DOCSLIB.ORG

Expression and Characterization of the IPM 150 Gene Ž / IMPG1 Product, a Novel Human Photoreceptor Cell-Associated Chondroitin

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Expression and Characterization of the IPM 150 Gene Ž / IMPG1 Product, a Novel Human Photoreceptor Cell-Associated Chondroitin Matrix Biology 18Ž. 1999 509]518 Expression and characterization of the IPM 150 gene ž/IMPG1 product, a novel human photoreceptor cell-associated chondroitin-sulfate proteoglycan Markus H. Kuehn, Gregory S. HagemanU Department of Ophthalmology and Visual Sciences, The Uni¨ersity of Iowa, 11190E PFP, 200 Hawkins Dri¨e, Iowa, IA 52240, USA Received 9 May 1999; received in revised form 29 July 1999; accepted 3 August 1999 Abstract The interphotoreceptor matrixŽ. IPM occupies the extracellular space between the apical surface of the retinal pigmented epithelium and the external limiting membrane of the neural retina. This space contains two chondroitin sulfate proteogly- cans, designated IPM 150 and IPM 200, which are likely to effect retinal adhesion and photoreceptor survival. In an effort to characterize human IPM 150, several cDNA clones encoding its core protein have been isolated from a human retinal cDNA library. Translation of overlapping cDNA sequences yields a novel core protein with a predicted molecular mass of 89.3 kDa. Northern and dot-blot analyses as well as the isolation of expressed sequence tags demonstrate that IPM 150 mRNA is expressed not only in the neural retina but also in several other non-ocular tissues. In situ hybridization analyses indicate that, in the eye, IPM 150 mRNA is expressed speci®cally by cone and rod photoreceptor cells. Characterization of IPM 150 proteoglycan core protein and identi®cation of its site of synthesis are important steps towards understanding the architecture and biology of the IPM. Q 1999 Elsevier Science B.V.rInternational Society of Matrix Biology. All rights reserved. Keywords: cDNA; Chondroitin-sulfate proteoglycan; Interphotoreceptor matrix; Photoreceptor; Retina 1. Introduction ates signi®cant functional interactions between the neural retina and the RPE, including the exchange of Invagination of the optic vesicle during vertebrate metabolites and catabolic byproducts, regulation of ocular morphogenesis results in the formation of a the ionic milieu, mediation of retinal adhesion, se- unique extracellularŽ. `subretinal' space between the questration of growth factors, and maintenance of apical surfaces of the neural retina and the retinal photoreceptor polarization, orientation, turnover and pigmented epitheliumŽ. RPE . Photoreceptor cell outer viabilityŽ Hewitt et al., 1990; Hageman and Johnson, segments project into this compartment which is oc- 1991a,b; Hageman et al., 1991. cupied by the interphotoreceptor matrixŽ. IPM , an IPM glycoconjugates mediate the physical attach- extracellular matrix comprised of an array of proteins, ment of the neural retina to the RPE, and although glycoproteins, and proteoglycansŽ Hageman and John- the precise molecular mechanisms involved have not son, 1991a; Mieziewska, 1996; Hageman and Kuehn, been elucidated, chondroitin sulfate proteoglycans ap- 1998. There is general consensus that the IPM medi- pear to be crucial in this functionŽ Holly®eld et al., 1989; Yao et al., 1990, 1992, 1994; Johnson and Hage- man, 1991; Lazarus and Hageman, 1992; Marmor et U Corresponding author. al., 1994; Hageman et al., 1995. Cone photoreceptor E-mail address: [email protected]Ž. G.S. Hageman cells are associated with cone matrix sheathsŽ. CMS , 0945-053Xr99r$ - see front matter Q 1999 Elsevier Science B.V.rInternational Society of Matrix Biology. All rights reserved. PII: S 0 9 4 5 - 0 5 3 XŽ. 9 9 0 0 0 4 3 - 8 510 M.H. Kuehn, G.S. Hageman Matrix Biology 18() 1999 509᎐518 distinct domains of the IPM that contain chondroitin 2. Materials and methods 6-sulfate proteoglycan and have ®rm attachments to both RPE cells and the neural retinaŽ Johnson et al., 2.1. Tissues 1986; Blanks et al., 1988. This adhesive system is suf®ciently strong to detach the RPE or tear