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Epigenetic Repression of RARRES1 Is Mediated by Methylation of a Proximal Promoter and a Loss of CTCF Binding
Epigenetic Repression of RARRES1 Is Mediated by Methylation of a Proximal Promoter and a Loss of CTCF Binding Zhengang Peng1,2, Rulong Shen3, Ying-Wei Li1,2, Kun-Yu Teng1,2, Charles L. Shapiro4, Huey-Jen L. Lin1,2,5* 1 Division of Medical Technology, School of Allied Medical Professions, the Ohio State University Medical Center, Columbus, Ohio, United States of America, 2 Molecular Biology and Cancer Genetics Program, Comprehensive Cancer Center, the Ohio State University Medical Center, Columbus, Ohio, United States of America, 3 Department of Pathology, the Ohio State University Medical Center, Columbus, Ohio, United States of America, 4 Department of Medical Oncology, the Ohio State University Medical Center, Columbus, Ohio, United States of America, 5 Department of Medical Technology, University of Delaware, Newark, Delaware, United States of America Abstract Background: The cis-acting promoter element responsible for epigenetic silencing of retinoic acid receptor responder 1 (RARRES1) by methylation is unclear. Likewise, how aberrant methylation interplays effectors and thus affects breast neoplastic features remains largely unknown. Methodology/Principal Findings: We first compared methylation occurring at the sequences (2664,+420) flanking the RARRES1 promoter in primary breast carcinomas to that in adjacent benign tissues. Surprisingly, tumor cores displayed significantly elevated methylation occurring solely at the upstream region (2664,286), while the downstream element (285,+420) proximal to the transcriptional start site (+1) remained largely unchanged. Yet, hypermethylation at the former did not result in appreciable silencing effect. In contrast, the proximal sequence displayed full promoter activity and methylation of which remarkably silenced RARRES1 transcription. This phenomenon was recapitulated in breast cancer cell lines, in which methylation at the proximal region strikingly coincided with downregulation. -
Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma
Anatomy and Pathology Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma Sarah L. Lake,1 Sarah E. Coupland,1 Azzam F. G. Taktak,2 and Bertil E. Damato3 PURPOSE. To detect deletions and loss of heterozygosity of disease is fatal in 92% of patients within 2 years of diagnosis. chromosome 3 in a rare subset of fatal, disomy 3 uveal mela- Clinical and histopathologic risk factors for UM metastasis noma (UM), undetectable by fluorescence in situ hybridization include large basal tumor diameter (LBD), ciliary body involve- (FISH). ment, epithelioid cytomorphology, extracellular matrix peri- ϩ ETHODS odic acid-Schiff-positive (PAS ) loops, and high mitotic M . Multiplex ligation-dependent probe amplification 3,4 5 (MLPA) with the P027 UM assay was performed on formalin- count. Prescher et al. showed that a nonrandom genetic fixed, paraffin-embedded (FFPE) whole tumor sections from 19 change, monosomy 3, correlates strongly with metastatic death, and the correlation has since been confirmed by several disomy 3 metastasizing UMs. Whole-genome microarray analy- 3,6–10 ses using a single-nucleotide polymorphism microarray (aSNP) groups. Consequently, fluorescence in situ hybridization were performed on frozen tissue samples from four fatal dis- (FISH) detection of chromosome 3 using a centromeric probe omy 3 metastasizing UMs and three disomy 3 tumors with Ͼ5 became routine practice for UM prognostication; however, 5% years’ metastasis-free survival. to 20% of disomy 3 UM patients unexpectedly develop metas- tases.11 Attempts have therefore been made to identify the RESULTS. Two metastasizing UMs that had been classified as minimal region(s) of deletion on chromosome 3.12–15 Despite disomy 3 by FISH analysis of a small tumor sample were found these studies, little progress has been made in defining the key on MLPA analysis to show monosomy 3. -
Biochemical Characterization of DDX43 (HAGE) Helicase
Biochemical Characterization of DDX43 (HAGE) Helicase A Thesis Submitted to the College of Graduate Studies and Research In Fulfillment of the Requirements For the Degree of Master of Science In the Department of Biochemistry University of Saskatchewan Saskatoon By Tanu Talwar © Copyright Tanu Talwar, March, 2017. All rights reserved PERMISSION OF USE STATEMENT I hereby present this thesis in partial fulfilment of the requirements for a postgraduate degree from the University of Saskatchewan and agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, either in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised this thesis or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts of it for any financial gain will not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis. Requests for permission to copy or to make other use of material in this thesis in whole or part should be addressed to: Head of the Department of Biochemistry University of Saskatchewan 107 Wiggins Road Saskatoon, Saskatchewan, Canada S7N 5E5 i ABSTRACT DDX43, DEAD-box polypeptide 43, also known as HAGE (helicase antigen gene), is a member of the DEAD-box family of RNA helicases. -
