Altered Nucleophosmin Transport in Acute Myeloid Leukaemia with Mutated NPM1: Molecular Basis and Clinical Implications
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Parameter IV Dose (1 Mg/Kg) Oral Dose (10 Mg/Kg)
AG-221, a First-in-Class Therapy Targeting Acute Myeloid Leukemia Harboring Oncogenic IDH2 Mutations Katharine Yen, Jeremy Travins, Fang Wang, Muriel D. David, Erin Artin, Kimberly Straley, Anil Padyana, Stefan Gross, Byron DeLaBarre, Erica Tobin, Yue Chen, Raj Nagaraja, Sung Choe, Lei Jin, Zenon Konteatis, Giovanni Cianchetta, Jeffrey O. Saunders, Francesco G. Salituro, Cyril Quivoron, Paule Opolon, Olivia Bawa, Véronique Saada, Angélo Paci, Sophie Broutin, Olivier Bernard, Stéphane de Botton, Benoît S. Marteyn, Monika Pilichowska, YingXia Xu, Cheng Fang, Fan Jiang, Wentao Wei, Shengfang Jin, Lee Silverman, Wei Liu, Hua Yang, Lenny Dang, Marion Dorsch, Virginie Penard-Lacronique, Scott A. Biller, Shin-San Michael Su SUPPLEMENTARY TABLES Supplementary Table 1. Drug metabolism and pharmacokinetic attributes of AG-221 Parameter IV dose (1 mg/kg) Oral dose (10 mg/kg) CL (l/h/kg) 0.83 ± 0.10 NA Vss (l/kg) 5.5 ± 1.6 NA AUC (h.ng/ml) 1,200 ± 130 5,000 ± 610 t1/2 (h) 5.4 ± 1.8 5.4 ± 1.2 F (%) NA 41 ± 5.0 IV and oral pharmacokinetic parameters of AG-221 in male Sprague-Dawley rats (mean ± s.d., n = 3). AUC, area under plasma concentration curve; CL, clearance; F, absolute oral bioavailability; IV, intravenous; NA, not applicable; t1/2, terminal half-life; Vss, volume of distribution at steady state. Page 1 of 12 Supplementary Table 2. Selectivity of AG-221 confirmed by testing against a panel of kinases Enzyme IC50 of AG-221 IC50 of reference Reference (nM) (nM) P13K >10,000 9.1 PI 103 JNK2 >10,000 5741.2 Staurosporine AKT1 >10,000 9.8 Staurosporine -
Nucleolin and Its Role in Ribosomal Biogenesis
NUCLEOLIN: A NUCLEOLAR RNA-BINDING PROTEIN INVOLVED IN RIBOSOME BIOGENESIS Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Heinrich-Heine-Universität Düsseldorf vorgelegt von Julia Fremerey aus Hamburg Düsseldorf, April 2016 2 Gedruckt mit der Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät der Heinrich-Heine-Universität Düsseldorf Referent: Prof. Dr. A. Borkhardt Korreferent: Prof. Dr. H. Schwender Tag der mündlichen Prüfung: 20.07.2016 3 Die vorgelegte Arbeit wurde von Juli 2012 bis März 2016 in der Klinik für Kinder- Onkologie, -Hämatologie und Klinische Immunologie des Universitätsklinikums Düsseldorf unter Anleitung von Prof. Dr. A. Borkhardt und in Kooperation mit dem ‚Laboratory of RNA Molecular Biology‘ an der Rockefeller Universität unter Anleitung von Prof. Dr. T. Tuschl angefertigt. 4 Dedicated to my family TABLE OF CONTENTS 5 TABLE OF CONTENTS TABLE OF CONTENTS ............................................................................................... 5 LIST OF FIGURES ......................................................................................................10 LIST OF TABLES .......................................................................................................12 ABBREVIATION .........................................................................................................13 ABSTRACT ................................................................................................................19 ZUSAMMENFASSUNG -
NPM1-ALK (Human) Recombinant Gene Summary: the 2;5 Chromosomal Translocation Is Protein Frequently Associated with Anaplastic Large Cell Lymphomas (Alcls)
