DOCSLIB.ORG

The Genetic Regulation of the Response of Hematopoietic Stem/Progenitor Cells to the Cytostatic Agent Hydroxyurea

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Genetic Regulation of the Response of Hematopoietic Stem/Progenitor Cells to the Cytostatic Agent Hydroxyurea University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2006 THE GENETIC REGULATION OF THE RESPONSE OF HEMATOPOIETIC STEM/PROGENITOR CELLS TO THE CYTOSTATIC AGENT HYDROXYUREA Jeffrey Lynn Yates University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Yates, Jeffrey Lynn, "THE GENETIC REGULATION OF THE RESPONSE OF HEMATOPOIETIC STEM/ PROGENITOR CELLS TO THE CYTOSTATIC AGENT HYDROXYUREA" (2006). University of Kentucky Doctoral Dissertations. 420. https://uknowledge.uky.edu/gradschool_diss/420 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Jeffrey Lynn Yates The Graduate School University of Kentucky 2006 THE GENETIC REGULATION OF THE RESPONSE OF HEMATOPOIETIC STEM/PROGENITOR CELLS TO THE CYTOSTATIC AGENT HYDROXYUREA ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The College of Medicine at the University of Kentucky By Jeffrey Lynn Yates Lexington, KY Co-Directors: Dr. Gary Van Zant, Professor of Medicine and Dr. Brian Jackson, Professor of Physiology 2006 Copyright © Jeffrey L. Yates 2006 ABSTRACT OF DISSERTATION THE GENETIC REGULATION OF THE RESPONSE OF HEMATOPOIETIC STEM/PROGENITOR CELLS TO THE CYTOSTATIC AGENT HYDROXYUREA Cellular proliferation is a key characteristic of hematopoietic stem and progenitor cells (HSC/HPCs) that allows for the production of all blood cell lineages during an individual’s lifetime. While this feature of stem cells is strictly regulated during steady- state and stress hematopoiesis, it also contributes to the development of myeloproliferative disorders, such as chronic myelogenous leukemia, essential thrombocythemia, and polycythemia vera. It should come as no surprise then, that common treatments for these diseases often target the proliferative nature of the dysfunctional HSC/HPCs. Thus, the identification of molecular determinants of cell cycle regulation associated with these disorders could serve as targets for novel therapies. Using the hematopoietic system of the inbred mouse strains, C57BL/6J (B6) and DBA/2J (D2), it was found that the HSC/HPCs of the long-lived B6 mouse strain were less susceptible to the cytostatic agent hydroxyurea (HU) than the short-lived D2 mouse strain. A quantitative trait locus (QTL) analysis revealed a region of proximal chromosome 7 that regulates this response to HU. Congenic mouse strains were generated and phenotypic analysis confirmed that the B6 and D2 loci confer a low and high sensitivity of the HSC/HPCs to HU, respectively. We then showed that while this response of the HSC/HPCs to HU is independent of their cell cycle status, the B6 allele of this QTL confers a proliferative advantage to bone marrow cells after bone marrow transplantation. Having shown that proximal chromosome 7 regulates the response of HSC/HPCs to HU, we found it necessary to characterize the gene and protein expression profiles in order to identify the responsible candidate genes. We first analyzed mRNA expression profiles of HPCs from the parental and congenic mouse strains using gene microarrays and found that four genes within the congenic interval were differentially expressed. Real-time PCR confirmed that the expression profile of only one gene, Ndufa3, is significantly different in HPCs of B6 and D2 mice. Concurrently, we assessed the protein expression profiles of HPC-enriched mononuclear cells. Significant differences were found between the cytoplasmic and nuclear fractions of both strains, with a skewing of protein expression towards the D2 congenic strain. KEYWORDS: Hematopoiesis, Hydroxyurea, Stem Cells, Genomics, Proteomics Jeffrey L. Yates_______________ 08/01/2006___________________ THE GENETIC REGULATION OF THE RESPONSE OF HEMATOPOIETIC STEM/PROGENITOR CELLS TO THE CYTOSTATIC AGENT HYDROXYUREA By Jeffrey Lynn Yates Gary Van Zant, Ph.D._____ Co-Director of Dissertation Brian Jackson, Ph.D.