the CMS Human eyes were obtained from MidAmerica following manual separation of the neural retina from Transplant ServicesŽ. St. Louis, MO, USA and the the RPEŽ. Hageman et al., 1995 . Furthermore, enzy- University of Iowa Lion's Eye BankŽ Iowa City, IA, matic cleavage of IPM-associated chondroitin sulfate USA. and processed within 3 h of cardiac cessation glycosaminoglycans leads to a rapid decrease of reti- under approved Institutional Review Board protocols. nal adhesiveness in both rabbits and primates in vivo Eyes and other organs were obtained from cynomol- Ž.Yao et al., 1990, 1994 . Adhesion is restored several gus macaque monkeys Ž.Macaca fascicularis immedi- days after injection, concomitant with the de novo ately after barbiturate-induced euthanasia. All ani- biosynthesis of IPM chondroitin sulfate proteoglycans mals were treated in conformity with the NIH `Guide Ž.Yao et al., 1992 . In addition, disruption of proteogly- for the Care and Use of Laboratory Animals', and the can synthesis in vivo leads to loss of CMS-associated established guidelines of St. Louis University and the chondroitin 6-sulfate proteoglycans, IPM disruption, University of Iowa. localized retinal detachments and photoreceptor outer segment degenerationŽ. Lazarus and Hageman, 1992 . 2.2. Isolation of IPM Other studies have documented a correlation between changes in IPM composition and photore- Human and monkey neural retinas were separated ceptor cell degeneration in various ocular diseases from the RPE and incubated in a 10-mM phosphate ŽLaVail et al., 1981; Blanks et al., 1987, 1993; Johnson buffered salineŽ. PBS , pH 7.4, containing a cocktail of et al., 1989; Hageman and Kuehn, 1998. In the RCS protease inhibitors as described earlierŽ Hageman et rat and the MPS VII mouse, for example, loss of IPM al., 1991. The isolated retinas were then placed in 4 chondroitin 6-sulfate proteoglycan precedes de- M urea solution in PBS containing 0.5% NP-40 and tectable photoreceptor degenerationŽ Porrello and protease inhibitors until the IPM dissociated from the LaVail, 1986; Johnson et al., 1989; Chu et al., 1992; photoreceptor cells. The resulting sheets of insoluble Lazarus et al., 1993. IPM were isolated, pelleted by centrifugation, resus- Ž.᎐ Immunohistochemical and biochemical investiga- pended in PBS and repelleted 7 10 times to remove tions have demonstrated that CMSs contain two ma- any remaining soluble components. jor chondroitin 6-sulfate proteoglycansŽ Hageman and Johnson, 1986, 1987. which, upon digestion with 2.3. Amino acid sequencing chondroitinase ABC, migrate in SDS-polyacrylamide gels with apparent molecular weights of 150 kDa and Aqueous-insoluble human and monkey IPM prepa- 200 kDaŽ. Hageman and Johnson, 1991a . These pro- rations were homogenized and digested with chon- teoglycans are herein referred to as IPM 150 and droitin ABC lyaseŽ.Ž. E.C. 4.2.2.4 Seikagaku in the Њ IPM 200, respectively. They comprise a signi®cant presence of protease inhibitors, for 2 h at 37 C. Pro- portion of the IPM and they are the only IPM con- teins were separated on SDS-polyacrylamide gels, transferred to PVDF membranes and brie¯y stained stituents bound by AC6S antibodies on Western blots with 0.1% Coomassie blue. The appropriate bands of IPM preparations, suggesting that they represent were excised and NH -terminal amino acid sequences the same molecules, which mediate retinal adhesion 2 for IPM 150 were determined by Edman degradation in vivo. Ž.Stone et al., 1992 . In order to characterize further the structure and Other amino acid sequences were obtained from function of IPM 150, we have determined the cDNA fragments of IPM 150 generated by an `in-gel' trypsin sequence encoding its core protein. The results pre- digestion protocol. Brie¯y, chondroitinase ABC- sented herein show that IPM 150 is expressed by rod treated IPM preparations were separated by SDS- and cone photoreceptor cells in the retina as well as PAGE, the gels were stained with 0.1% Coomassie various other tissues and possesses a unique se- and IPM 150 was identi®ed and excised. Gel strips quence, bearing