NPM1-ALK (Human) Recombinant Gene Summary: The 2;5 chromosomal translocation is Protein frequently associated with anaplastic large cell lymphomas (ALCLs). The translocation creates a fusion Catalog Number: P5782 gene consisting of the ALK (anaplastic lymphoma kinase) gene and the nucleophosmin (NPM) gene: the 3' Regulation Status: For research use only (RUO) half of ALK, derived from chromosome 2, is fused to the 5' portion of NPM from chromosome 5. A recent study Product Description: Human NPM1-ALK (BAA08343.1, shows that the product of the NPM-ALK fusion gene is 1 a.a. - 680 a.a.) partial recombinant protein with GST oncogenic. The deduced amino acid sequences reveal tag expressed in Baculovirus infected Sf21 cells. that ALK is a novel receptor protein-tyrosine kinase having a putative transmembrane domain and an Host: Insect extracellular domain. These sequences are absent in the product of the transforming NPM-ALK gene. ALK shows Theoretical MW (kDa): 103 the greatest sequence similarity to LTK (leukocyte tyrosine kinase). ALK plays an important role in the Applications: Func, SDS-PAGE development of the brain and exerts its effects on (See our web site product page for detailed applications specific neurons in the nervous system. [provided by information) RefSeq] Protocols: See our web site at http://www.abnova.com/support/protocols.asp or product page for detailed protocols Form: Liquid Preparation Method: Baculovirus infected insect cell (Sf21) expression system Purification: Glutathione sepharose chromatography Purity: 81 % by SDS-PAGE/CBB staining Activity: The activity was measured by off-chip mobility shift assay. The enzyme was incubated with fluorescence-labeled substrate and Mg (or Mn)/ATP. -
Transcriptome-Wide Profiling of Cerebral Cavernous Malformations
www.nature.com/scientificreports OPEN Transcriptome-wide Profling of Cerebral Cavernous Malformations Patients Reveal Important Long noncoding RNA molecular signatures Santhilal Subhash 2,8, Norman Kalmbach3, Florian Wegner4, Susanne Petri4, Torsten Glomb5, Oliver Dittrich-Breiholz5, Caiquan Huang1, Kiran Kumar Bali6, Wolfram S. Kunz7, Amir Samii1, Helmut Bertalanfy1, Chandrasekhar Kanduri2* & Souvik Kar1,8* Cerebral cavernous malformations (CCMs) are low-fow vascular malformations in the brain associated with recurrent hemorrhage and seizures. The current treatment of CCMs relies solely on surgical intervention. Henceforth, alternative non-invasive therapies are urgently needed to help prevent subsequent hemorrhagic episodes. Long non-coding RNAs (lncRNAs) belong to the class of non-coding RNAs and are known to regulate gene transcription and involved in chromatin remodeling via various mechanism. Despite accumulating evidence demonstrating the role of lncRNAs in cerebrovascular disorders, their identifcation in CCMs pathology remains unknown. The objective of the current study was to identify lncRNAs associated with CCMs pathogenesis using patient cohorts having 10 CCM patients and 4 controls from brain. Executing next generation sequencing, we performed whole transcriptome sequencing (RNA-seq) analysis and identifed 1,967 lncRNAs and 4,928 protein coding genes (PCGs) to be diferentially expressed in CCMs patients. Among these, we selected top 6 diferentially expressed lncRNAs each having signifcant correlative expression with more than 100 diferentially expressed PCGs. The diferential expression status of the top lncRNAs, SMIM25 and LBX2-AS1 in CCMs was further confrmed by qRT-PCR analysis. Additionally, gene set enrichment analysis of correlated PCGs revealed critical pathways related to vascular signaling and important biological processes relevant to CCMs pathophysiology. -
Cancer Stem Cells and Nucleolin As Drivers of Carcinogenesis
pharmaceuticals Review Cancer Stem Cells and Nucleolin as Drivers of Carcinogenesis Laura Sofia Carvalho 1,Nélio Gonçalves 1 , Nuno André Fonseca 1,2 and João Nuno Moreira 1,3,* 1 CNC—Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine (Polo 1), University of Coimbra, Rua Larga, 3004-504 Coimbra, Portugal; laurasofi[email protected] (L.S.C.); [email protected] (N.G.); [email protected] (N.A.F.) 2 TREAT U, SA—Parque Industrial de Taveiro, Lote 44, 3045-508 Coimbra, Portugal 3 UC—University of Coimbra, CIBB, Faculty of Pharmacy (FFUC), Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal * Correspondence: [email protected]; Tel.: +351-239-820-190 Abstract: Cancer, one of the most mortal diseases worldwide, is