______ Co-Director of Dissertation Steven Estus, Ph.D._______ Director of Graduate Studies Rules for the Use of Dissertations Unpublished dissertations submitted for the Doctor’s degree and deposited in the University of Kentucky Library are as a rule open for inspection, but are to be used only with due regard as to the rights of the authors. Bibliographical references may be noted, but quotations or summaries of parts may be published only with the permission of the author, and with the usual scholarly acknowledgements. Extensive copying or publication of the dissertation in whole or in part also requires the consent of the Dean of the Graduate School of the University of Kentucky. A library that borrows this dissertation for use by its patrons is expected to secure the signature of each user. Name Date DISSERTATION Jeffrey Lynn Yates The Graduate School University of Kentucky 2006 THE GENETIC REGULATION OF THE RESPONSE OF HEMATOPOIETIC STEM/PROGENITOR CELLS TO THE CYTOSTATIC AGENT HYDROXYUREA DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Medicine at the University of Kentucky By Jeffrey Lynn Yates Lexington, KY Co-Directors: Dr. Gary Van Zant, Professor of Medicine and Dr. Brian Jackson, Professor of Physiology Copyright © Jeffrey L. Yates 2006 I would like to dedicate this dissertation first and foremost to my wife Shannon whose unwavering support made this endeavor possible. ACKNOWLEDGEMENTS I would first like to thank my savior and creator Jesus Christ for blessing me with the abilities that allowed me to complete this dissertation, Furthermore, I would like to give my heartfelt gratitude to Dr. Gary Van Zant, for his patience, support, advice, and friendship in the development and completion of the research outlined in this dissertation. Furthermore, I would like to thank my dissertation committee, Dr.Brian Jackson, Dr. Scott Diamond, and Dr. Brett Spear for their critical comments and support along the way. I would also like to thank Dr. Bob Dickson for agreeing to serve as the outside examiner and his useful comments regarding this dissertation. I would finally like to thank my lab mates who are too numerous to name here. It would suffice to say that there were a lot of women in the lab who always kept me on my toes and grounded. I will be eternally grateful to all of you for the impact you have made in my life. iii TABLE OF CONTENTS ACKNOWLEDGEMENTS ........................................................................................... xi LIST OF TABLES......................................................................................................... vi LIST OF FIGURES ...................................................................................................... vii CHAPTER ONE: INTRODUCTION............................................................................. 1 Characteristics of the hematopoietic system ................................................................ 1 Organization and identification of the pluripotent HSC ............................................... 2 Systemic versus cellular aging..................................................................................... 3 Model systems of stem cell aging................................................................................ 5 Regulation of HSC proliferation.................................................................................. 6 DNA repair and genomic instability during aging........................................................ 9 Genetic regulation of stem cell proliferation.............................................................. 11 The CAFC assay: High throughput identification of the hematopoietic heirarchy..... 13 The cytostatic action of hydroxyurea......................................................................... 15 Experimental goals and significance.......................................................................... 17 CHAPTER TWO: MAPPING AND CONFIRMATION OF A QTL REGULATING THE RESPONSE OF HEMATOPOIETIC STEM/PROGENITOR CELLS TO HYDROXYUREA........................................................................................................ 20 Summary................................................................................................................... 20 Introduction .............................................................................................................. 22 Materials and Methods ............................................................................................. 25 Results ...................................................................................................................... 28 Discussion................................................................................................................. 31 CHAPTER THREE: INVESTIGATION INTO THE MECHANISMS UNDERLYING THE STRAIN-SPECIFIC RESPONSE OF HEMATOPOIETIC STEM/PROGENITOR CELLS TO HYDROXYUREA..................................................................................... 41 Summary................................................................................................................... 41 Introduction .............................................................................................................