no signi®cant homology to any other were incubated at 37ЊC for 24 h in a 1:25Ž. ww ratio protein. It is anticipated that this information will not of trypsin to protein. Following incubation, the pep- only aid in subsequent studies of the role of IPM tides were extractedŽ. Stone and Williams, 1993 and constituents in the retina but during molecular char- fractionated by reverse phase HPLC in 0.2 ml of 2 M acterization of other tissues expressing this proteogly- urea solution. Separated peptides were subjected to can as well. amino acid sequencing. M.H. Kuehn, G.S. Hageman Matrix Biology 18() 1999 509᎐518 511 2.4. Reerse transcription-polymerase chain reaction 2.6. cDNA sequencing ()RT-PCR Subcloned cDNA fragments were manually se- Total retinal RNA was isolated from monkey and quenced by dideoxy nucleotide chain termination Ž. human retinas using RNAStat-60 reagentŽ. Tel-Test Sanger et al., 1977 using the Sequenase 2.0 sequenc- Ž. and 100 ngtube were reverse-transcribed using ran- ing Kit Amersham . Both strands were analyzed at dom hexamer primers and the GeneAmpᮋ RNA PCR least twice using either vector-speci®c primers or cus- KitŽ. Perkin Elmer Cetus . For the initial experiments, tom oligonucleotide primers. Comparisons between monkey retinal cDNA was ampli®ed for 25 cycles the obtained sequences and those in the NCBI using a degenerate sense PCR primerŽ 5Ј-TATTAG- databases were executed using the BLAST algorithm Ž. GAAT TCCATYTTYT TYCCIAAYGG-3Ј., designed Altschul et al., 1990 in the MacVector software Ž. using the amino acid sequence of the monkey IPM package Kodak International Biotechnologies or the 150 amino-terminus and a degenerate antisense NCBI web server. primerŽ 5Ј-TTICCIGCIA GYTCYTGRTA RTAIGG- 3Ј. which was designed based on the sequence of 2.7. Northern blot analyses tryptic peptide ࠻70, derived from human IPM 150. During the synthesis of these primers, inosine residues Total RNA from various ocular and non-ocular were used in positions of complete degeneracy. An tissues was isolated as described above and separated ampli®cation product of 580 bp was isolated and on agarose gels containing formaldehyde.
Load more

Recommended publications
  • Genome Sequence of the Basal Haplorrhine Primate Tarsius Syrichta Reveals Unusual Insertions
    ARTICLE Received 29 Oct 2015 | Accepted 17 Aug 2016 | Published 6 Oct 2016 DOI: 10.1038/ncomms12997 OPEN Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions Ju¨rgen Schmitz1,2, Angela Noll1,2,3, Carsten A. Raabe1,4, Gennady Churakov1,5, Reinhard Voss6, Martin Kiefmann1, Timofey Rozhdestvensky1,7,Ju¨rgen Brosius1,4, Robert Baertsch8, Hiram Clawson8, Christian Roos3, Aleksey Zimin9, Patrick Minx10, Michael J. Montague10, Richard K. Wilson10 & Wesley C. Warren10 Tarsiers are phylogenetically located between the most basal strepsirrhines and the most derived anthropoid primates. While they share morphological features with both groups, they also possess uncommon primate characteristics, rendering their evolutionary history somewhat obscure. To investigate the molecular basis of such attributes, we present here a new genome assembly of the Philippine tarsier (Tarsius syrichta), and provide extended analyses of the genome and detailed history of transposable element insertion events. We describe the silencing of Alu monomers on the lineage leading to anthropoids, and recognize an unexpected abundance of long terminal repeat-derived and LINE1-mobilized transposed elements (Tarsius interspersed elements; TINEs). For the first time in mammals, we identify a complete mitochondrial genome insertion within the nuclear genome, then reveal tarsier-specific, positive gene selection and posit population size changes over time. The genomic resources and analyses presented here will aid efforts to more fully understand the ancient characteristics of primate genomes. 1 Institute of Experimental Pathology, University of Mu¨nster, 48149 Mu¨nster, Germany. 2 Mu¨nster Graduate School of Evolution, University of Mu¨nster, 48149 Mu¨nster, Germany. 3 Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Go¨ttingen, Germany.
