells show constitutive activation of a plethora of transcription factors involved in immediate-early gene regulation, we postulated that (TFs) that are physiologically only transiently activated, and that alterations of the ubiquitin system contribute to their simulta- are implicated in cellular activation and immediate-early gene neous activation. Based on a literature search in combination with induction. Among these TFs, nuclear factor-κB (NF-κB), signal gene expression data of HRS and non-Hodgkin (NH) B cell-derived transducer and activator of transcription (STAT) 3, 5 and 6, cell lines,17 we focused on PDLIM2 (also known as mystique or activator protein-1 (AP-1) and interferon regulatory factor-5 (IRF5) SLIM).18–20 PDLIM2 has been shown to act as ubiquitin E3-ligase – play key roles in HL pathogenesis.4 8 inducing inactivation and degradation of TFs.19,21 In addition, The mechanisms leading to activation of these TFs in HRS cells ubiquitin-independent mechanisms of PDLIM2 have been are complex and affect various layers of control of respective described.19 By these mechanisms, PDLIM2 controls the activity pathway components.1 These include deleterious mutations of of TFs, such as NF-κB-p65, STAT1 and STAT3,19,21–23 that are highly negative regulators of receptor-proximal activation modules,9 activated in HRS cells. Furthermore, alterations of PDLIM2 gene 1Max-Delbrück-Center for Molecular Medicine, Berlin, Germany; 2Hematology, Oncology, and Tumor Immunology, Charité–Universitätsmedizin Berlin, Berlin, Germany; 3Institute of Human Genetics, Christian-Albrechts University Kiel, Kiel, Germany; 4Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; 5Dr Senckenberg Institute of Pathology, University of Frankfurt, Medical School, Frankfurt, Germany; 6Research Unit Cellular Signal Integration, Helmholtz Zentrum München für Gesundheit und Umwelt, Neuherberg, Germany; 7Department of Pathology, Haematopathology Section and Lymph Node Registry, Christian-Albrechts University Kiel, Kiel, Germany; 8Institute of Pathology, Charité–Universitätsmedzin Berlin, Berlin, Germany; 9Division of Translational Oncology, Department of Medicine A, University Hospital Münster, and Cluster of Excellence EXC 1003, Cells in Motion, Münster, Germany; 10German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany and 11Institute of Human Genetics, University Hospital Ulm, Ulm, Germany. Correspondence: Dr S Mathas, Max-Delbrück-Center for Molecular Medicine, and Charité - Universitätsmedizin Berlin, Hematology, Oncology and Tumor Immunology, Robert-Rössle-Straße 10, D-13125 Berlin, Germany. E-mail: [email protected] Received 19 January 2016; revised 2 August 2016; accepted 9 August 2016; accepted article preview online 19 August 2016 Loss of PDLIM2 in human lymphoma KD Wurster et al 2 expression have been observed in malignancies,23–25 and the RNA preparation and reverse transcriptase-PCR analyses PDLIM2 gene locus in 8p21.3 is in the minimal commonly deleted Total RNA preparation, complementary DNA synthesis and semiquantita- region in 8p21.3 in several B-cell non-Hodgkin lymphomas.26,27 tive PCR and real-time quantitative PCR analyses were performed as Here, we describe an inactivation of the putative ubiquitin previously described.17,28 Primers are listed in Supplementary Table 1. E3-ligase PDLIM2 as unifying defect of HRS cells. PDLIM2 loss of All PCR products were verified by sequencing. expression is associated