Load more

Recommended publications
  • Loss of Fam60a, a Sin3a Subunit, Results in Embryonic Lethality and Is Associated with Aberrant Methylation at a Subset of Gene
    RESEARCH ARTICLE Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters Ryo Nabeshima1,2, Osamu Nishimura3,4, Takako Maeda1, Natsumi Shimizu2, Takahiro Ide2, Kenta Yashiro1†, Yasuo Sakai1, Chikara Meno1, Mitsutaka Kadota3,4, Hidetaka Shiratori1†, Shigehiro Kuraku3,4*, Hiroshi Hamada1,2* 1Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan; 2Laboratory for Organismal Patterning, RIKEN Center for Developmental Biology, Kobe, Japan; 3Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan; 4Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan Abstract We have examined the role of Fam60a, a gene highly expressed in embryonic stem cells, in mouse development. Fam60a interacts with components of the Sin3a-Hdac transcriptional corepressor complex, and most Fam60a–/– embryos manifest hypoplasia of visceral organs and die in utero. Fam60a is recruited to the promoter regions of a subset of genes, with the expression of these genes being either up- or down-regulated in Fam60a–/– embryos. The DNA methylation level of the Fam60a target gene Adhfe1 is maintained at embryonic day (E) 7.5 but markedly reduced at –/– *For correspondence: E9.5 in Fam60a embryos, suggesting that DNA demethylation is enhanced in the mutant. [email protected] (SK); Examination of genome-wide DNA methylation identified several differentially methylated regions, [email protected] (HH) which were preferentially hypomethylated, in Fam60a–/– embryos. Our data suggest that Fam60a is †These authors contributed required for proper embryogenesis, at least in part as a result of its regulation of DNA methylation equally to this work at specific gene promoters.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Supplementary Table 1
    Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7
    [Show full text]
  • Genome-Wide CRISPR Screen for Essential Cell Growth Mediators in Mutant KRAS Colorectal Cancers Edwin H
    Published OnlineFirst September 27, 2017; DOI: 10.1158/0008-5472.CAN-17-2043 Cancer Therapeutics, Targets, and Chemical Biology Research Genome-Wide CRISPR Screen for Essential Cell Growth Mediators in Mutant KRAS Colorectal Cancers Edwin H. Yau1,2,3, Indrasena Reddy Kummetha1, Gianluigi Lichinchi1, Rachel Tang1, Yunlin Zhang1, and Tariq M. Rana1,3 Abstract Targeting mutant KRAS signaling pathways continues to established synthetic enhancers or synthetic lethals for KRASMUT attract attention as a therapeutic strategy for KRAS-driven colorectal cancer, including targetable metabolic genes. Notably, tumors. In this study, we exploited the power of the CRISPR- genetic disruption or pharmacologic inhibition of the metabolic Cas9 system to identify genes affecting the tumor xenograft enzymes NAD kinase or ketohexokinase was growth inhibitory growth of human mutant KRAS (KRASMUT) colorectal cancers. in vivo. In addition, the chromatin remodeling protein INO80C Using pooled lentiviral single-guide RNA libraries, we con- was identified as a novel tumor suppressor in KRASMUT colo- ducted a genome-wide loss-of-function genetic screen in an rectal and pancreatic tumor xenografts. Our findings define a isogenic pair of human colorectal cancer cell lines harboring novel targetable set of therapeutic targets for KRASMUT tumors. mutant or wild-type KRAS. The screen identified novel and Cancer Res; 77(22); 6330–9. Ó2017 AACR. Introduction specific genome engineering in mammalian cells (3–5). By target- ing the Cas9 nuclease gene using specific single-guide RNAs The RAS family of oncogenes (KRAS, NRAS, and HRAS) is the (sgRNA) and inducing targeted double-strand DNA breaks that target of intense research for two reasons: the crucial role of are repaired by error-prone nonhomologous end joining, inser- mutant RAS proteins in tumorigenesis and the continued unmet 0 tion or deletion mutations can be introduced into 5 exons of need for therapeutic options for RAS-mutated human cancers.
