Glatiramer Acetate Treatment Effects on Gene Expression in Monocytes of Multiple Sclerosis Patients
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Nuclear and Mitochondrial Genome Defects in Autisms
UC Irvine UC Irvine Previously Published Works Title Nuclear and mitochondrial genome defects in autisms. Permalink https://escholarship.org/uc/item/8vq3278q Journal Annals of the New York Academy of Sciences, 1151(1) ISSN 0077-8923 Authors Smith, Moyra Spence, M Anne Flodman, Pamela Publication Date 2009 DOI 10.1111/j.1749-6632.2008.03571.x License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California THE YEAR IN HUMAN AND MEDICAL GENETICS 2009 Nuclear and Mitochondrial Genome Defects in Autisms Moyra Smith, M. Anne Spence, and Pamela Flodman Department of Pediatrics, University of California, Irvine, California In this review we will evaluate evidence that altered gene dosage and structure im- pacts neurodevelopment and neural connectivity through deleterious effects on synap- tic structure and function, and evidence that the latter are key contributors to the risk for autism. We will review information on alterations of structure of mitochondrial DNA and abnormal mitochondrial function in autism and indications that interactions of the nuclear and mitochondrial genomes may play a role in autism pathogenesis. In a final section we will present data derived using Affymetrixtm SNP 6.0 microar- ray analysis of DNA of a number of subjects and parents recruited to our autism spectrum disorders project. We include data on two sets of monozygotic twins. Col- lectively these data provide additional evidence of nuclear and mitochondrial genome imbalance in autism and evidence of specific candidate genes in autism. We present data on dosage changes in genes that map on the X chromosomes and the Y chro- mosome. -
Pathway-Based Genome-Wide Association Analysis of Coronary Heart Disease Identifies Biologically Important Gene Sets
European Journal of Human Genetics (2012) 20, 1168–1173 & 2012 Macmillan Publishers Limited All rights reserved 1018-4813/12 www.nature.com/ejhg ARTICLE Pathway-based genome-wide association analysis of coronary heart disease identifies biologically important gene sets Lisa de las Fuentes1,4, Wei Yang2,4, Victor G Da´vila-Roma´n1 and C Charles Gu*,2,3 Genome-wide association (GWA) studies of complex diseases including coronary heart disease (CHD) challenge investigators attempting to identify relevant genetic variants among hundreds of thousands of markers being tested. A selection strategy based purely on statistical significance will result in many false negative findings after adjustment for multiple testing. Thus, an integrated analysis using information from the learned genetic pathways, molecular functions, and biological processes is desirable. In this study, we applied a customized method, variable set enrichment analysis (VSEA), to the Framingham Heart Study data (404 467 variants, n ¼ 6421) to evaluate enrichment of genetic association in 1395 gene sets for their contribution to CHD. We identified 25 gene sets with nominal Po0.01; at least four sets are previously known for their roles in CHD: vascular genesis (GO:0001570), fatty-acid biosynthetic process (GO:0006633), fatty-acid metabolic process (GO:0006631), and glycerolipid metabolic process (GO:0046486). Although the four gene sets include 170 genes, only three of the genes contain a variant ranked among the top 100 in single-variant association tests of the 404 467 variants tested. Significant enrichment for novel gene sets less known for their importance to CHD were also identified: Rac 1 cell-motility signaling pathway (h_rac1 Pathway, Po0.001) and sulfur amino-acid metabolic process (GO:0000096, Po0.001). -
309 in PTPRCAP Is Associated with Susceptibility to Diffuse-Type Gastric