with various mechanisms, including genomic alterations and promoter DNA methylation. Functionally, Analysis of apoptosis and proliferation loss of PDLIM2 promotes growth of HRS cells, facilitates the The percentage of viable and apoptotic cells was determined by Annexin activation of inflammatory TFs and results in deregulation of V-fluorescein isothiocyanate/propidium iodide double staining (Bender fl 7 differentially expressed cHL-associated genes, suggesting a MedSystems, Vienna, Austria) and ow cytometry as previously described. Proliferation of cells was determined by measurement of [3H]-thymidine pathogenic role in cHL. Furthermore, we demonstrate loss of incorporation using standard protocols. PDLIM2 expression in anaplastic large cell lymphoma (ALCL) that shares key biological aspects with cHL. Western blot analyses Whole-cell and nuclear extract preparation and western blotting were performed as described5 with 30 μg whole-cell or 20 μg nuclear extracts. MATERIALS AND METHODS Primary antibodies were: PDLIM2 (sc-79988), IκBα (sc-371; both from Santa Cell lines and culture conditions Cruz, Heidelberg, Germany), PDLIM2 (ab68220; Abcam, Cambridge, UK) β HRS (L428, L1236, KM-H2, L591 (EBV+), U-HO1, SUP-HD1, HDLM-2, L540, and -actin (A5316, Sigma-Aldrich). L540Cy), pro-B lymphoblastic leukemia (Reh), Burkitt lymphoma (Namalwa, BL-60, BJAB), diffuse large B-cell lymphoma (SU-DHL-4), ALCL (K299, SU- Immunohistochemistry DHL-1, DEL, JB6, all anaplastic lymphoma kinase (ALK) positive; Mac-1, Mac- Immunohistochemical stainings of 20 primary cHL, 10 follicular lymphoma, 2A, FE-PD, DL40, all ALK negative), T-cell leukemia-derived (Jurkat, KE-37, 15 diffuse large B-cell lymphoma and 10 Burkitt lymphoma cases Molt-14, H9) and HEK293 cells were cultured as previously described.28 were performed as previously described.33 Primary antibodies (PDLIM2, Cells were electroporated in OPTI-MEM I using Gene-Pulser Xcell (Bio-Rad, PA5-31484, Thermo Scientific, Darmstadt, Germany; PDLIM2, ab68220, Munich, Germany) with 950 μF and 0.18 kV (L540Cy, HEK293) or 500 μF Abcam; IκBα, sc-371, Santa Cruz) were applied in a dilution of 1:100 and 0.3 kV (Reh, L591). Transfection efficiency was determined by pEGFP- (PDLIM2 antibodies) or 1:500 (IκBα) overnight. N3 (Clontech Laboratories, Mountain View, CA, USA) co-transfection. L591 and L540Cy cells were transfected with 40 μg of a pcDNA3-PDLIM2 Interphase cytogenetics transcript variant 2 (tv 2) construct along with 10 μg pEGFP-N3. GFP+ cells Fluorescence
Recommended publications
  • Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-Like Mouse Models: Tracking the Role of the Hairless Gene
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2006 Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene Yutao Liu University of Tennessee - Knoxville Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Life Sciences Commons Recommended Citation Liu, Yutao, "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino- like Mouse Models: Tracking the Role of the Hairless Gene. " PhD diss., University of Tennessee, 2006. https://trace.tennessee.edu/utk_graddiss/1824 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Yutao Liu entitled "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Life Sciences. Brynn H. Voy, Major Professor We have read this dissertation and recommend its acceptance: Naima Moustaid-Moussa, Yisong Wang, Rogert Hettich Accepted for the Council: Carolyn R.
