T3DB - the Toxin, Toxin- Target Database
Total Page：16
File Type：pdf, Size：1020Kb
Load more
Recommended publications
-
Toxicogenomics Applications of New Functional Genomics Technologies in Toxicology
\-\w j Toxicogenomics Applications of new functional genomics technologies in toxicology Wilbert H.M. Heijne Proefschrift ter verkrijging vand egraa dva n doctor opgeza gva nd e rector magnificus vanWageninge n Universiteit, Prof.dr.ir. L. Speelman, in netopenbaa r te verdedigen op maandag6 decembe r200 4 des namiddagst e half twee ind eAul a - Table of contents Abstract Chapter I. page 1 General introduction [1] Chapter II page 21 Toxicogenomics of bromobenzene hepatotoxicity: a combined transcriptomics and proteomics approach[2] Chapter III page 48 Bromobenzene-induced hepatotoxicity atth etranscriptom e level PI Chapter IV page 67 Profiles of metabolites and gene expression in rats with chemically induced hepatic necrosis[4] Chapter V page 88 Liver gene expression profiles in relation to subacute toxicity in rats exposed to benzene[5] Chapter VI page 115 Toxicogenomics analysis of liver gene expression in relation to subacute toxicity in rats exposed totrichloroethylen e [6] Chapter VII page 135 Toxicogenomics analysis ofjoin t effects of benzene and trichloroethylene mixtures in rats m Chapter VII page 159 Discussion and conclusions References page 171 Appendices page 187 Samenvatting page 199 Dankwoord About the author Glossary Abbreviations List of genes Chapter I General introduction Parts of this introduction were publishedin : Molecular Biology in Medicinal Chemistry, Heijne etal., 2003 m NATO Advanced Research Workshop proceedings, Heijne eral., 2003 81 Chapter I 1. General introduction 1.1 Background /.1.1 Toxicologicalrisk -
Genomic Dose Response
Genomic Dose Response: The Picture NTP Genomic Dose Response Modeling Expert Panel Meeting October 23, 2017 Russell Thomas Director National Center for Computational Toxicology The views expressed in this presentation are those of the author and do not necessarily reflect the views or policies of the U.S. EPA Scott May Want To Rethink Asking Me To Be The “Big Picture Guy”… National Center for Computational Toxicology It is a Well Known Fact that Toxicology Continues to Have a Data Problem US National Research Council, 1984 Size of Estimate Mean Percent Category Category In the Select Universe Pesticides and Inert Ingredients of Pesticides 3,350 Formulations 10 24 2 26 38 Cosmetic Ingredients 3,410 2 14 10 18 56 Drugs and Excipients Used in Drug Formulations 1,815 18 18 3 36 25 Food Additives 8,627 • Major challenge is too many 5 14 1 34 46 Chemicals in Commerce: chemicals and not enough At Least 1 Million 12,860 Pounds/Year data 11 11 78 Chemicals in Commerce: • Total # chemicals = 65,725 Less than 1 Million 13,911 Pounds/Year • Chemicals with no toxicity 12 12 76 data of any kind = ~46,000 Chemicals in Commerce: Production Unknown or 21,752 Inaccessible 10 8 82 Complete Partial Minimal Some No Toxicity Health Health Toxicity Toxicity Information Hazard Hazard Information Information Available Assessment Assessment Available Available 2 Possible Possible (But Below Minimal) National Center for Computational Toxicology It is a Well Known Fact that Toxicology Continues to Have a Data Problem 70 60 50 40 30 20 Percent of Chemicals <1% 10 0 Acute Cancer Gentox Dev Tox Repro Tox EDSP Tier 1 Modified from Judson et al., EHP 2009 3 National Center for Computational Toxicology For Those With Data, Have We Been Truly Predictive or Just Protective? …data compiled from 150 compounds with 221 human toxicity events reported. -
Next-Generation Sequencing Data for Use in Risk Assessment Bruce Alexander Merrick
Available online at www.sciencedirect.com Current Opinion in ScienceDirect Toxicology Next-generation sequencing data for use in risk assessment Bruce Alexander Merrick Abstract fluorescently labeled nucleotides and capillary electro- Next-generation sequencing (NGS) represents several phoresis that gave rise to automated sequencing in- powerful platforms that have revolutionized RNA and DNA struments such as the Applied Biosystems, Inc. model analysis. The parallel sequencing of millions of DNA molecules 370A sequencers and others, on the basis of Sanger can provide mechanistic insights into toxicology and provide chemistries [2]. Read length per each sample was at 500e new avenues for biomarker discovery with growing relevance 800 nucleotides, and sample throughput was limited. for risk assessment. The evolution of NGS technologies has improved over the last decade with increased sensitivity and Sanger-based DNA sequencing instruments are accuracy to foster new biomarker assays from tissue, blood, considered first-generation platforms. Instruments that and other biofluids. NGS technologies can identify transcrip- perform multiple sequencing reactions simultaneously tional changes and genomic targets with base pair precision in in a ‘massively parallel’ fashion have been dubbed, response to chemical exposure. Furthermore, there are ‘NextGeneration’ or NextGen Sequencing [3]. How several exciting movements within the toxicology community NGS came about compared with other genomic plat- that incorporate NGS platforms into new strategies for more forms is interlinked with microarray technology rapid toxicological characterizations. These include the Tox21 (Figure 1). Both platforms can provide whole genomic in vitro high-throughput transcriptomic screening program, approaches to research problems. Microarrays are a development of organotypic spheroids, alternative animal fluorescent probe hybridization-based technology with models, mining archival tissues, liquid biopsy, and epige- origins in the mid-1990s that are now a mature genomic nomics. -
In Vitro RNA-Seq-Based Toxicogenomics Assessment Shows