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Volume 11 Number 12 December 2009 pp. 1340–1347 1340 www.neoplasia.com Hyoungseok Ju*, Byungho Lim*, Minjin Kim*, A Regulatory Polymorphism at † ‡ § Yong Sung Kim , Woo Ho Kim , Chunhwa Ihm , − PTPRCAP Seung-Moo Noh¶,DongSooHan#, Hang-Jong Yu**, Position 309 in Is †† Associated with Susceptibility Bo Youl Choi and Changwon Kang* to Diffuse-type Gastric Cancer *Department of Biological Sciences, Korea Advanced 1 Institute of Science and Technology, Daejeon, South Korea; and Gene Expression †Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea; ‡Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea; §Department of Laboratory Medicine, Eulji University College of Medicine, Daejeon, South Korea; ¶Department of General Surgery, Chungnam National University College of Medicine, Daejeon, South Korea; #Department of Medicine, Hanyang University Guri Hospital, Guri, South Korea; **Korea Gastric Cancer Center, Seoul Paik Hospital, Seoul, South Korea; ††Department of Preventive Medicine, Hanyang University College of Medicine, Seoul, South Korea Abstract PTPRCAP (CD45-AP) is a positive regulator of protein tyrosine phosphatase PTPRC (CD45), which activates Src family kinases implicated in tumorigenesis. Single-nucleotide polymorphism (SNP) rs869736 located at position −309 of the PTPRCAP promoter was associated with susceptibility to diffuse-type gastric cancer in the current case-control study. The minor-allele homozygote was significantly associated with a 2.5-fold increased susceptibility to diffuse- type gastric cancer (P = .0021, n = 252), but not to intestinal-type (P =.30,n =178),versus the major-allele homo- zygote, when comparing unrelated Korean patients with healthy controls (n = 406). -
Supporting Information
Supporting Information Pouryahya et al. SI Text Table S1 presents genes with the highest absolute value of Ricci curvature. We expect these genes to have significant contribution to the network’s robustness. Notably, the top two genes are TP53 (tumor protein 53) and YWHAG gene. TP53, also known as p53, it is a well known tumor suppressor gene known as the "guardian of the genome“ given the essential role it plays in genetic stability and prevention of cancer formation (1, 2). Mutations in this gene play a role in all stages of malignant transformation including tumor initiation, promotion, aggressiveness, and metastasis (3). Mutations of this gene are present in more than 50% of human cancers, making it the most common genetic event in human cancer (4, 5). Namely, p53 mutations play roles in leukemia, breast cancer, CNS cancers, and lung cancers, among many others (6–9). The YWHAG gene encodes the 14-3-3 protein gamma, a member of the 14-3-3 family proteins which are involved in many biological processes including signal transduction regulation, cell cycle pro- gression, apoptosis, cell adhesion and migration (10, 11). Notably, increased expression of 14-3-3 family proteins, including protein gamma, have been observed in a number of human cancers including lung and colorectal cancers, among others, suggesting a potential role as tumor oncogenes (12, 13). Furthermore, there is evidence that loss Fig. S1. The histogram of scalar Ricci curvature of 8240 genes. Most of the genes have negative scalar Ricci curvature (75%). TP53 and YWHAG have notably low of p53 function may result in upregulation of 14-3-3γ in lung cancer Ricci curvatures. -
Emery and Rimoin's Principles and Practice Of
9 Disorders of the Venous System Pascal Brouillard,1 Nisha Limaye,1 Laurence M. Boon,1,2 Miikka Vikkula1,3 1Human Molecular Genetics, de Duve Institute, Université catholique de Louvain, Brussels, Belgium, 2Center for Vascular Anomalies, Division of Plastic Surgery, Cliniques Universitaires St-Luc, Université catholique de Louvain, Brussels, Belgium, 3Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Université catholique de Louvain, Brussels, Belgium 9.1 INTRODUCTION hemangioma) and more slow-growing vascular malfor- mations. The latter are subcategorized according to the The vasculature is the first organ system to develop during type(s) of vessel(s) altered [5–7] into capillary, venous, embryogenesis, delivering nutrients, growth factors, and arteriovenous, lymphatic, and combined malformations. oxygen to tissues and removing wastes. It is made up of four major types of vessels: arteries, capillaries, veins, and