    [Show full text]
  • A Draft Map of the Human Proteome
    ARTICLE doi:10.1038/nature13302 A draft map of the human proteome Min-Sik Kim1,2, Sneha M. Pinto3, Derese Getnet1,4, Raja Sekhar Nirujogi3, Srikanth S. Manda3, Raghothama Chaerkady1,2, Anil K. Madugundu3, Dhanashree S. Kelkar3, Ruth Isserlin5, Shobhit Jain5, Joji K. Thomas3, Babylakshmi Muthusamy3, Pamela Leal-Rojas1,6, Praveen Kumar3, Nandini A. Sahasrabuddhe3, Lavanya Balakrishnan3, Jayshree Advani3, Bijesh George3, Santosh Renuse3, Lakshmi Dhevi N. Selvan3, Arun H. Patil3, Vishalakshi Nanjappa3, Aneesha Radhakrishnan3, Samarjeet Prasad1, Tejaswini Subbannayya3, Rajesh Raju3, Manish Kumar3, Sreelakshmi K. Sreenivasamurthy3, Arivusudar Marimuthu3, Gajanan J. Sathe3, Sandip Chavan3, Keshava K. Datta3, Yashwanth Subbannayya3, Apeksha Sahu3, Soujanya D. Yelamanchi3, Savita Jayaram3, Pavithra Rajagopalan3, Jyoti Sharma3, Krishna R. Murthy3, Nazia Syed3, Renu Goel3, Aafaque A. Khan3, Sartaj Ahmad3, Gourav Dey3, Keshav Mudgal7, Aditi Chatterjee3, Tai-Chung Huang1, Jun Zhong1, Xinyan Wu1,2, Patrick G. Shaw1, Donald Freed1, Muhammad S. Zahari2, Kanchan K. Mukherjee8, Subramanian Shankar9, Anita Mahadevan10,11, Henry Lam12, Christopher J. Mitchell1, Susarla Krishna Shankar10,11, Parthasarathy Satishchandra13, John T. Schroeder14, Ravi Sirdeshmukh3, Anirban Maitra15,16, Steven D. Leach1,17, Charles G. Drake16,18, Marc K. Halushka15, T. S. Keshava Prasad3, Ralph H. Hruban15,16, Candace L. Kerr19{, Gary D. Bader5, Christine A. Iacobuzio-Donahue15,16,17, Harsha Gowda3 & Akhilesh Pandey1,2,3,4,15,16,20 The availability of human genome sequence has transformed biomedical research over the past decade. However, an equiv- alent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here we present a draft map of the human proteome using high-resolution Fourier-transform mass spectrometry.
    [Show full text]
  • University of London Thesis
    REFERENCE ONLY UNIVERSITY OF LONDON THESIS Degree pWvO Y e a r Name of Author ^ COPYRIGHT This is a thesis accepted for a Higher Degree of the University of London. It is an unpublished typescript and the copyright is held by the author. All persons consulting the thesis must read and abide by the Copyright Declaration below. COPYRIGHT DECLARATION I recognise that the copyright of the above-described thesis rests with the author and that no quotation from it or information derived from it may be published without the prior written consent of the author. LOANS Theses may not be lent to individuals, but the Senate House Library may lend a copy to approved libraries within the United Kingdom, for consultation solely on the premises of those libraries. Application should be made to: Inter-Library Loans, Senate House Library, Senate House, Malet Street, London WC1E 7HU. REPRODUCTION University of London theses may not be reproduced without explicit written permission from the Senate House Library. Enquiries should be addressed to the Theses Section of the Library. Regulations concerning reproduction vary according to the date of acceptance of the thesis and are listed below as guidelines. A. Before 1962. Permission granted only upon the prior written consent of the author. (The Senate House Library will provide addresses where possible). B. 1962 - 1974. In many cases the author has agreed to permit copying upon completion of a Copyright Declaration. C. 1975 - 1988. Most theses may be copied upon completion of a Copyright Declaration. D. 1989 onwards. Most theses may be copied. This thesis comes within category D.