    [Show full text]
  • Molecular and Epigenetic Features of Melanomas and Tumor Immune
    Seremet et al. J Transl Med (2016) 14:232 DOI 10.1186/s12967-016-0990-x Journal of Translational Medicine RESEARCH Open Access Molecular and epigenetic features of melanomas and tumor immune microenvironment linked to durable remission to ipilimumab‑based immunotherapy in metastatic patients Teofila Seremet1,3*† , Alexander Koch2†, Yanina Jansen1, Max Schreuer1, Sofie Wilgenhof1, Véronique Del Marmol3, Danielle Liènard3, Kris Thielemans4, Kelly Schats5, Mark Kockx5, Wim Van Criekinge2, Pierre G. Coulie6, Tim De Meyer2, Nicolas van Baren6,7 and Bart Neyns1 Abstract Background: Ipilimumab (Ipi) improves the survival of advanced melanoma patients with an incremental long-term benefit in 10–15 % of patients. A tumor signature that correlates with this survival benefit could help optimizing indi- vidualized treatment strategies. Methods: Freshly frozen melanoma metastases were collected from patients treated with either Ipi alone (n: 7) or Ipi combined with a dendritic cell vaccine (TriMixDC-MEL) (n: 11). Samples were profiled by immunohistochemistry (IHC), whole transcriptome (RNA-seq) and methyl-DNA sequencing (MBD-seq). Results: Patients were divided in two groups according to clinical evolution: durable benefit (DB; 5 patients) and no clinical benefit (NB; 13 patients). 20 metastases were profiled by IHC and 12 were profiled by RNA- and MBD-seq. 325 genes were identified as differentially expressed between DB and NB. Many of these genes reflected a humoral and cellular immune response. MBD-seq revealed differences between DB and NB patients in the methylation of genes linked to nervous system development and neuron differentiation. DB tumors were more infiltrated by CD8+ and PD-L1+ cells than NB tumors.
    [Show full text]
  • PDLIM2 Antibody A
    Revision 1 C 0 2 - t PDLIM2 Antibody a e r o t S Orders: 877-616-CELL (2355) [email protected] Support: 877-678-TECH (8324) 4 4 Web: [email protected] 1 www.cellsignal.com 8 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source: UniProt ID: Entrez-Gene Id: WB H M Endogenous 38 Rabbit Q96JY6 64236 Product Usage Information Application Dilution Western Blotting 1:1000 Storage Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA and 50% glycerol. Store at –20°C. Do not aliquot the antibody. Specificity / Sensitivity PDLIM2 Antibody recognizes endogenous levels of total PDLIM2 protein. Species Reactivity: Human, Mouse Source / Purification Polyclonal antibodies are produced by immunizing animals with a synthetic peptide corresponding to residues surrounding Gly255 of human PDLIM2 protein. Antibodies are purified by protein A and peptide affinity chromatography. Background PDLIM2, also known as Mystique, contains an amino-terminal PDZ domain and a carboxy-terminal LIM domain. PDLIM2 was orginally found to be associated with cytoskeletal proteins in epithelial cells to promote cell attachment and migration (1,2). Subsequent studies have shown that PDLIM2 can also inhibit NF-κB activity by acting as a nuclear ubiquitin E3 ligase for p65 (3). PDLIM2 is suppressed in cancer cell lines by DNA methylation (4,5). Expression of PDLIM2 can inhibit anchorage-independent growth and tumor formation. 1. Torrado, M. et al. (2004) Invest Ophthalmol Vis Sci 45, 3955-63. 2. Loughran, G.