lymphatic vessels, all of which have a single layer of endo- 9.2 THE VENOUS SYSTEM thelial cells (ECs) forming the innermost layer. In blood Veins collect CO2-rich blood from the capillary net- vessels, the endothelial tubes are supported by a layer of work and contain about 75%–80% of the total volume of vascular smooth muscle cells (vSMCs) and/or pericytes blood in the body. They have larger lumens than arteries, (together called mural cells) of variable thickness. A base- with thinner, less muscular walls. Venous flow is passive, ment membrane separates the endothelial and vSMC essentially mediated by physical movements of the body layers, with an extracellular matrix (ECM) of fibrous and and the aspirating effect exerted by the heart. The pres- elastic proteins and carbohydrate polymers forming the ence of valves ensures correct orientation of blood flow. -
WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T (51) International Patent Classification: David [US/US]; 13539 N . 95th Way, Scottsdale, AZ C12Q 1/68 (2006.01) 85260 (US). (21) International Application Number: (74) Agent: AKHAVAN, Ramin; Caris Science, Inc., 6655 N . PCT/US20 12/0425 19 Macarthur Blvd., Irving, TX 75039 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 14 June 2012 (14.06.2012) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, English (25) Filing Language: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, Publication Language: English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/497,895 16 June 201 1 (16.06.201 1) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/499,138 20 June 201 1 (20.06.201 1) US OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, 61/501,680 27 June 201 1 (27.06.201 1) u s SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 61/506,019 8 July 201 1(08.07.201 1) u s TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
Genetic and Chemical Modifiers of EGFR Dependence in Non- Small Cell Lung Cancer
Genetic and Chemical Modifiers of EGFR Dependence in Non- Small Cell Lung Cancer The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Sharifnia, Tanaz. 2014. Genetic and Chemical Modifiers of EGFR Dependence in Non-Small Cell Lung Cancer. Doctoral dissertation, Harvard University. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11745725 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Genetic and Chemical Modifiers of EGFR Dependence in Non-Small Cell Lung Cancer A dissertation presented by Tanaz Sharifnia to The Division of Medical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biological and Biomedical Sciences Harvard University Cambridge, Massachusetts December 2013 © 2013 Tanaz Sharifnia All rights reserved. Dissertation Advisor: Professor Matthew Meyerson Tanaz Sharifnia Genetic and Chemical Modifiers of EGFR Dependence in Non-Small Cell Lung Cancer ABSTRACT The term ‘oncogene addiction’ has been used to describe the phenomenon whereby tumor cells exhibit singular reliance on an oncogene or oncogenic pathway for their survival, despite the accumulation of multiple genetic lesions. In non-small cell lung cancer (NSCLC), this principle is perhaps best exemplified with the finding that epidermal growth factor receptor (EGFR) mutations predict response to EGFR-targeted therapies and thus represent a dependency in the subset of tumors harboring these alterations. -
Research Article Sex Difference of Ribosome in Stroke-Induced Peripheral Immunosuppression by Integrated Bioinformatics Analysis
Hindawi BioMed Research International Volume 2020, Article ID 3650935, 15 pages https://doi.org/10.1155/2020/3650935 Research Article Sex Difference of Ribosome in Stroke-Induced Peripheral Immunosuppression by Integrated Bioinformatics Analysis Jian-Qin Xie ,1,2,3 Ya-Peng Lu ,1,3 Hong-Li Sun ,1,3 Li-Na Gao ,2,3 Pei-Pei Song ,2,3 Zhi-Jun Feng ,3 and Chong-Ge You 2,3 1Department of Anesthesiology, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China 2Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China 3The Second Clinical Medical College of Lanzhou University, Lanzhou, Gansu 730030, China Correspondence should be addressed