    [Show full text]
  • Nº Ref Uniprot Proteína Péptidos Identificados Por MS/MS 1 P01024
    Document downloaded from http://www.elsevier.es, day 26/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Nº Ref Uniprot Proteína Péptidos identificados 1 P01024 CO3_HUMAN Complement C3 OS=Homo sapiens GN=C3 PE=1 SV=2 por 162MS/MS 2 P02751 FINC_HUMAN Fibronectin OS=Homo sapiens GN=FN1 PE=1 SV=4 131 3 P01023 A2MG_HUMAN Alpha-2-macroglobulin OS=Homo sapiens GN=A2M PE=1 SV=3 128 4 P0C0L4 CO4A_HUMAN Complement C4-A OS=Homo sapiens GN=C4A PE=1 SV=1 95 5 P04275 VWF_HUMAN von Willebrand factor OS=Homo sapiens GN=VWF PE=1 SV=4 81 6 P02675 FIBB_HUMAN Fibrinogen beta chain OS=Homo sapiens GN=FGB PE=1 SV=2 78 7 P01031 CO5_HUMAN Complement C5 OS=Homo sapiens GN=C5 PE=1 SV=4 66 8 P02768 ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 66 9 P00450 CERU_HUMAN Ceruloplasmin OS=Homo sapiens GN=CP PE=1 SV=1 64 10 P02671 FIBA_HUMAN Fibrinogen alpha chain OS=Homo sapiens GN=FGA PE=1 SV=2 58 11 P08603 CFAH_HUMAN Complement factor H OS=Homo sapiens GN=CFH PE=1 SV=4 56 12 P02787 TRFE_HUMAN Serotransferrin OS=Homo sapiens GN=TF PE=1 SV=3 54 13 P00747 PLMN_HUMAN Plasminogen OS=Homo sapiens GN=PLG PE=1 SV=2 48 14 P02679 FIBG_HUMAN Fibrinogen gamma chain OS=Homo sapiens GN=FGG PE=1 SV=3 47 15 P01871 IGHM_HUMAN Ig mu chain C region OS=Homo sapiens GN=IGHM PE=1 SV=3 41 16 P04003 C4BPA_HUMAN C4b-binding protein alpha chain OS=Homo sapiens GN=C4BPA PE=1 SV=2 37 17 Q9Y6R7 FCGBP_HUMAN IgGFc-binding protein OS=Homo sapiens GN=FCGBP PE=1 SV=3 30 18 O43866 CD5L_HUMAN CD5 antigen-like OS=Homo
    [Show full text]
  • Whole Exome Sequencing in the Rat Julie F
    Foley et al. BMC Genomics (2018) 19:487 https://doi.org/10.1186/s12864-018-4858-8 METHODOLOGY ARTICLE Open Access Whole exome sequencing in the rat Julie F. Foley1* , Dhiral P. Phadke4, Owen Hardy5, Sara Hardy5, Victor Miller5, Anup Madan6, Kellie Howard7, Kimberly Kruse7, Cara Lord6, Sreenivasa Ramaiahgari1, Gregory G. Solomon2, Ruchir R. Shah4, Arun R. Pandiri3, Ronald A. Herbert3, Robert C. Sills3 and B. Alex Merrick1 Abstract Background: The rat genome was sequenced in 2004 with the aim to improve human health altered by disease and environmental influences through gene discovery and animal model validation. Here, we report development and testing of a probe set for whole exome sequencing (WES) to detect sequence variants in exons and UTRs of the rat genome. Using an in-silico approach, we designed probes targeting the rat exome and compared captured mutations in cancer-related genes from four chemically induced rat tumor cell lines (C6, FAT7, DSL-6A/C1, NBTII) to validated cancer genes in the human database, Catalogue of Somatic Mutations in Cancer (COSMIC) as well as normal rat DNA. Paired, fresh frozen (FF) and formalin-fixed, paraffin-embedded (FFPE) liver tissue from naive rats were sequenced to confirm known dbSNP variants and identify any additional variants. Results: Informatics analysis of available gene annotation from rat RGSC6.0/rn6 RefSeq and Ensembl transcripts provided 223,636 unique exons representing a total of 26,365 unique genes and untranslated regions. Using this annotation and the Rn6 reference genome, an in-silico probe design generated 826,878 probe sequences of which 94.2% were uniquely aligned to the rat genome without mismatches.