    [Show full text]
  • Development and Validation of a Six-RNA Binding Proteins Prognostic Signature and Candidate Drugs for Prostate Cancer
    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.28.175984; this version posted June 29, 2020. 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. Development and validation of a six-RNA binding proteins prognostic signature and candidate drugs for prostate cancer Lei Gao1†, Jialin Meng2†, Yong Zhang1, Junfei Gu1, Zhenwei Han1, Shenglin Gao3*, Xiaolu Wang1* 1Department of Urology, the second Hospital of Hebei Medical University, Shijiazhuang, China 2Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China 3 Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China † Authors contributed equally Correspondence: Xiaolu Wang: [email protected] Shenglin Gao: [email protected] Abstract The dysregulation of RNA binding proteins (RBPs) play critical roles in the progression of several cancers. However, the overall functions of RBPs in prostate cancer (PCa) remain poorly understood. Therefore, we first identified 144 differentially expressed RBPs in tumors compared to normal tissues based on the TCGA dataset. Next, six RBP genes (MSI1, MBNL2, LENG9, REXO2, RNASE1, PABPC1L) were screened out as prognosis hub genes by univariate, LASSO and multivariate Cox regression and used to establish the prognostic signature. Further analysis indicated that high risk group was significantly associated with poor RFS, which was validated in the MSKCC cohort.
    [Show full text]
  • 1 Novel Expression Signatures Identified by Transcriptional Analysis
    ARD Online First, published on October 7, 2009 as 10.1136/ard.2009.108043 Ann Rheum Dis: first published as 10.1136/ard.2009.108043 on 7 October 2009. Downloaded from Novel expression signatures identified by transcriptional analysis of separated leukocyte subsets in SLE and vasculitis 1Paul A Lyons, 1Eoin F McKinney, 1Tim F Rayner, 1Alexander Hatton, 1Hayley B Woffendin, 1Maria Koukoulaki, 2Thomas C Freeman, 1David RW Jayne, 1Afzal N Chaudhry, and 1Kenneth GC Smith. 1Cambridge Institute for Medical Research and Department of Medicine, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY, UK 2Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK Correspondence should be addressed to Dr Paul Lyons or Prof Kenneth Smith, Department of Medicine, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY, UK. Telephone: +44 1223 762642, Fax: +44 1223 762640, E-mail: [email protected] or [email protected] Key words: Gene expression, autoimmune disease, SLE, vasculitis Word count: 2,906 The Corresponding Author has the right to grant on behalf of all authors and does grant on behalf of all authors, an exclusive licence (or non-exclusive for government employees) on a worldwide basis to the BMJ Publishing Group Ltd and its Licensees to permit this article (if accepted) to be published in Annals of the Rheumatic Diseases and any other BMJPGL products to exploit all subsidiary rights, as set out in their licence (http://ard.bmj.com/ifora/licence.pdf). http://ard.bmj.com/ on September 29, 2021 by guest. Protected copyright. 1 Copyright Article author (or their employer) 2009.
    [Show full text]
  • Molecular Mechanisms of Nuclear Hormone Receptor Transcriptional Synergy and Autoinduction
    MOLECULAR MECHANISMS OF NUCLEAR HORMONE RECEPTOR TRANSCRIPTIONAL SYNERGY AND AUTOINDUCTION by Pia D. Bagamasbad A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Molecular, Cellular and Developmental Biology) in the University of Michigan 2012 Doctoral Committee: Professor Robert J. Denver, Chair Professor Kenneth M. Cadigan Professor Cunming Duan Professor Audrey F. Seasholtz ©Pia D. Bagamasbad All rights Reserved 2012 To my father whose last wish was for me to pursue and finish my doctoral degree To my mother for her endless, unconditional love and support, and for teaching me the value of a good education and hardwork ii ACKNOWLEDGEMENTS I would like to thank my thesis advisor Dr. Robert J. Denver for his guidance, support and patience, not only in science but also through the personal obstacles that I have encountered through graduate school. He has been an excellent mentor and has greatly influenced my scientific growth and outlook. I thank my committee members, Dr. Kenneth Cadigan, Dr. Cunming Duan and Dr. Audrey Seasholtz for their insight and guidance. Their expertise in the different disciplines of biology was of significant importance in shaping my dissertation research. I thank the MCDB administrative staff, particularly Mary Carr and Kelly Campbell, for consistently helping me out with administrative paper works and concerns. I am grateful for the funding support provided by the Rackham Predoctoral Fellowship and the Edwin H. Edwards Scholarship given by the Department of Molecular, Cellular and Developmental Biology. I am lucky to have worked with people like Chris, Yoshi, Melissa, Joe and Rose who are always willing to help in experiments and have provided an intellectually stimulating and friendly lab environment.