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. -
And Embryo-Expressed KHDC1/DPPA5/ECAT1/OOEP Gene Family
Available online at www.sciencedirect.com Genomics 90 (2007) 583–594 www.elsevier.com/locate/ygeno Atypical structure and phylogenomic evolution of the new eutherian oocyte- and embryo-expressed KHDC1/DPPA5/ECAT1/OOEP gene family Alice Pierre a, Mathieu Gautier b, Isabelle Callebaut c, Martine Bontoux a, Eric Jeanpierre a, ⁎ Pierre Pontarotti d, Philippe Monget a, a Physiologie de la Reproduction et des Comportements, UMR 6175 INRA–CNRS–Université F. Rabelais de Tours Haras Nationaux, 37380 Nouzilly, France b Laboratoire de Génétique Biochimique et de Cytogénétique, Domaine de Vilvert, INRA, 78352 Jouy-en-Josas, France c Département de Biologie Structurale, Institut de Minéralogie et de Physique des Milieux Condensés, UMR CNRS 7590, Université Pierre et Marie Curie–Paris 6, Université Denis Diderot–Paris 7, IPGP, 140 Rue de Lourmel, 75015 Paris, France d EA 3781 Evolution Biologique, Université d’Aix Marseille I, 13331 Marseille Cedex 3, France Received 12 April 2007; accepted 12 June 2007 Available online 3 October 2007 Abstract Several recent studies have shown that genes specifically expressed by the oocyte are subject to rapid evolution, in particular via gene duplication mechanisms. In the present work, we have focused our attention on a family of genes, specific to eutherian mammals, that are located in unstable genomic regions. We have identified two genes specifically expressed in the mouse oocyte: Khdc1a (KH homology domain containing 1a, also named Ndg1 for Nur 77 downstream gene 1, a target gene of the Nur77 orphan receptor), and another gene structurally related to Khdc1a that we have renamed Khdc1b. In this paper, we show that Khdc1a and Khdc1b belong to a family of several members including the so-called developmental pluripotency A5 (Dppa5) genes, the cat/dog oocyte expressed protein (cat OOEP and dog OOEP) genes, and the ES cell- associated transcript 1 (Ecat1) genes. -
Evaluation of the FHIT Gene in Colorectal Cancers1
[CANCER RESEARCH 56, 2936-2939. July I. 1996] Advances in Brief Evaluation of the FHIT Gene in Colorectal Cancers1 Sam Thiagalingam, Nikolai A. Lisitsyn, Masaaki Hamaguchi, Michael H. Wigler, James K. V. Willson, Sanford D. Markowitz, Frederick S. Leach, Kenneth W. Kinzler, and Bert Vogelstein2 The Johns Hopkins Oncology Center. Baltimore, Maryland 21231 [S. T.. F. S. L., K. W. K., B. V.]; Department of Genetics. University of Pennsylvania, Philadelphia, Pennsylvania 9094 ¡N.A. LI: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 ¡M.H., M. H. W.]; Department of Medicine and Ireland Cancer Center, University Hospitals of Cleveland and Case Western Resene University. Cleveland. Ohio 44106 ¡J.K. V. W., and S. D. M.¡; and Howard Hughes Medical Institute [B. V.¡,The Johns Hopkins Oncology Center, Baltimore, Maryland 21231 Abstract suppressor genes (13), the RDA results strongly supported the exist ence of a tumor suppressor gene in this area (14). A variety of studies suggests that tumor suppressor loci on chromosome Finally, Ohta et al. (15) have recently used a positional cloning 3p are important in various forms of human neoplasia. Recently, a chro approach to identify a novel gene that spanned the t(3;8) breakpoint. mosome 3pl4.2 gene called FHIT was discovered and proposed as a They named this gene FHIT (fragile histidine triad gene), reflecting its candidate tumor suppressor gene in coloréela!and other cancers. We evaluated the FHIT gene in a panel of colorectal cancer cell lines and homology to the Schizosaccharomyces pombe gene encoding Ap4A xenografts, which allowed a comprehensive mutational analysis. -
Initial Sequencing and Comparative Analysis of the Mouse Genome
articles Initial sequencing and comparative analysis of the mouse genome Mouse Genome Sequencing Consortium* *A list of authors and their af®liations appears at the end of the paper ........................................................................................................................................................................................................................... The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identi®cation of intraspecies polymorphism. With the complete sequence of the human genome nearly in hand1,2, covering about 90% of the euchromatic human genome, with about the next challenge is to extract the extraordinary trove of infor- 35% in ®nished form1. Since then, progress towards a complete mation encoded within its roughly 3 billion nucleotides. This human sequence has proceeded swiftly, with approximately 98% of information includes the blueprints for all RNAs and proteins, the genome now available in draft form and about 95% in ®nished the regulatory elements that ensure proper expression of all genes, form. -
METTL1 Promotes Let-7 Microrna Processing Via M7g Methylation