    [Show full text]
  • Assessment of the Interphotoreceptor Matrix Proteoglycan-1 (IMPG1) Gene Localised to Disease (ADSTGD), Progressive Bifocal Chori
    JtMed Genet 1998;35:641-645 641 Assessment of the interphotoreceptor matrix proteoglycan- 1 (IMPG1) gene localised to J Med Genet: first published as 10.1136/jmg.35.8.641 on 1 August 1998. Downloaded from 6ql3-ql5 in autosomal dominant Stargardt-like disease (ADSTGD), progressive bifocal chorioretinal atrophy (PBCRA), and North Carolina macular dystrophy (MCDR1) Andrea Gehrig, Ute Felbor, Rosemary E Kelsell, David M Hunt, Irene H Maumenee, Bernhard H F Weber Abstract assessment of the functional properties of the We have recently characterised the geno- gene product with regard to the disease pathol- mic organisation of a novel interphotore- ogy. Several criteria, such as tissue specificity of ceptor matrix proteoglycan, IMPG1, and gene expression, cellular localisation of the have mapped the gene locus to chromo- transcript, immunohistochemical data, possibly some 6ql3-ql5 by fluorescence in situ in combination with interspecies nucleotide/ hybridisation. As the interphotoreceptor protein sequence comparison or protein pattern matrix (IPM) is thought to play a critical database searches, may provide helpful infor- role in retinal adhesion and the mainte- mation on the probable function of a candidate nance of photoreceptor cells, it is conceiv- gene. With an increasing number of mapped able that a defect in one of the IPM genes and expressed sequence tags (ESTs) components may cause degenerative le- available through the international efforts ofthe sions in retinal structures and thus may be Human Genome Project, the positional candi-
    [Show full text]
  • 319 a Novel Locus for Leber Congenital Amaurosis
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Letters to the Editor 319 Rich AM, Brock WA, Pena A (1988) Spectrum of genitourinary The incidence of LCA is 3 in 100,000 persons and malformations in patients with imperforate anus. Pediatr accounts for у5% of all inherited retinal dystrophies Surg Int 3:110–113 (Perrault et al. 1996). Clinical and genetic heterogeneity Ross AJ, Ruiz-Perez V, Wang Y, Hagan D-M, Scherer S, Lynch have been demonstrated (Wardenburg 1961; Camuzat SA, Lindsay S, et al (1998) A homeobox gene, HLXB9, is et al. 1996). The phenotype has been associated with the major locus for dominantly inherited sacral agenesis. Nat Genet 20:358–361 familial juvenile nephronophthisis and cone-shaped Seri M, Martucciello G, Paleari L, Bolino A, Priolo M, Salemi epiphyses (Saldino-Mainzer syndrome) and with kidney G, Caroli F, et al (1999) Exclusion of the Sonic Hedgehog disease (Senior-Loken syndrome), osteoporosis, meta- gene as responsible for Currarino syndrome and anorectal bolic diseases, and neurological abnormalities (Loken et malformations with sacral hypodevelopment. Hum Genet al. 1961; Senior et al. 1961; Dekaban 1969; Mainzer et 104:108–110 al. 1970; Ellis et al. 1984). The first locus for LCA was mapped to 17p13 with ∗ Present affiliation: Department of Experimental Oncology, Institute of On- cology, Milan. the use of homozygosity mapping in consanguineous Address for correspondence and reprints: Dr. Steve Scherer, Department of families of North African descent (Camuzat et al. 1996). Genetics, Room 9107, The Hospital for Sick Children, 555 University Avenue, Mutations in the retina-specific guanylate cyclase gene Toronto, Ontario M5G 1X8, Canada.