    [Show full text]
  • E2F in Vivo Binding Specificity: Comparison of Consensus Versus Nonconsensus Binding Sites
    Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Letter E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites Alina Rabinovich,1 Victor X. Jin,2 Roman Rabinovich,1 Xiaoqin Xu,1 and Peggy J. Farnham1,3 1Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA; 2The Bioinformatics Program and the Department of Biology, University of Memphis, Memphis, Tennessee 38152, USA We have previously shown that most sites bound by E2F family members in vivo do not contain E2F consensus motifs. However, differences between in vivo target sites that contain or lack a consensus E2F motif have not been explored. To understand how E2F binding specificity is achieved in vivo, we have addressed how E2F family members are recruited to core promoter regions that lack a consensus motif and are excluded from other regions that contain a consensus motif. Using chromatin immunoprecipitation coupled with DNA microarray analysis (ChIP-chip) assays, we have shown that the predominant factors specifying whether E2F is recruited to an in vivo binding site are (1) the site must be in a core promoter and (2) the region must be utilized as a promoter in that cell type. We have tested three models for recruitment of E2F to core promoters lacking a consensus site, including (1) indirect recruitment, (2) looping to the core promoter mediated by an E2F bound to a distal motif, and (3) assisted binding of E2F to a site that weakly resembles an E2F motif. To test these models, we developed a new in vivo assay, termed eChIP, which allows analysis of transcription factor binding to isolated fragments.
    [Show full text]
  • Genome-Wide CRISPR Screen for Essential Cell Growth Mediators in Mutant KRAS Colorectal Cancers
    Author Manuscript Published OnlineFirst on September 27, 2017; DOI: 10.1158/0008-5472.CAN-17-2043 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Genome-wide CRISPR screen for essential cell growth mediators in mutant KRAS colorectal cancers Edwin H. Yau1,2,3, Indrasena Reddy Kummetha1, Gianluigi Lichinchi1, Rachel Tang1, Yunlin Zhang1, and Tariq M. Rana1,3 1Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, California, 92093, USA. 2Division of Hematology-Oncology, Department of Internal Medicine, University of California San Diego School of Medicine, La Jolla, CA 92037 3Solid Tumor Therapeutics Program, Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093 *Corresponding and Lead Contact: T.M.R. ([email protected]) Conflict of Interest: The authors declare no competing financial interests Running Title: Genome-wide CRISPR screen of KRAS mutant tumor xenografts Key Words: KRAS, CRISPR-Cas9, genome-wide, NADK, KHK, INO80C, cancer metabolism Financial Support: This work was supported in part by the National Institutes of Health (CA177322). E.H.Y. was supported by the National Cancer Institute of the National Institutes of Health under Award Number T32CA121938 1 Downloaded from cancerres.aacrjournals.org on October 1, 2021. © 2017 American Association for Cancer Research. Author Manuscript Published OnlineFirst on September 27, 2017; DOI: 10.1158/0008-5472.CAN-17-2043 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. ABSTRACT Targeting mutant KRAS signaling pathways continues to attract attention as a therapeutic strategy for KRAS-driven tumors.