    [Show full text]
  • Views for Entrez
    BASIC RESEARCH www.jasn.org Phosphoproteomic Analysis Reveals Regulatory Mechanisms at the Kidney Filtration Barrier †‡ †| Markus M. Rinschen,* Xiongwu Wu,§ Tim König, Trairak Pisitkun,¶ Henning Hagmann,* † † † Caroline Pahmeyer,* Tobias Lamkemeyer, Priyanka Kohli,* Nicole Schnell, †‡ †† ‡‡ Bernhard Schermer,* Stuart Dryer,** Bernard R. Brooks,§ Pedro Beltrao, †‡ Marcus Krueger,§§ Paul T. Brinkkoetter,* and Thomas Benzing* *Department of Internal Medicine II, Center for Molecular Medicine, †Cologne Excellence Cluster on Cellular Stress | Responses in Aging-Associated Diseases, ‡Systems Biology of Ageing Cologne, Institute for Genetics, University of Cologne, Cologne, Germany; §Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; ¶Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; **Department of Biology and Biochemistry, University of Houston, Houston, Texas; ††Division of Nephrology, Baylor College of Medicine, Houston, Texas; ‡‡European Molecular Biology Laboratory–European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom; and §§Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany ABSTRACT Diseases of the kidney filtration barrier are a leading cause of ESRD. Most disorders affect the podocytes, polarized cells with a limited capacity for self-renewal that require tightly controlled signaling to maintain their integrity, viability, and function. Here, we provide an atlas of in vivo phosphorylated, glomerulus- expressed
    [Show full text]
  • Downloaded, Each with Over 20 Samples for AD-Specific Pathways, Biological Processes, and Driver Each Specific Brain Region in Each Condition
    Xiang et al. BMC Medical Genomics 2018, 11(Suppl 6):115 https://doi.org/10.1186/s12920-018-0431-1 RESEARCH Open Access Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimer’s disease patients Shunian Xiang1,2, Zhi Huang4, Wang Tianfu1, Zhi Han3, Christina Y. Yu3,5, Dong Ni1*, Kun Huang3* and Jie Zhang2* From 29th International Conference on Genome Informatics Yunnan, China. 3-5 December 2018 Abstract Background: Gene co-expression network (GCN) mining is a systematic approach to efficiently identify novel disease pathways, predict novel gene functions and search for potential disease biomarkers. However, few studies have systematically identified GCNs in multiple brain transcriptomic data of Alzheimer’s disease (AD) patients and looked for their specific functions. Methods: In this study, we first mined GCN modules from AD and normal brain samples in multiple datasets respectively; then identified gene modules that are specific to AD or normal samples; lastly, condition-specific modules with similar functional enrichments were merged and enriched differentially expressed upstream transcription factors were further examined for the AD/normal-specific modules. Results: We obtained 30 AD-specific modules which showed gain of correlation in AD samples and 31 normal- specific modules with loss of correlation in AD samples compared to normal ones, using the network mining tool lmQCM. Functional and pathway enrichment analysis not only confirmed known gene functional categories related to AD, but also identified novel regulatory factors and pathways. Remarkably, pathway analysis suggested that a variety of viral, bacteria, and parasitic infection pathways are activated in AD samples.
    [Show full text]
  • Transdifferentiation of Human Mesenchymal Stem Cells
    Transdifferentiation of Human Mesenchymal Stem Cells Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Julius-Maximilians-Universität Würzburg vorgelegt von Tatjana Schilling aus San Miguel de Tucuman, Argentinien Würzburg, 2007 Eingereicht am: Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Martin J. Müller Gutachter: PD Dr. Norbert Schütze Gutachter: Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am: Hiermit erkläre ich ehrenwörtlich, dass ich die vorliegende Dissertation selbstständig angefertigt und keine anderen als die von mir angegebenen Hilfsmittel und Quellen verwendet habe. Des Weiteren erkläre ich, dass diese Arbeit weder in gleicher noch in ähnlicher Form in einem Prüfungsverfahren vorgelegen hat und ich noch keinen Promotionsversuch unternommen habe. Gerbrunn, 4. Mai 2007 Tatjana Schilling Table of contents i Table of contents 1 Summary ........................................................................................................................ 1 1.1 Summary.................................................................................................................... 1 1.2 Zusammenfassung..................................................................................................... 2 2 Introduction.................................................................................................................... 4 2.1 Osteoporosis and the fatty degeneration of the bone marrow..................................... 4 2.2 Adipose and bone