to Chong-Ge You; [email protected] Received 13 April 2020; Revised 8 October 2020; Accepted 18 November 2020; Published 3 December 2020 Academic Editor: Rudolf K. Braun Copyright © 2020 Jian-Qin Xie et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Ischemic stroke (IS) greatly threatens human health resulting in high mortality and substantial loss of function. Recent studies have shown that the outcome of IS has sex specific, but its mechanism is still unclear. This study is aimed at identifying the sexually dimorphic to peripheral immune response in IS progression, predicting potential prognostic biomarkers that can lead to sex- specific outcome, and revealing potential treatment targets. Gene expression dataset GSE37587, including 68 peripheral whole blood samples which were collected within 24 hours from known onset of symptom and again at 24-48 hours after onset (20 women and 14 men), was downloaded from the Gene Expression Omnibus (GEO) datasets. -
Genetic Syndromes with Vascular Malformations – Update on Molecular Background and Diagnostics
State of the art paper Genetics Genetic syndromes with vascular malformations – update on molecular background and diagnostics Adam Ustaszewski1,2, Joanna Janowska-Głowacka2, Katarzyna Wołyńska2, Anna Pietrzak3, Magdalena Badura-Stronka2 1Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland Corresponding author: 2Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Adam Ustaszewski Poland Institute of Human Genetics 3Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland Polish Academy of Sciences 32 Strzeszynska St Submitted: 19 April 2018; Accepted: 9 September 2018 60-479 Poznan, Poland Online publication: 25 February 2020 Phone: +48 61 65 79 223 E-mail: adam.ustaszewski@ Arch Med Sci 2021; 17 (4): 965–991 igcz.poznan.pl DOI: https://doi.org/10.5114/aoms.2020.93260 Copyright © 2020 Termedia & Banach Abstract Vascular malformations are present in a great variety of congenital syn- dromes, either as the predominant or additional feature. They pose a major challenge to the clinician: due to significant phenotype overlap, a precise diagnosis is often difficult to obtain, some of the malformations carry a risk of life threatening complications and, for many entities, treatment is not well established. To facilitate their recognition and aid in differentiation, we present a selection of notable congenital disorders of vascular system development, distinguishing between the heritable germinal and sporadic somatic mutations as their causes. Clinical features, genetic background and comprehensible description of molecular mechanisms is provided for each entity. Key words: arteriovenous malformation, vascular malformation, capillary malformation, venous malformation, arterial malformation, lymphatic malformation. Introduction Congenital vascular malformations (VMs) are disorders of vascular architecture development. -
MIKULASOVA Et Al. MMEJ DRIVES 8Q24 REARRANGEMENTS in MYELOMA
MIKULASOVA et al. MMEJ DRIVES 8q24 REARRANGEMENTS IN MYELOMA Microhomology-mediated end joining drives complex rearrangements and over-expression of MYC and PVT1 in multiple myeloma Authors Aneta Mikulasova1,2, Cody Ashby1, Ruslana G. Tytarenko1, Pingping Qu3, Adam Rosenthal3, Judith A. Dent1, Katie R. Ryan1, Michael A. Bauer1, Christopher P. Wardell1, Antje Hoering3, Konstantinos Mavrommatis4, Matthew Trotter5, Shayu Deshpande1, Erming Tian1, Jonathan Keats6, Daniel Auclair7, Graham H. Jackson8, Faith E. Davies1, Anjan Thakurta4, Gareth J. Morgan1, and Brian A. Walker1 Affiliations 1Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA 2Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom 3Cancer Research and Biostatistics, Seattle, WA, USA 4Celgene Corporation, Summit, NJ, USA 5Celgene Institute for Translational Research Europe, Seville, Spain 6Translational Genomics Research Institute, Phoenix, AZ, USA. 7Multiple Myeloma Research Foundation, Norwalk, CT, USA. 8Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom MIKULASOVA et al. MMEJ DRIVES 8q24 REARRANGEMENTS IN MYELOMA Contents Supplementary Methods ............................................................................................................... 2 Data Analysis .............................................................................................................................. 2 External Datasets ...................................................................................................................... -