characterized by the gain of specific features and cellular heterogeneity. Clonal evolution is an established theory to explain heterogeneity, but the discovery of cancer stem cells expanded the concept to include the hierarchical growth and plasticity of cancer cells. The activation of epithelial-to-mesenchymal transition and its molecular players are widely correlated with the presence of cancer stem cells in tumors. Moreover, the acquisition of certain oncological features may be partially attributed to alterations in the levels, location or function of nucleolin, a multifunctional protein involved in several cellular processes. This review aims at integrating the established hallmarks of cancer with the plasticity of cancer cells as an emerging hallmark; responsible for tumor heterogeneity; therapy resistance and relapse. The discussion will contextualize the involvement of nucleolin in the establishment of cancer hallmarks and its application as a marker protein for targeted anticancer therapies Keywords: tumor heterogeneity; drug resistance; cancer stem cells; nucleolin; targeted therapies; epithelial-to-mesenchymal transition Citation: Carvalho, L.S.; Gonçalves, N.; Fonseca, N.A.; Moreira, J.N. -
Increased Expression of NPM1 Suppresses P27kip1 Function in Cancer Cells
cancers Article Increased Expression of NPM1 Suppresses p27Kip1 Function in Cancer Cells Tatsuya Kometani, Takuya Arai and Taku Chibazakura * Department of Bioscience, Tokyo University of Agriculture 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan; [email protected] (T.K.); [email protected] (T.A.) * Correspondence: [email protected] Received: 4 August 2020; Accepted: 5 October 2020; Published: 8 October 2020 Simple Summary: Cancer malignancy frequently correlates with a low expression of p27Kip1, a major cyclin-dependent kinase inhibitor, and the p27 protein level has been reportedly responsible for its antiproliferative function. However, we found the function of overexpressed p27 is suppressed in some cancer cells, suggesting that p27 function is also regulated independently of its protein level. The aim of this study was to clarify this unknown p27 regulatory mechanism and its impact on cancer proliferation. We isolated nucleophosmin isoform 1 (NPM1), which is highly expressed in variety of cancers, as a novel p27-interacting protein. Overexpressing NPM1 in normal cells suppressed and silencing NPM1 in cancer cells rescued the p27 function, respectively, in vitro. Moreover, NPM1 silencing and p27 induction in cancer cells significantly suppressed their proliferation in mouse xenografts. Our findings reveal that NPM1 is a novel p27 functional suppressor and a potential anti-cancer target, especially in cancers with normal p27 expression. Abstract: p27Kip1, a major cyclin-dependent kinase inhibitor, is frequently expressed at low levels in cancers, which correlates with their malignancy. However, in this study, we found a qualitative suppression of p27 overexpressed in some cancer cells. By proteomic screening for factors interacting with p27, we identified nucleophosmin isoform 1 (NPM1) as a novel p27-interacting factor and observed that NPM1 protein was expressed at high levels in some cancer cells. -
Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol . -
Core Transcription Factors, Oct4, Sox2 and Nanog, Individually Form Complexes with Nucleophosmin (Npm1) to Control Embryonic Stem