    [Show full text]
  • Type of the Paper (Article
    Supplementary Methods Microarray Experiments (Single Color Mode) The Microarray utilized in this study represents a refined version of the Whole Human Genome Oligo Microarray 4 × 44K v2 (Design ID 026652, Agilent Technologies, (Santa Clara, CA, USA), called ‘054261On1M’ (Design ID 066335) developed at the Research Core Unit Transcriptomics (RCUT) of Hannover Medical School (Hannover, Germany). The microarray design was created in Agilent’s eArray portal using a 1 × 1 M design format for mRNA expression as template. All non-control probes of design ID 026652 have been printed five times within a region comprising a total of 181,560 Features (170 columns × 1068 rows). Four of such regions were placed within one 1 M region giving rise to four microarray fields per slide to be hybridized individually (Customer Specified Feature Layout). Control probes required for proper Feature Extraction software operation were determined and placed automatically by eArray using recommended default settings. An amount of 250 ng of total RNA were used for synthesis of aminoallyl-UTP-modified (aaUTP) cRNA with the ‘Quick Amp Labeling kit, no dye’ (#5190-0447, Agilent Technologies) according to the manufacturer’s recommendations, except that reaction volumes were quartered and contained NTP- mix was exchanged by NTP Set (ATP, CTP, GTP, UTP) and aminoallyl-UTP (Fermentas, Thermo Fisher Scientific; Waltham, MA, USA); order numbers R1091, R0481, respectively). Final NTP concentrations used for in-vitro transcription were 2.5 mM (ATP, CTP, GTP), 1.88 mM UTP, and 0.62 mM aaUTP. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies) as described in the Amino Allyl MessageAmp™ II Kit Manual (#AM1753; Life Technologies, Carlsbad, CA, USA) except that reaction volumes were quartered.
    [Show full text]
  • Downloaded Per Proteome Cohort Via the Web- Site Links of Table 1, Also Providing Information on the Deposited Spectral Datasets
    www.nature.com/scientificreports OPEN Assessment of a complete and classifed platelet proteome from genome‑wide transcripts of human platelets and megakaryocytes covering platelet functions Jingnan Huang1,2*, Frauke Swieringa1,2,9, Fiorella A. Solari2,9, Isabella Provenzale1, Luigi Grassi3, Ilaria De Simone1, Constance C. F. M. J. Baaten1,4, Rachel Cavill5, Albert Sickmann2,6,7,9, Mattia Frontini3,8,9 & Johan W. M. Heemskerk1,9* Novel platelet and megakaryocyte transcriptome analysis allows prediction of the full or theoretical proteome of a representative human platelet. Here, we integrated the established platelet proteomes from six cohorts of healthy subjects, encompassing 5.2 k proteins, with two novel genome‑wide transcriptomes (57.8 k mRNAs). For 14.8 k protein‑coding transcripts, we assigned the proteins to 21 UniProt‑based classes, based on their preferential intracellular localization and presumed function. This classifed transcriptome‑proteome profle of platelets revealed: (i) Absence of 37.2 k genome‑ wide transcripts. (ii) High quantitative similarity of platelet and megakaryocyte transcriptomes (R = 0.75) for 14.8 k protein‑coding genes, but not for 3.8 k RNA genes or 1.9 k pseudogenes (R = 0.43–0.54), suggesting redistribution of mRNAs upon platelet shedding from megakaryocytes. (iii) Copy numbers of 3.5 k proteins that were restricted in size by the corresponding transcript levels (iv) Near complete coverage of identifed proteins in the relevant transcriptome (log2fpkm > 0.20) except for plasma‑derived secretory proteins, pointing to adhesion and uptake of such proteins. (v) Underrepresentation in the identifed proteome of nuclear‑related, membrane and signaling proteins, as well proteins with low‑level transcripts.
