DOCSLIB.ORG

Bisphenol Aassociated Alterations in the Expression and Epigenetic

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Bisphenol Aassociated Alterations in the Expression and Epigenetic Environmental and Molecular Mutagenesis 55:184^195 (2014) Research Article Bisphenol A-Associated Alterations in the Expression and Epigenetic Regulation of Genes Encoding Xenobiotic Metabolizing Enzymes in Human Fetal Liver Muna S. Nahar,1 Jung H. Kim,1 Maureen A. Sartor,2 and Dana C. Dolinoy1* 1Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 2Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan Alterations in xenobiotic metabolizing enzyme were evaluated in silico, putative binding sites (XME) expression across the life course, along for the E-twenty-six (ETS) and activator protein1 with genetic, nutritional, and environmental reg- (AP1) related transcription factor families were ulation, can influence how organisms respond identified and unique to 97% of all candidate to toxic insults. In this study, we investigated transcripts. Interestingly, many ETS binding sites the hypothesis that in utero exposure to the contain cytosine-guanine dinucleotides (CpGs) endocrine active compound, bisphenol A (BPA), within their consensus sequences. Thus, quantita- influences expression and epigenetic regulation tive analysis of CpG methylation of three candi- of phase I and II XME genes during develop- date genes was conducted across n 5 50 ment. Using healthy 1st to 2nd trimester human samples. Higher BPA levels were associated fetal liver specimens quantified for internal BPA with increased site-specific methylation at levels, we examined XME gene expression COMT (P < 0.005) and increased average using PCR Array (n 5 8) and RNA-sequencing methylation at SULT2A1 (P < 0.020) promoters. (n 5 12) platforms. Of the greater than 160 While toxicological studies have traditionally XME genes assayed, 2 phase I and 12 phase focused on high-dose effects and hormonal II genes exhibited significantly reduced expres- receptor mediated regulation, our findings sug- sion with higher BPA levels, including isoforms gest the importance of low-dose effects and from the carboxylesterase, catechol O-methyl- nonclassical mechanisms of endocrine disruption transferase, glutathione S-transferase, sulfotrans- during development. Environ. Mol. Mutagen. ferase, and UDP-glucuronosyltransferase families. 55:184–195, 2014. VC 2013 Wiley Periodicals, Inc. When the promoters of these candidate genes Key words: xenobiotic metabolism; bisphenol A; liver; DNA methylation; transcription factor INTRODUCTION A compound’s absorption, distribution, metabolism, and Grant sponsor: National Institute of Health; Grant number: ES017524. excretion via biotransformation pathways dictate its thera- Grant sponsor: University of Michigan (UM) National Institute of Envi- ronmental Health Science (NIEHS) Core Center; Grant number: P30 peutic or toxic potential. Specifically, changes in xenobiotic ES017885. metabolizing enzyme (XME) gene expression and activity Grant sponsor: UM NIEHS Institutional Training Grant; Grant number: can alter drug efficacy and toxicity, with the greatest dis- T32 ES007062. crepancies observed in children compared with adults *Correspondence to: Dana C. Dolinoy, 6638 SPH Tower, 1415 Wash- [Alcorn and McNamara, 2003]. In general, the oxidizing ington Heights, Ann Arbor, MI 48109-2029, USA. E-mail: ddolinoy@ phase I XMEs functionalize compounds into active metabo- umich.edu lites while the conjugating phase II XMEs increase the Received 23 July 2013; provisionally accepted 19 September 2013; and molecular weight of compounds for rapid excretion of toxic in final form 30 September 2013 metabolites [Caldwell et al., 1995]. Preliminary studies DOI 10.1002/em.21823 indicate that relative XME expression and activity among Published online 9 November 2013 in different classes and isoforms change drastically throughout Wiley Online Library (wileyonlinelibrary.com). VC 2013 Wiley Periodicals, Inc. Environmental and Molecular Mutagenesis. DOI 10.1002/em BPA and Xenobiotic Metabolism in Fetal Liver 185 the life course [Hines, 2008]. For example, the phase II limited to animal and in vitro models. For example, rat UDP-glucuronosyltransferase isoforms, UGT1A1 and hepatic microsome studies show that BPA inhibits CYP UGT1A6, are both expressed at low levels in the human enzymes, including activity for CYP1A2, CYP2C11, and fetus; while UGT1A1 attains adult levels within months CYP2E1 [Hanioka et al., 2000; Pfeiffer and Metzler after birth, the UGT1A6 isoform reaches adult levels at 10 2004]; yeast and human liver microsome studies associate years of age [McCarver and Hines, 2002]. Therefore, the BPA with both competitive and noncompetitive inhibition extent of metabolism of a xenobiotic chemical is dependent of UGT1A6 [Hanioka et al., 2008]; and human endome- on age and ontogeny, or the maturation of specific XMEs trial Ishikawa cell line studies show increased ALDH3A1 [Allegaert et al., 2007]. Much of our understanding of expression following BPA exposure [Naciff et al., 2010]. human XME ontogeny arises from adverse pharmaceutical Interspecies differences in metabolism and/or relatively exposures or diseases throughout birth and infancy, or high BPA exposure doses, however, limit the translation extrapolations from rodent models [Saghir et al., 2012]. of these findings for human risk assessment. Comprehensive studies examining metabolism in early The influence of xenoestrogens on the maturation and