The Effect of Phototherapy on Cancer Predisposition Genes of Diabetic and Normal Human Skin Fibroblasts
Hindawi BioMed Research International Volume 2017, Article ID 7604861, 9 pages https://doi.org/10.1155/2017/7604861 Research Article The Effect of Phototherapy on Cancer Predisposition Genes of Diabetic and Normal Human Skin Fibroblasts Pongsathorn Chotikasemsri,1 Boonsin Tangtrakulwanich,2 and Surasak Sangkhathat3 1 Biomedical Engineering Institute, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand 2Department of Orthopedic Surgery and Physical Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand 3Department of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand Correspondence should be addressed to Pongsathorn Chotikasemsri; [email protected] Received 3 October 2016; Accepted 19 February 2017; Published 12 March 2017 Academic Editor: Tokuya Omi Copyright © 2017 Pongsathorn Chotikasemsri et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The purpose of this study was to investigate whether LED light at different wavelengths affects the expression profile of 143cancer predisposition genes in both diabetic and normal human fibroblasts. In this study, both diabetic and normal fibroblast cell lines were 2 cultured and irradiated with red (635 nm), green (520 nm), and blue (465 nm) LED light for 10 minutes at 0.67 J/cm each. After that, mRNA from all cell lines was extracted for microarray analysis. We found that green light activates EPHB2, KIT, ANTXR2, ESCO2, MSR1, EXT1, TSC1, KIT, NF1, BUB1B, FANCD2, EPCAM, FANCD2, NF, DIS3L2, and RET in normal fibroblast cells, while blue and red light can upregulate RUNX1, PDGFRA, EHBP1, GPC3, AXIN2, KDR, GLMN, MSMB, EPHB2, MSR1, KIT, FANCD2, BMPR1A, BUB1B, PDE11A, and RET. -
HSP90-Incorporating Chaperome Networks As Biosensor for Disease-Related Pathways in Patient- Specific Midbrain Dopamine Neurons
ARTICLE DOI: 10.1038/s41467-018-06486-6 OPEN HSP90-incorporating chaperome networks as biosensor for disease-related pathways in patient- specific midbrain dopamine neurons Sarah Kishinevsky1,2,3,4, Tai Wang3, Anna Rodina3, Sun Young Chung1,2, Chao Xu3, John Philip5, Tony Taldone3, Suhasini Joshi3, Mary L. Alpaugh3,14, Alexander Bolaender3, Simon Gutbier6, Davinder Sandhu7, Faranak Fattahi1,2, Bastian Zimmer1,2, Smit K. Shah3, Elizabeth Chang5, Carmen Inda3,15, John Koren 3rd3,16, Nathalie G. Saurat1,2, Marcel Leist 6, Steven S. Gross7, Venkatraman E. Seshan8, Christine Klein9, Mark J. Tomishima1,2,10, Hediye Erdjument-Bromage11,12, Thomas A. Neubert 11,12, Ronald C. Henrickson5, 1234567890():,; Gabriela Chiosis3,13 & Lorenz Studer1,2 Environmental and genetic risk factors contribute to Parkinson’s Disease (PD) pathogenesis and the associated midbrain dopamine (mDA) neuron loss. Here, we identify early PD pathogenic events by developing methodology that utilizes recent innovations in human pluripotent stem cells (hPSC) and chemical sensors of HSP90-incorporating chaperome networks. We show that events triggered by PD-related genetic or toxic stimuli alter the neuronal proteome, thereby altering the stress-specific chaperome networks, which produce changes detected by chemical sensors. Through this method we identify STAT3 and NF-κB signaling activation as examples of genetic stress, and phospho-tyrosine hydroxylase (TH) activation as an example of toxic stress-induced pathways in PD neurons. Importantly, pharmacological inhibition of the stress chaperome network reversed abnormal phospho- STAT3 signaling and phospho-TH-related dopamine levels and rescued PD neuron viability. The use of chemical sensors of chaperome networks on hPSC-derived lineages may present a general strategy to identify molecular events associated with neurodegenerative diseases.