    [Show full text]
  • Pharmacogenomics of Ventricular Conduction in Multi-Ethnic Populations
    PHARMACOGENOMICS OF VENTRICULAR CONDUCTION IN MULTI-ETHNIC POPULATIONS Amanda Anne Seyerle A dissertation submitted to the faculty at the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Epidemiology in the Gillings School of Global Public Health. Chapel Hill 2016 Approved by: Christy L. Avery Kari E. North Eric A. Whitsel Til Stürmer Craig Lee ©2016 Amanda Anne Seyerle ALL RIGHTS RESERVED ii ABSTRACT Amanda Anne Seyerle: Pharmacogenomics of Ventricular Conduction in Multi-Ethnic Populations (Under the direction of Christy L. Avery) Adverse drug reactions (ADRs) pose a serious public health burden, yet the role of genetics in drug response remains incompletely characterized. Thiazide diuretics, commonly used anti-hypertensives, may cause QT interval (QT) prolongation, a major drug development barrier that increases risk for highly fatal and difficult to predict ventricular arrhythmias. We thus examined whether common SNPs modified the association between thiazide use (17% mean prevalence) and QT or its component parts (QRS interval, JT interval) by performing ancestry-specific, trans-ethnic, and cross-phenotype genome-wide analyses of European (66%), African American (15%), and Hispanic (19%) populations (N- 78,199). Analyses leveraged longitudinal data, incorporated corrected standard errors to account for underestimation of interaction estimate variances, and evaluated evidence for pathway enrichment. Although no loci achieved genome-side significance (P<5x10-8), we found suggestive evidence (P<5x10-6) for SNPs modifying the thiazide-QT association at 22 loci, including biologically plausible ion transport loci (e.g. NELL1, KCNQ3). Given our highly plausible, but only suggestive findings and our observational cohort setting, we next examined the influence of prevalent user bias and exposure misclassification on pharmacogenomics studies conducted in observational settings.
    [Show full text]
  • A Genome-Wide Scan of Cleft Lip Triads Identifies Parent
    F1000Research 2019, 8:960 Last updated: 03 AUG 2021 RESEARCH ARTICLE A genome-wide scan of cleft lip triads identifies parent- of-origin interaction effects between ANK3 and maternal smoking, and between ARHGEF10 and alcohol consumption [version 2; peer review: 2 approved] Øystein Ariansen Haaland 1, Julia Romanowska1,2, Miriam Gjerdevik1,3, Rolv Terje Lie1,4, Håkon Kristian Gjessing 1,4, Astanand Jugessur1,3,4 1Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway 2Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway 3Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway 4Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway v2 First published: 24 Jun 2019, 8:960 Open Peer Review https://doi.org/10.12688/f1000research.19571.1 Latest published: 19 Jul 2019, 8:960 https://doi.org/10.12688/f1000research.19571.2 Reviewer Status Invited Reviewers Abstract Background: Although both genetic and environmental factors have 1 2 been reported to influence the risk of isolated cleft lip with or without cleft palate (CL/P), the exact mechanisms behind CL/P are still largely version 2 unaccounted for. We recently developed new methods to identify (revision) report parent-of-origin (PoO) interactions with environmental exposures 19 Jul 2019 (PoOxE) and now apply them to data from a genome-wide association study (GWAS) of families with children born with isolated CL/P. version 1 Methods: Genotypes from 1594 complete triads and 314 dyads (1908 24 Jun 2019 report report nuclear families in total) with CL/P were available for the current analyses.