Article METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation Graphical Abstract Authors Luca Pandolfini, Isaia Barbieri, Andrew J. Bannister, ..., Mara d’Onofrio, Shankar Balasubramanian, Tony Kouzarides Correspondence [email protected] In Brief Pandolfini, Barbieri, et al. show that a subgroup of tumor suppressor microRNAs, including let-7e, contain 7-methylguanosine (m7G). Methyltransferase METTL1 is required for m7G modification of miRNAs, their efficient processing, and the inhibition of lung cancer cell migration. Structurally, m7G in miRNA precursors antagonizes RNA secondary structures that would otherwise inhibit their maturation. Highlights Data Resource d Internal m7G is identified in miRNAs by two independent GSE112182 sequencing techniques GSE112180 GSE112181 d Methyltransferase METTL1 mediates m7G modification of GSE120454 specific miRNAs GSE120455 d METTL1 promotes miRNA maturation and suppresses lung cancer cell migration d m7G promotes processing by antagonizing G-quadruplex structures in miRNA precursors Pandolfini et al., 2019, Molecular Cell 74, 1278–1290 June 20, 2019 ª 2019 The Author(s). Published by Elsevier Inc. https://doi.org/10.1016/j.molcel.2019.03.040 Molecular Cell Article METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation Luca Pandolfini,1,9 Isaia Barbieri,1,2,9 Andrew J. Bannister,1 Alan Hendrick,3 Byron Andrews,3 Natalie Webster,3 Pierre Murat,4,7 Pia Mach,1 Rossella Brandi,5 Samuel C. Robson,1,8 Valentina Migliori,1 Andrej Alendar,1 Mara d’Onofrio,5,6 Shankar Balasubramanian,4 -
Análise Integrativa De Perfis Transcricionais De Pacientes Com
UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
Original Article Association of AXIN2 and MMP7 Polymorphisms with Non-Small Cell Lung Cancer in Chinese Han Population
Int J Clin Exp Pathol 2016;9(2):2253-2258 www.ijcep.com /ISSN:1936-2625/IJCEP0009888 Original Article Association of AXIN2 and MMP7 polymorphisms with non-small cell lung cancer in Chinese Han population Shuguang Han, Lei Lv, Xinhua Wang, Xun Wang, Hongqing Zhao Department of Respiratory Medicine, Second People’s Hospital of Wuxi, Wuxi, Jiangsu, China Received May 4, 2015; Accepted June 23, 2015; Epub February 1, 2016; Published February 15, 2016 Abstract: Objectives: This study aimed to explore the effect of AXIN2 and MMP7 polymorphisms on non-small cell lung cancer (NSCLC) susceptibility; in addition, the interaction between gene polymorphisms and environment was also displayed. Methods: The genotyping was conducted by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 102 patients with NSCLC and 120 healthy controls. Odds ratio (OR) and 95% con- fidence interval (CI) were calculated to assess the relevance strength of AXIN2 and MMP7 polymorphisms with NSCLC. The x² test was used to compare to the frequencies difference of genotypes and alleles in cases and controls and Hardy-Weinberg equilibrium (HWE) test. The haplotype and interaction analyses were performed by haploview and MDR software, respectively. Results: The genotype frequencies of all polymorphisms in the control group conformed to HWE. GG genotype frequency of AXIN2 rs2240307 polymorphism was significantly higher in cases than controls (P=0.041). Similarly, rs2240308 in AXIN2 gene was also increased the susceptibility to NSCLC remarkably (OR=2.412, 95% CI=1.025-5.674). What’s more, haplotype A-G-G in AXIN2 might play a protective role in NSCLC (OR=0.462, 95% CI=0.270-0.790). -
Genetic and Epigenetic Profiling of Human Prostate Cancer Cell-Subsets
Genetic and Epigenetic Profiling of Human Prostate Cancer Cell-Subsets Alberto John Taurozzi PhD University of York Biology September 2016 Abstract Perturbation of androgen signalling drives progression of human prostate cancer (CaP) to castration-resistant prostate cancer (CRPC). Additionally, CaP is initiated and maintained by cancer stem cells (CSC)s which are analogous to normal prostate stem cells (SC)s. This study presents a qPCR assay to detect androgen receptor gene amplification (GAAR), which is the most common mechanism of castration resistance (>30%). Also, the epigenetic regulation and function of two SC-silenced genes with tumour-suppressive activity (Latexin (LXN) and Retinoic Acid Receptor Responder 1 (RARRES1)) were interrogated using micro-ChIP, transcriptional profiling and mass spectrometry. Traditionally, GAAR is detected using FISH which is labour-intensive and semi- quantitative, limiting clinical applicability. The mechanism of action of LXN or RARRES1 in CaP is unknown, and epigenetic regulation by DNA methylation has been ruled-out in primary CaP. The qPCR assay can detect GAAR in minor cell populations (~1%) within a heterogeneous sample and also quantifies X chromosome aneuploidy (XCA) - a predictor of poor- prognosis in CaP. GAAR and XCA were detected in near-patient xenografts derived from CRPC-tissue indicating that these abnormalities are present in cells capable of in vivo tumour-reconstitution. Micro-ChIP analysis of fractionated primary CaP cultures identified bivalent chromatin at LXN and RARRES1 promoters. Transcriptomic profiling failed to reveal significant changes in gene expression after transduction with LXN or RARRES1. However, an interactome for LXN and RARRES1 was successfully generated in PC3 cells. Additionally, confocal microscopy of mVenus-tagged LXN revealed a pan-cellular distribution which is reflected in the interactome.