    [Show full text]
  • Survival Analysis of Infected Mice Reveals Pathogenic Variations in The
    OPEN Survival analysis of infected mice reveals SUBJECT AREAS: pathogenic variations in the genome of COMPUTATIONAL BIOLOGY AND avian H1N1 viruses BIOINFORMATICS ECOLOGY Zeynep A. Koçer1, Yiping Fan2, Robert Huether2*, John Obenauer2{, Richard J. Webby1, Jinghui Zhang2, Robert G. Webster1 & Gang Wu2 Received 3 October 2014 1Department of Infectious Diseases, Division of Virology, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, United States, 2Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, United Accepted States. 24 November 2014 Published Most influenza pandemics have been caused by H1N1 viruses of purely or partially avian origin. Here, using 12 December 2014 Cox proportional hazard model, we attempt to identify the genetic variations in the whole genome of wild-type North American avian H1N1 influenza A viruses that are associated with their virulence in mice by residue variations, host origins of virus (Anseriformes-ducks or Charadriiformes-shorebirds), and Correspondence and host-residue interactions. In addition, through structural modeling, we predicted that several polymorphic requests for materials sites associated with pathogenicity were located in structurally important sites, especially in the polymerase complex and NS genes. Our study introduces a new approach to identify pathogenic variations in wild-type should be addressed to viruses circulating in the natural reservoirs and ultimately to understand their infectious risks to humans as R.G.W. (robert. part of risk assessment efforts towards the emergence of future pandemic strains. [email protected]) or G.W. (gang.wu@ stjude.org) nfluenza A viruses (IAVs), which belong to the Orthomyxoviridae family, typically replicate in the intestinal tract of wild aquatic birds causing no overt disease and are transmitted through open-water sources via the I fecal-oral route1.
    [Show full text]
  • Supporting Information Extendend Materials and Methods Animals A
    Supporting Information Extendend Materials and Methods Animals A BAC clone, RP23-443K20, that contains the translational start site of the Epb41l5 gene was obtained from BACPAC Resources (http://bacpac.chori.org/), and targeting and control vectors were constructed as described. Following primers were used: the 32 bp p1 (5’-CAGAAAGTCGACGCTAGATCCCCTCGCCTACC-3’) and 23bp p2 (5’- GGTGTGGGGTCTGGGAATGAAGG-3’) to amplify the 2.5kb 5’ arm of the targeting vector, the 19bp p3 (5’-GGTCAAACAGCTCCTGTCC-3’) and 36bp p4 (5’- GACTGGCTCGAGGGTAGGGTTGAGAGGGATTAGTAG-3’) sequences to amplify the 1.1kb 3’ arm of the targeting vector. Their locations are indicated in Figure S7. The six underlined nucleotides in p1 and p4 sequences were converted into Accl and Xhol recognition sequences, GTCGAC and CTCGAG, respectively, to generate each primers. The amplified products were digested by each restriction enzyme: Accl and Xhol for the 2.5 kb 5’ arm and Spel and Notl for the 1.1kb 3’ arm, respectively. To construct the targeting vector, the 5’ 2.5kb and 3’ 1.1kb arms were inserted into the Accl/Notl sites and Nhel/Xhol sites of 5’ and 3’ cloning sites, respectively, of the LacZ/Neo-DTA vector. To generate podocyte specific knockout mice the well established hNPHS2-Cre allele was intercrossed to Epb41l5 conditional mice (provided by Lawrence Holzman - Renal, Electrolyte and Hypertension Division, University of Pennsylvania School of Medicine Philadelphia, PA, USA). As an inducible podocyte specific mouse line we made use of a mouse line expressing a rtTA cassette under control of the hNPHS2 promotor (1). Induction of the respective inducible mouse models was performed according to following protocol: animals at the age of 4 weeks received doxycycline hydrochloride (Fagron) via the drinking water (2mg/ml with 5% (wt/vol) sucrose, protected from light) for a periode of 14 days.