www.impactaging.com AGING, November 2010, Vol 2 N 11 Research Paper Core transcription factors, Oct4, Sox2 and Nanog, individually form complexes with nucleophosmin (Npm1) to control embryonic stem (ES) cell fate determination Helena Johansson and Stina Simonsson Department of Medical Biochemistry and Cell Biology; Institute of Biomedicine; University of Gothenburg, box 440, 405 30 Gothenburg, Västra Götaland; Sweden Key words: Npm1, Oct4, Sox2, Nanog, ES cells, Tpt1 Received: 10/25/10; accepted: 11/10/10; published on line: 11/12/10 Corresponding author: Stina Simonsson, PhD; E‐mail: [email protected] Copyright: © Johansson and Simonsson. This is an open‐access article distributed under the terms of the Creative Commons A ttribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Abstract: Embryonic stem (ES) cells have therapeutic potential in regenerative medicine, although the molecular mechanism controlling their pluripotency is not completely understood. Depending on interaction partners most proteins can be involved in several different cellular mechanisms. We screened for novel protein‐protein interactions using in situ proximity ligation assays together with specific antibodies directed against known important ES cell proteins. We found that all three core transcription factors, namely Oct4, Sox2 and Nanog, individually formed complexes with nucleophosmin (Npm1). We showed that the Npm1/Sox2 complex was sustained when cells were induced to differentiate by retinoic acid, while decreased in the other differentiation pathways. Moreover, Oct4 also formed individual complexes with translationally controlled tumor protein (Tpt1). Downregulation of Npm1 or Tpt1 increased mRNA levels for genes involved in mesoderm and ectoderm differentiation pathways, respectively, indicative of their involvement in ES cell maintenance. -
Next Generation Gene Sequencing -Solid Tumor
Cancer‐related Mutaon Analysis Next Generaon Gene Sequencing for Solid Tumors Assay Summary IU Health Molecular Pathology Laboratory now offers high throughput sequencing for hot spot mutations found in clinically relevant cancer genes. In addition to a general panel of 48 genes, selected panels have been developed for a more tailored application in specific cancers. Comparing to single gene assay, these panels offer a more comprehensive and economic way to assess prognosis and/or treatment options for cancer patients at the initial diagnosis or at the relapse. Orderable Name: Use IU Health Molecular Pathology requisition; Call 317.491.6417 for requisition. Panels include: Lung cancer panel AKT1, ALK, BRAF, EGFR, KRAS, MET, NRAS, PIK3CA, PTEN Colon cancer panel APC, AKT1, BRAF, KRAS, NRAS, PIK3CA, PTEN, SMAD4 Gastrointestinal stromal tumor (GIST) panel BRAF, KIT, PDGFRA Melanoma panel BRAF, CTNNB1, GNA11, GNAQ, KIT, NRAS Ovarian cancer panel BRAF, KRAS, PIK3CA, PTEN Thyroid cancer panel KIT, BRAF, RET Breast cancer panel AKT1, ERBB2, PIK3CA Oncology sequencing panel ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A, CSF1R, CTNNB1, EGFR, ERBB2, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, JAK2, JAK3, KDR, KIT, KRAS, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, VHL Clinical Utility: This test is useful for the assessment of prognosis and/or treatment options for individuals with cancers at initial diagnosis or at replase1. Clinical Information: The Oncology Sequencing Solid Tumor Panel is a highly multiplexed targeted resequencing assay for detecting somatic mutations across hundreds of mutational hotspots in cancer genomes. -
Supplementary Table 1
Supplementary Table 1. Phosphoryl I-Area II-Area II-Debunker III-Area Gene Symbol Protein Name Phosphorylated Peptide I-R2 I-Debunker score II-R2 III-R2 ation Site Ratio Ratio score Ratio 92154 ABBA-1 Actin-bundling protein with BAIAP2 homologyK.TPTVPDS*PGYMGPTR.A S601 1.76 0.95 0.999958250 1.18 0.98 0.999971836 0.98 0.98 92154 ABBA-1 Actin-bundling protein with BAIAP2 homologyR.AGS*EECVFYTDETASPLAPDLAK.A S612 1.40 0.99 0.999977464 1.03 0.99 0.999986373 1.00 0.99 92154 ABBA-1 Actin-bundling protein with BAIAP2 homologyK.GGGAPWPGGAQTYS*PSSTCR.Y S300 0.49 0.98 0.999985406 0.97 0.99 0.999983906 2.03 0.97 23 ABCF1 ATP-binding cassette sub-family F memberK.QQPPEPEWIGDGESTS*PSDK.V 1 S22 1.09 0.98 0.872361494 0.81 1.00 0.847115585 0.97 0.97 27 ABL2 Isoform IA of Tyrosine-protein kinase ABL2K.VPVLIS*PTLK.H S936 0.76 0.98 0.999991559 1.06 0.99 0.999989547 0.99 0.96 3983 ABLIM1 Actin binding LIM protein 1 R.TLS*PTPSAEGYQDVR.D S433 1.27 0.99 0.999994010 1.16 0.98 0.999989861 1.11 0.99 31 ACACA acetyl-Coenzyme A carboxylase alpha isoformR.FIIGSVSEDNS*EDEISNLVK.L 1 S29 1.23 0.99 0.999992898 0.72 0.99 0.999992499 0.83 0.99 65057 ACD Adrenocortical dysplasia protein homologR.TPS*SPLQSCTPSLSPR.S S424 1.51 0.90 0.999936226 0.82 0.88 0.997623142 0.46 0.93 22985 ACIN1 Apoptotic chromatin condensation inducerK.ASLVALPEQTASEEET*PPPLLTK.E in the nucleus T414 0.90 0.92 0.922696554 0.91 0.92 0.993049132 0.95 0.99 22985 ACIN1 Apoptotic chromatin condensation inducerK.ASLVALPEQTAS*EEETPPPLLTK.E in the nucleus S410 1.02 0.99 0.997470008 0.80 0.99 0.999702808 0.96 -