human fetal development are limited; for example, recent regulation of phase I and II xenobiotic metabolizing studies characterize only a handful of XMEs, such as ster- enzymes has yet to be studied in humans. Here, utilizing oidogenic enzymes in 2nd trimester fetal liver [O’Shaugh- a comprehensive approach evaluating XME expression, nessy et al., 2013] or cytochrome p450s (CYP) and we identify multiple XME genes that are associated with glutathione s-transferases in fetal liver and adrenals [Wang physiologically relevant concentrations of total BPA, et al., 2008]. Evaluating ontogeny, especially throughout assess relative abundance of these XME mRNAs in the human gestation, is thus of great importance in assessing developing human fetal liver, and investigate DNA meth- toxicity; however, obtaining suitable human specimens may ylation as a potential mechanism influencing biotransfor- pose ethical and technical challenges. mation response to BPA exposure. In addition to drug metabolism, XMEs play an impor- tant role in steroid homeostasis, neuroendocrine function, and growth. Both endogenous and exogenous compounds METHODS AND MATERIALS help regulate XME ontogeny and subsequently, metabolic function. More recently, studies demonstrating the impor- Tissue Samples tance of hormonal regulation on the establishment of Human fetal liver samples were procured from the NIH- hepatic metabolism throughout pregnancy and develop- funded University of Washington Birth Defects Research ment have emerged [Kennedy, 2008; Jeong, 2010]. Xeno- Laboratory fetal biobank (2R24HD000836-47), and charac- biotics that can mimic endogenous hormones, such as terized for BPA concentrations by the Kannan Laboratory endocrine active compounds (EAC), can potentially mod- at the Wadsworth Center (New York State Department of ify baseline hormonal regulation of xenobiotic metabo- Health). As previously described [Nahar et al., 2012], fol- lism and response to environmental stressors during lowing surgery and consent from volunteers undergoing critical windows of development. elective abortions during 1st and 2nd trimester of preg- Bisphenol A (BPA), a synthetic estrogen used in the nancy (gestational day 74–120), healthy tissue specimens production of polycarbonate plastics and epoxy resin, is a were flash frozen and immediately stored in polycarbonate- controversial EAC that is of concern primarily in the free tubing at 280C until processed for BPA analysis and developing organism [Rubin, 2011]. Presence of BPA in RNA/DNA extraction. No identifying clinical data were fetal tissue [Cao et al., 2012; Nahar et al., 2012], reduced available on samples except for sex and gestational age. capacity for BPA metabolism in the fetus [Nahar et al., Total BPA concentrations measured in liver tissue ranged 2012], and the ability for BPA transfer across the pla- from below the limit of quantification at 0.071 ng/g (LOQ/ centa [Schonfelder et al., 2002; Balakrishnan et al., 2010; ͱ2, where LOQ 5 0.1 ng/g) up to 96.8 ng/g [Nahar et al., Jimenez-Dıaz et al., 2010], place the developing human 2012]. fetus at a higher risk for BPA toxicity. Although the human health consequences of BPA exposures are dis- RNA Extraction and cDNA Synthesis puted, several rodent studies suggest that developmental exposure to BPA can alter susceptibility to disease later Total RNA was isolated from frozen liver tissue using in life by modifying the epigenome [Ho et al., 2006; the AllPrep DNA/RNA/Protein kit (Qiagen, Valencia, Bromer et al., 2010; Kundakovic and Champagne, 2011; CA) according to the manufacturer’s instructions. Anderson et al., 2012]. Thus, we hypothesize that BPA Approximately 10 to 20 mg of homogenized tissue was dependent changes to epigenetic regulation of XME dur- added to 600 mL of Buffer RLT (containing 1% b-mer- ing development may also result in latent effects on dis- captoethanol) in a 2 mL round bottom polypropylene ease susceptibility. To date, research addressing BPAs eppendorf tube with a 5 mm stainless steel bead. Samples influence on XME expression and activity has been were further homogenized in solution for 2 min at 20 Hz Environmental
Load more

Recommended publications
  • Environmental Influences on Endothelial Gene Expression
    ENDOTHELIAL CELL GENE EXPRESSION John Matthew Jeff Herbert Supervisors: Prof. Roy Bicknell and Dr. Victoria Heath PhD thesis University of Birmingham August 2012 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Tumour angiogenesis is a vital process in the pathology of tumour development and metastasis. Targeting markers of tumour endothelium provide a means of targeted destruction of a tumours oxygen and nutrient supply via destruction of tumour vasculature, which in turn ultimately leads to beneficial consequences to patients. Although current anti -angiogenic and vascular targeting strategies help patients, more potently in combination with chemo therapy, there is still a need for more tumour endothelial marker discoveries as current treatments have cardiovascular and other side effects. For the first time, the analyses of in-vivo biotinylation of an embryonic system is performed to obtain putative vascular targets. Also for the first time, deep sequencing is applied to freshly isolated tumour and normal endothelial cells from lung, colon and bladder tissues for the identification of pan-vascular-targets. Integration of the proteomic, deep sequencing, public cDNA libraries and microarrays, delivers 5,892 putative vascular targets to the science community.