    [Show full text]
  • Mai Muuttunut Pihlution Uniti
    MAIMUUTTUNUT US009994893B2 PIHLUTION UNITI (12 ) United States Patent ( 10 ) Patent No. : US 9 , 994 ,893 B2 Tischfield et al. (45 ) Date of Patent: Jun . 12, 2018 (54 ) COMPOSITIONS AND METHODS FOR OTHER PUBLICATIONS FUNCTIONAL QUALITY CONTROL FOR HUMAN BLOOD - BASED GENE Opitz et al ., Imparct of RNA Degradation on Gene Expression EXPRESSION PRODUCTS Profiling, BMC Medical Genomics , 2010 , 3 ( 36 ) , 1 - 14 . * Shmueli et al. , GeneNote : Whole Genome Expression Profiles in ( 71 ) Applicant: Rutgers, The State University of New Normal Human Tissues , Molecular Biology and Genetics, 2003 , Jersey, New Brunswick , NJ (US ) 326 , 1067 - 1072 . ( Year : 2003 ) . * International Search Report PCT/ US2012 /069561 , dated Apr. 5 , (72 ) Inventors : Jay Tischfield , Martinsville , NJ (US ) ; 2013 . 16 Pages. Andrew Brooks, New York , NY (US ) ; Auer et al. , “ Chipping away at the chip bias : RNA degradation in Stephanie Frahm , Flemington , NJ (US ) microarray analysis .” Nat Genet . Dec. 2003 ;35 ( 4 ) :292 - 3 . Baechler et al ., “ Expression levels for many genes in human (73 ) Assignee: Rutgers, The State University of New peripheral blood cells are highly sensitive to ex vivo incubation .” Jersey , New Brunswick , NJ (US ) Genes Immun . Aug . 2004 ; 5 ( 5 ) : 347 - 53 . Becker et al ., “ mRNA and microRNA quality control for RT- PCR ( * ) Notice : Subject to any disclaimer , the term of this analysis . ” Methods . Apr. 2010 ;50 ( 4 ) :237 - 43 . patent is extended or adjusted under 35 Beelman et al ., “ Degradation of mRNA in eukaryotes” Cell. Apr . 21, U . S . C . 154 ( b ) by 851 days . 1995 ;81 ( 2 ) : 179 - 83 . Bijlani et al ., “ Prediction of biologically significant components (21 ) Appl. No .: 14 / 365 , 060 from microarray data : Independently Consistent Expression Dis criminator ( ICED ) .” Bioinformatics .
    [Show full text]
  • Pengrong Yan
    REGULATION OF HTLV-I ONCOPROTEIN TAX BY PDLIM2 by Pengrong Yan Biological Sciences B.S., Fudan University, 2005 Submitted to the Graduate Faculty of School of Medicine in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2010 UNIVERSITY OF PITTSBURGH School of Medicine This thesis/dissertation was presented by Pengrong Yan It was defended on Aug 5th, 2010 and approved by Thomas Smithgall, Ph.D., Professor, Department of Microbiology and Molecular Genetics Patrick Moore, M.D. M.P.H., Professor, Department of Microbiology and Molecular Genetics Paul Robbins, Ph.D., Professor, Department of Microbiology and Molecular Genetics Jing Hu, Ph.D., Assistant Professor, Department of Pharmacology and Chemical Biology Thesis Director and Advisor: Gutian Xiao, Ph.D., Associate Professor, Department of Microbiology and Molecular Genetics ii REGULATION OF HTLV-I ONCOPROTEIN TAX BY PDLIM2 Pengrong Yan, PhD University of Pittsburgh, 2010 Portions of the research in Chapter 2 were originally published in Blood. Pengrong Yan, Jing Fu, Zhaoxia Qu, Shirong Li, Takashi Tanaka, Michael J Grusby and Gutian Xiao. (2009) PDLIM2 suppresses human T-cell leukemia virus type I Tax – mediated tumorigenesis by targeting Tax into the nuclear matrix for proteasomal degradation. Blood. 113(18): 4370-80. © The American Society of Hematology (ASH). Portions of the research in Chapter 3 are currently in press at Oncogene. Jing Fu, Pengrong Yan, Shirong Li, Zhaoxia Qu and Gutian Xiao. Molecular determinants of PDLIM2 in suppressing HTLV-I Tax-mediated tumorigenesis. Oncogene. © Nature Publishing Group. Portions of the research in Chapter 4 were originally published in Neoplasia.
    [Show full text]