Rnascope® Probes for Stem Cells Research Get Probes for Your Gene of Interest Designed and Manufactured in Two Weeks
Probe List Series Stem Cell Research RNAscope® Probes for Stem Cells Research Get probes for your gene of interest designed and manufactured in two weeks. Featured Publications using Detection of Stem Cell Markers gene of interest, as for example long non-coding RNAscope® Technology RNA. The RNAscope® assay allows you to visualize The rapid and expansive field of stem cell biology and quantify virtually any gene from any genome in Wnts produced by Osterix- has demonstrated the remarkable capabilities any tissue. expressing osteolineage cells of these cells to self-renew, differentiate, and regulate their proliferation and reprogram. Yet the field is still burgeoning with differentiation. studies trying to elucidate stem cell populations, Tan SH. et. al. Proc Natl Acad Sci USA. 2014. Dec 9;111(49): characterize stem cell markers, and identify the ® E5262-71.PMID: 25422448 signals secreted from stem cells. RNAscope in situ hybridization (ISH) technology enables cell- Characterization of LGR5 stem specific localization of RNA transcripts quickly cells in colorectal adenomas and and precisely for markers of stem cell populations. carcinomas. The RNAscope® assay can be used to: Baker AM. et. al. Sci Rep. 2015 Mar 2;5:8654.PMID: 25728748 • Identify, characterize, and locate stem PMID: 25728748 cell populations • Reveal markers of stem cell maintenance Pontin functions as an essential coactivator for Oct4-dependent and regeneration lincRNA expression in mouse • Identify long non-coding RNAs in stem cells FIGURE 1. Detection of TP63 mRNA expression in embryonic stem cells. ® • Detect stem cell markers when no reliable human prostate FFPE tissue using RNAscope 2.0 HD Boo K. -
Molecular Pathology Tests
Cleveland Clinic Laboratories Molecular Pathology Tests Molecular Cytogenetics IGK PCR (BIOMED-2 Primers) Chromosome Studies TCRB PCR (BIOMED-2 Primers) Postnatal: TCRG PCR (BIOMED-2 Primers) Peripheral blood IGH (Southern blot) Fibroblasts TCRß (Southern blot) Products of Conception: BCL2 mbr (PCR) CVS (chorionic villi) p210 BCR/ABL1( RT-PCR, quantitative) Placenta p190 BCR/ABL1( RT-PCR, quantitative) Skin BCR/ABL Kinase Domain Mutation Analysis Bone PML/RARA RT-PCR, qualitative Cancer: Nucleophosmin gene (NPM1) mutation analysis ** Bone Marrow FLT3 Gene Mutations Leukemic blood JAK2 V617F mutation (PCR) Lymph node Fluorescence in-situ hybridization Fatty tumors 5q Renal tissue ALK Chromosomal Microarray BCL2 Whole Genome microarray (Oligo array) BCL6 BCR/ABL1 Molecular Genetic Pathology BIRC3(API2)/MALT1 Alpha-1-Antitrypsin genotyping (S and Z alleles) CBFB/MYH11 (inv 16) CYP2C9 and VKORC1 Warfarin PGX CLL (13q,11q, 17p,+12) CYP2C19 Clopidogrel PGX ETV6/RUNX1 (TEL/AML1) CYP2D6 FGFR1 CYP2D6 Tamoxifen PGX IGH Cystic fibrosis [ACOG panel] (PCR) IGH/BCL2 DNA fingerprinting for identity (STR;PCR) IGH/CCND1 Factor V Leiden (PCR) IGH/MALT1 Fragile X syndrome (FMR1) DNA analysis (PCR) IGH/MYC HFE [Hereditary Hemochromatosis] (PCR) MALT1(18q21) MTHFR (PCR) MLL PLA1, PLA2 (PCR) MYC Progenitor cell engraftment monitoring (STR;PCR) Myelodysplasia (-5/5q, -7/7q,+8,-20q) Prothrombin G20210A (PCR) Plasma cell myeloma [13q, IGH, TP53, t(11,14), t(4;14), Transthyretin (TTR) exon sequencing t(14;16)] VWF exon 28 sequencing PDGFRA PDGFRB Molecular Hematopathology