    [Show full text]
  • Transcriptome Characterization of Human Mammary Cell Lines Expressing Different Levels of ERBB2 by Serial Analysis of Gene Expression
    1441-1461 26/4/06 13:24 Page 1441 INTERNATIONAL JOURNAL OF ONCOLOGY 28: 1441-1461, 2006 Transcriptome characterization of human mammary cell lines expressing different levels of ERBB2 by serial analysis of gene expression MARIANA LOPES DOS SANTOS1, CAROLINA GONÇALVES PALANCH1, SIBELI SALAORNI1, WILSON ARAUJO DA SILVA Jr2 and MARIA APARECIDA NAGAI1 1Disciplina de Oncologia, Departamento de Radiologia da Faculdade de Medicina da Universidade de São Paulo, São Paulo; 2Departamento de Genética, Faculdade de Medicina de Ribeirão Preto-USP, Ribeirão Preto, Brazil Received October 31, 2005; Accepted December 27, 2005 Abstract. Over-expression of ERBB2, a member of the family Introduction of transmembrane receptor tyrosine kinases, occurs in 15-30% of primary breast tumors and is associated with poor prognosis The ERBB2 gene, also known as HER2/NEU, encodes a and chemoresistance to a variety of anticancer drugs. In this 185-kDa transmembrane glycoprotein with intrinsic tyrosine study, aiming to identify differentially-expressed genes kinase activity that belongs to the epidermal growth factor involved in erbB2-mediated transformation of the breast, we receptor (EGFR) family (1). This family of receptor tyrosine generated SAGE libraries from two human mammary cell kinases (RTKs) comprises four members, EGFR (ERBB1), lines, derived from normal luminal cells, expressing different ERBB2 (HER2), ERBB3 and ERBB4 that play important roles levels of erbB2. The parental cell line HB4a expresses basal in several signal transduction pathways regulating cell prolifer- levels and the C5.2 expresses high levels of erbB2. A total of ation, differentiation, cytoskeletal rearrangement and survival 161,632 tags was generated by sequencing, 81,684 from HB4a (1,2).
    [Show full text]
  • Membranes of Human Neutrophils Secretory Vesicle Membranes And
    Downloaded from http://www.jimmunol.org/ by guest on September 30, 2021 is online at: average * The Journal of Immunology , 25 of which you can access for free at: 2008; 180:5575-5581; ; from submission to initial decision 4 weeks from acceptance to publication J Immunol doi: 10.4049/jimmunol.180.8.5575 http://www.jimmunol.org/content/180/8/5575 Comparison of Proteins Expressed on Secretory Vesicle Membranes and Plasma Membranes of Human Neutrophils Silvia M. Uriarte, David W. Powell, Gregory C. Luerman, Michael L. Merchant, Timothy D. Cummins, Neelakshi R. Jog, Richard A. Ward and Kenneth R. McLeish cites 44 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2008/04/01/180.8.5575.DC1 This article http://www.jimmunol.org/content/180/8/5575.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* • Why • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2008 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 30, 2021. The Journal of Immunology Comparison of Proteins Expressed on Secretory Vesicle Membranes and Plasma Membranes of Human Neutrophils1 Silvia M.
    [Show full text]
  • Thesis Final 140410
    SUMO-1 mapping in the human genome and its implications for transcription control DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Hui-wen Liu Graduate Program in Molecular, Cellular and Developmental Biology The Ohio State University 2014 Dissertation Committee: Jeffrey D. Parvin, M.D., Ph.D., Advisor Ching-shih Chen, Ph.D., Mark Parthun, Ph.D., Amanda Toland, Ph.D. Copyright by Hui-wen Liu 2014 Abstract SUMOylation, a post-translational modification with SUMO proteins covalently conjugated to a variety of proteins, regulates a range of cellular processes, including cell proliferation and maintenance of genome stability. In this study, we investigated how SUMO-1 functions as a chromatin mark on the human genome during cell cycle progression by ChIP-seq approach. Surprisingly, despite the known repressive role of SUMOylation on histones, we found that SUMO-1 localizes to the promoters of constitutively active genes involved in protein translation and proliferation during interphase. For example, ribosomal protein genes; and SUMO-1 marks on these promoters were absent during mitosis. In addition, SUMO-1 association on the promoters recruits RNAPII, and depletion of SUMO-1 leads to down regulation of those ribosomal protein genes, suggesting a positive role of SUMO-1 in gene activation. To further elucidate how SUMOylation regulates transcription process related to protein synthesis, we identified that SUMO-1 marks the promoters via the Scaffold Associated Factor B (SAFB) protein. The results showed that SAFB is SUMOylated, and depletion of SAFB caused the decrease of SUMO-1 marks on the promoters of those housekeeping genes transcribed by RNAPII.
    [Show full text]