    [Show full text]
  • Towards a Comprehensive Description of the Human Retinal Transcriptome
    Towards a Comprehensive Description of the Human Retinal Transcriptome: Identification and Characterization of Differentially Expressed Genes Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Heidi Schulz aus Argentinien Würzburg 2003 Eingereicht am 10. September 2003 Bei der Fakultät für Biologie Mitglieder der Promotionskommission Vorsitzender: Prof. Dr. R. Hedrich Gutachter: Prof. Dr. Bernhard H.F. Weber Gutachter: Prof. Dr. Ricardo Benavente Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am: Erklärung gemäß §4, Absatz 3 der Promotionsordnung für die Fakultät für Biologie der Universität Würzburg: Hiermit erkläre ich, dass ich die vorliegende Dissertation selbständig durchgeführt und verfasst habe. Andere Quellen als die angegebenen Hilfsmittel und Quellen wurden nicht verwendet. Die Dissertation wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Es wurde zuvor kein anderer akademischer Grad erworben. Die vorliegende Arbeit wurde am Institut für Humangenetik der Universität Würzburg unter der Leitung von Prof. Bernhard H.F. Weber angefertigt. Würzburg, den 10. September 2003 ACKNOWLEDGMENTS I would like to thank Prof. Bernhard Weber for giving me the possibility to do my Ph.D. research in his group and for coaching me in the fine art of scientific investigation and writing. My gratitude also extends to Prof. Ricardo Benavente who as a member of the Faculty of Biology of the University of Würzburg accepted to be supervisor of this thesis. I would like to acknowledge Dr. Heidi Stöhr for introducing me to the world of gene identification and characterization. I would also like to express my gratitude to past and present lab members of the AG Weber who helped me and contributed to a very pleasant working atmosphere.
    [Show full text]
  • AGE-RELATED MACULAR DEGENERATION UITNODIGING Eveline Kersten Was Born on December 12Th, 1989 in Voor Het Bijwonen Van De Nijmegen, the Netherlands
    AGE-RELATED MACULAR DEGENERATION MACULAR AGE-RELATED UITNODIGING Eveline Kersten was born on December 12th, 1989 in voor het bijwonen van de Nijmegen, the Netherlands. In 2007, she graduated from secondary school at “Lindenholt College” in openbare verdediging van Nijmegen, and started her medical studies at the mijn proefschrift Radboud University in Nijmegen. During the internships AGE-RELATED MACULAR she developed her interest in ophthalmology, which AGE-RELATED lead her to do a research internship at the department DEGENERATION MACULAR of Ophthalmology of the Radboud university medical DEGENERATION center under supervision of prof. dr. Carel B. Hoyng. After her graduation from medical school in 2014, she joined the scientific Clinical and Molecular Studies Clinical and molecular research group of prof. dr. C.B. Hoyng and started her PhD project on age- studies related macular degeneration. Her research results are presented in this thesis. In November 2017, she started a residency in Ophthalmology at the door same institute. Eveline Kersten Vrijdag 5 juli 2019 om 12:30 uur precies Radboud Universiteit Nijmegen Aula Major Comeniuslaan 2 6525 HP Nijmegen Na afloop bent u van harte welkom op de receptie in de aula Paranimfen: Eveline Kersten Eveline Madelon Kersten 06-31793885 Eveline Kersten [email protected] Maartje Geerlings 06-26204642 Age‐related macular degeneration Clinical and molecular studies Eveline Kersten The work presented in this thesis was carried out within the Radboud Institute for Health Sciences. Research described in this thesis financially supported by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 634479, the European Research Council under the European Union’s Seventh Framework Programme (FP/2007–2013)/ERC grant agreement no.
    [Show full text]
  • Complete Transcriptome Profiling of Normal and Age-Related Macular
    bioRxiv preprint doi: https://doi.org/10.1101/143917; this version posted May 30, 2017. 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. Complete Transcriptome Profiling of Normal and Age-Related Macular Degeneration Eye Tissues Reveals Changes in Regulation of Non-Coding RNA and Extreme Disregulation of Anti-Sense Transcription Eun Ji Kim3, , Gregory G. Grant3,, Anita S. Bowman1,2, Naqi Haider1, Harini V. Gudiseva1, Venkata Ramana Murthy Chavali1,2* 1 Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania 2 Functional Genomics Lab, University of Pennsylvania, Philadelphia, Pennsylvania 3 Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania *Corresponding author These authors contributed equally E-mail: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/143917; this version posted May 30, 2017. 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. Abstract Strand specific RNA sequencing of retina and RPE-Choroid-Scleara (RCS) in age-related macular degeneration (AMD) and matched normal controls reveals striking impact on anti-sense transcription and changes in the regulation of non-coding RNA that has not previously been reported. Hundreds of genes, which do not express anti-sense transcripts in normal retina and RCS, demonstrate extreme anti-sense expression in AMD.
    [Show full text]