    [Show full text]
  • Contig Protein Description Symbol Anterior Posterior Ratio
    Table S2. List of proteins detected in anterior and posterior intestine pooled samples. Data on protein expression are mean ± SEM of 4 pools fed the experimental diets. The number of the contig in the Sea Bream Database (http://nutrigroup-iats.org/seabreamdb) is indicated. Contig Protein Description Symbol Anterior Posterior Ratio Ant/Pos C2_6629 1,4-alpha-glucan-branching enzyme GBE1 0.88±0.1 0.91±0.03 0.98 C2_4764 116 kDa U5 small nuclear ribonucleoprotein component EFTUD2 0.74±0.09 0.71±0.05 1.03 C2_299 14-3-3 protein beta/alpha-1 YWHAB 1.45±0.23 2.18±0.09 0.67 C2_268 14-3-3 protein epsilon YWHAE 1.28±0.2 2.01±0.13 0.63 C2_2474 14-3-3 protein gamma-1 YWHAG 1.8±0.41 2.72±0.09 0.66 C2_1017 14-3-3 protein zeta YWHAZ 1.33±0.14 4.41±0.38 0.30 C2_34474 14-3-3-like protein 2 YWHAQ 1.3±0.11 1.85±0.13 0.70 C2_4902 17-beta-hydroxysteroid dehydrogenase 14 HSD17B14 0.93±0.05 2.33±0.09 0.40 C2_3100 1-acylglycerol-3-phosphate O-acyltransferase ABHD5 ABHD5 0.85±0.07 0.78±0.13 1.10 C2_15440 1-phosphatidylinositol phosphodiesterase PLCD1 0.65±0.12 0.4±0.06 1.65 C2_12986 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta-1 PLCD1 0.76±0.08 1.15±0.16 0.66 C2_4412 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2 PLCG2 1.13±0.08 2.08±0.27 0.54 C2_3170 2,4-dienoyl-CoA reductase, mitochondrial DECR1 1.16±0.1 0.83±0.03 1.39 C2_1520 26S protease regulatory subunit 10B PSMC6 1.37±0.21 1.43±0.04 0.96 C2_4264 26S protease regulatory subunit 4 PSMC1 1.2±0.2 1.78±0.08 0.68 C2_1666 26S protease regulatory subunit 6A PSMC3 1.44±0.24 1.61±0.08
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Enzyme DHRS7
    Toward the identification of a function of the “orphan” enzyme DHRS7 Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Selene Araya, aus Lugano, Tessin Basel, 2018 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Alex Odermatt (Fakultätsverantwortlicher) und Prof. Dr. Michael Arand (Korreferent) Basel, den 26.6.2018 ________________________ Dekan Prof. Dr. Martin Spiess I. List of Abbreviations 3α/βAdiol 3α/β-Androstanediol (5α-Androstane-3α/β,17β-diol) 3α/βHSD 3α/β-hydroxysteroid dehydrogenase 17β-HSD 17β-Hydroxysteroid Dehydrogenase 17αOHProg 17α-Hydroxyprogesterone 20α/βOHProg 20α/β-Hydroxyprogesterone 17α,20α/βdiOHProg 20α/βdihydroxyprogesterone ADT Androgen deprivation therapy ANOVA Analysis of variance AR Androgen Receptor AKR Aldo-Keto Reductase ATCC American Type Culture Collection CAM Cell Adhesion Molecule CYP Cytochrome P450 CBR1 Carbonyl reductase 1 CRPC Castration resistant prostate cancer Ct-value Cycle threshold-value DHRS7 (B/C) Dehydrogenase/Reductase Short Chain Dehydrogenase Family Member 7 (B/C) DHEA Dehydroepiandrosterone DHP Dehydroprogesterone DHT 5α-Dihydrotestosterone DMEM Dulbecco's Modified Eagle's Medium DMSO Dimethyl Sulfoxide DTT Dithiothreitol E1 Estrone E2 Estradiol ECM Extracellular Membrane EDTA Ethylenediaminetetraacetic acid EMT Epithelial-mesenchymal transition ER Endoplasmic Reticulum ERα/β Estrogen Receptor α/β FBS Fetal Bovine Serum 3 FDR False discovery rate FGF Fibroblast growth factor HEPES 4-(2-Hydroxyethyl)-1-Piperazineethanesulfonic Acid HMDB Human Metabolome Database HPLC High Performance Liquid Chromatography HSD Hydroxysteroid Dehydrogenase IC50 Half-Maximal Inhibitory Concentration LNCaP Lymph node carcinoma of the prostate mRNA Messenger Ribonucleic Acid n.d.
    [Show full text]
  • Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories
    Supplementary Table 1: Association of Gene Ontology Categories with Decay Rate for HepG2 Experiments These tables show details for all Gene Ontology categories. Inferences for manual classification scheme shown at the bottom. Those categories used in Figure 1A are highlighted in bold. Standard Deviations are shown in parentheses. P-values less than 1E-20 are indicated with a "0". Rate r (hour^-1) Half-life < 2hr. Decay % GO Number Category Name Probe Sets Group Non-Group Distribution p-value In-Group Non-Group Representation p-value GO:0006350 transcription 1523 0.221 (0.009) 0.127 (0.002) FASTER 0 13.1 (0.4) 4.5 (0.1) OVER 0 GO:0006351 transcription, DNA-dependent 1498 0.220 (0.009) 0.127 (0.002) FASTER 0 13.0 (0.4) 4.5 (0.1) OVER 0 GO:0006355 regulation of transcription, DNA-dependent 1163 0.230 (0.011) 0.128 (0.002) FASTER 5.00E-21 14.2 (0.5) 4.6 (0.1) OVER 0 GO:0006366 transcription from Pol II promoter 845 0.225 (0.012) 0.130 (0.002) FASTER 1.88E-14 13.0 (0.5) 4.8 (0.1) OVER 0 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism3004 0.173 (0.006) 0.127 (0.002) FASTER 1.28E-12 8.4 (0.2) 4.5 (0.1) OVER 0 GO:0006357 regulation of transcription from Pol II promoter 487 0.231 (0.016) 0.132 (0.002) FASTER 6.05E-10 13.5 (0.6) 4.9 (0.1) OVER 0 GO:0008283 cell proliferation 625 0.189 (0.014) 0.132 (0.002) FASTER 1.95E-05 10.1 (0.6) 5.0 (0.1) OVER 1.50E-20 GO:0006513 monoubiquitination 36 0.305 (0.049) 0.134 (0.002) FASTER 2.69E-04 25.4 (4.4) 5.1 (0.1) OVER 2.04E-06 GO:0007050 cell cycle arrest 57 0.311 (0.054) 0.133 (0.002)
    [Show full text]
  • Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 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. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 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 The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes.
    [Show full text]
  • 140503 IPF Signatures Supplement Withfigs Thorax
    Supplementary material for Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis Daryle J. DePianto1*, Sanjay Chandriani1⌘*, Alexander R. Abbas1, Guiquan Jia1, Elsa N. N’Diaye1, Patrick Caplazi1, Steven E. Kauder1, Sabyasachi Biswas1, Satyajit K. Karnik1#, Connie Ha1, Zora Modrusan1, Michael A. Matthay2, Jasleen Kukreja3, Harold R. Collard2, Jackson G. Egen1, Paul J. Wolters2§, and Joseph R. Arron1§ 1Genentech Research and Early Development, South San Francisco, CA 2Department of Medicine, University of California, San Francisco, CA 3Department of Surgery, University of California, San Francisco, CA ⌘Current address: Novartis Institutes for Biomedical Research, Emeryville, CA. #Current address: Gilead Sciences, Foster City, CA. *DJD and SC contributed equally to this manuscript §PJW and JRA co-directed this project Address correspondence to Paul J. Wolters, MD University of California, San Francisco Department of Medicine Box 0111 San Francisco, CA 94143-0111 [email protected] or Joseph R. Arron, MD, PhD Genentech, Inc. MS 231C 1 DNA Way South San Francisco, CA 94080 [email protected] 1 METHODS Human lung tissue samples Tissues were obtained at UCSF from clinical samples from IPF patients at the time of biopsy or lung transplantation. All patients were seen at UCSF and the diagnosis of IPF was established through multidisciplinary review of clinical, radiological, and pathological data according to criteria established by the consensus classification of the American Thoracic Society (ATS) and European Respiratory Society (ERS), Japanese Respiratory Society (JRS), and the Latin American Thoracic Association (ALAT) (ref. 5 in main text). Non-diseased normal lung tissues were procured from lungs not used by the Northern California Transplant Donor Network.
    [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]
  • Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
    Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement.
    [Show full text]
  • Molecular Mechanisms Regulating Copper Balance in Human Cells
    MOLECULAR MECHANISMS REGULATING COPPER BALANCE IN HUMAN CELLS by Nesrin M. Hasan A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland August 2014 ©2014 Nesrin M. Hasan All Rights Reserved Intended to be blank ii ABSTRACT Precise copper balance is essential for normal growth, differentiation, and function of human cells. Loss of copper homeostasis is associated with heart hypertrophy, liver failure, neuronal de-myelination and other pathologies. The copper-transporting ATPases ATP7A and ATP7B maintain cellular copper homeostasis. In response to copper elevation, they traffic from the trans-Golgi network (TGN) to vesicles where they sequester excess copper for further export. The mechanisms regulating activity and trafficking of ATP7A/7B are not well understood. Our studies focused on determining the role of kinase-mediated phosphorylation in copper induced trafficking of ATP7B, and identifying and characterizing novel regulators of ATP7A. We have shown that Ser- 340/341 region of ATP7B plays an important role in interactions between the N-terminus and the nucleotide-binding domain and that mutations in these residues result in vesicular localization of the protein independent of the intracellular copper levels. We have determined that structural changes that alter the inter-domain interactions initiate exit of ATP7B from the TGN and that the role of copper-induced kinase-mediated hyperphosphorylation might be to maintain an open interface between the domains of ATP7B. In a separate study, seven proteins were identified, which upon knockdown result in increased intracellular copper levels. We performed an initial characterization of the knock-downs and obtained intriguing results indicating that these proteins regulate ATP7A protein levels, post-translational modifications, and copper-dependent trafficking.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2003/0082511 A1 Brown Et Al
    US 20030082511A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2003/0082511 A1 Brown et al. (43) Pub. Date: May 1, 2003 (54) IDENTIFICATION OF MODULATORY Publication Classification MOLECULES USING INDUCIBLE PROMOTERS (51) Int. Cl." ............................... C12O 1/00; C12O 1/68 (52) U.S. Cl. ..................................................... 435/4; 435/6 (76) Inventors: Steven J. Brown, San Diego, CA (US); Damien J. Dunnington, San Diego, CA (US); Imran Clark, San Diego, CA (57) ABSTRACT (US) Correspondence Address: Methods for identifying an ion channel modulator, a target David B. Waller & Associates membrane receptor modulator molecule, and other modula 5677 Oberlin Drive tory molecules are disclosed, as well as cells and vectors for Suit 214 use in those methods. A polynucleotide encoding target is San Diego, CA 92121 (US) provided in a cell under control of an inducible promoter, and candidate modulatory molecules are contacted with the (21) Appl. No.: 09/965,201 cell after induction of the promoter to ascertain whether a change in a measurable physiological parameter occurs as a (22) Filed: Sep. 25, 2001 result of the candidate modulatory molecule. Patent Application Publication May 1, 2003 Sheet 1 of 8 US 2003/0082511 A1 KCNC1 cDNA F.G. 1 Patent Application Publication May 1, 2003 Sheet 2 of 8 US 2003/0082511 A1 49 - -9 G C EH H EH N t R M h so as se W M M MP N FIG.2 Patent Application Publication May 1, 2003 Sheet 3 of 8 US 2003/0082511 A1 FG. 3 Patent Application Publication May 1, 2003 Sheet 4 of 8 US 2003/0082511 A1 KCNC1 ITREXCHO KC 150 mM KC 2000000 so 100 mM induced Uninduced Steady state O 100 200 300 400 500 600 700 Time (seconds) FIG.
    [Show full text]
  • Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
    Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A.
    [Show full text]