www.nature.com/scientificreports OPEN In vitro RNA-seq-based toxicogenomics assessment shows reduced biological efect of tobacco Received: 11 August 2017 Accepted: 5 January 2018 heating products when compared Published: xx xx xxxx to cigarette smoke Linsey E. Haswell, Sarah Corke, Ivan Verrastro, Andrew Baxter, Anisha Banerjee, Jason Adamson, Tomasz Jaunky, Christopher Proctor, Marianna Gaça & Emmanuel Minet The battery of regulatory tests used to evaluate the risk of novel tobacco products such as heated tobacco products (THPs) presents some limitations including a bias towards the apical endpoint tested, and limited information on the mode of action. This is driving a paradigm shift to more holistic systems biology approaches. In this study, we used RNA-sequencing to compare the transcriptomic perturbations following acute exposure of a 3D airway tissue to the aerosols from two commercial THPs and a reference 3R4F cigarette. 2809 RNAs were diferentially expressed for the 3R4F treatment and 115 and 2 RNAs for the two THPs (pFDR < 0.05, FC > 1.5), respectively. The relationship between the identifed RNA features and gene ontologies were mapped showing a strong association with stress response, xenobiotics metabolism, and COPD-related terms for 3R4F. In contrast, fewer ontologies were found enriched for the THPs aerosols. “Response to wounding” was a common COPD-related term over-represented for the two THPs but at a reduced signifcance. Quantifcation of a cytokine panel post-exposure confrmed a pro-infammatory efect of cigarette smoke but not for THPs. In conclusion, THPs have a reduced impact on gene expression compared to 3R4F. Te health risk associated with smoking cigarettes and tobacco regulations have been driving a wave of develop- ment and innovation in next generation tobacco and nicotine delivery systems1. -
IPA Analysis of Metabolomics Data Including Cross-Platform Integration with Transcriptomics Data from a Diabetic Mouse Model
IPA Analysis of Metabolomics Data Including Cross-Platform Integration with Transcriptomics Data from a Diabetic Mouse Model CONTENTS Overview ........................................................................................................................................................................ 3 Introduction ................................................................................................................................................................... 3 Metabolomics Background ........................................................................................................................................ 3 Integration of Metabolomic and Transcriptomic data .............................................................................................. 5 The Ingenuity Platform .............................................................................................................................................. 5 Case Study Background ............................................................................................................................................. 5 Methods ........................................................................................................................................................................ 6 Establishing a Metabolite profile for db/db mice and identification of exploratory biomarkers .............................. 6 IPA-Metabolomics™ Analysis: ................................................................................................................................... -
Toxicogenomics: Toward the Future of Toxic Tort Causation
NORTH CAROLINA JOURNAL OF LAW & TECHNOLOGY VOLUME 5, ISSUE 1: FALL 2003 Toxicogenomics: Toward the Future of Toxic Tort Causation Jon R. Pierce and Terrence Sexton1 I. Introduction Plaintiff suspects that a chemical in her city’s water supply has caused her to develop a rare form of liver cancer. Defendant, a company in Plaintiff’s city, has been discharging the chemical into the water for a number of years. Both parties in the toxic tort litigation are at the mercy of an unevenly developed and often- insufficient body of science to establish or rebut the required causation element. This article will examine the current causation paradigm in toxic tort litigation, pointing out its specific weaknesses. The article will then introduce an emerging discipline, toxicogenomics, which will eventually make it possible to specifically describe the molecular pathways leading from exposure to injury, and in so doing will greatly improve the reliability of causation evidence in toxic tort cases to the benefit of both plaintiffs and defendants. To illustrate its potential usefulness, this article will walk through a hypothetical toxicogenomics experiment involving a suspected liver toxin. The article will conclude by suggesting that judges controlled by Daubert v. Merrell Dow Pharmaceuticals, Inc.2 would be wise not to admit such evidence until more research can definitively link the described molecular pathways to the specific injury. 1 Jon R. Pierce, J.D. Candidate, University of North Carolina School of Law, 2004. Terrence Sexton is a trial attorney with the international law firm of Shook Hardy & Bacon LLP. He represents clients nationwide in cases involving toxic torts, products liability, white collar crime and commercial disputes. -
Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment
nanomaterials Review Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment Angela Serra 1,2 , Michele Fratello 1,2 , Luca Cattelani 1,2 , Irene Liampa 3 , Georgia Melagraki 4 , Pekka Kohonen 5,6 , Penny Nymark 5,6 , Antonio Federico 1,2 , Pia Anneli Sofia Kinaret 1,2,7 , Karolina Jagiello 8,9, My Kieu Ha 10,11,12, Jang-Sik Choi 10,11,12, Natasha Sanabria 13 , Mary Gulumian 13,14, Tomasz Puzyn 8,9 , Tae-Hyun Yoon 10,11,12 , Haralambos Sarimveis 3 , Roland Grafström 5,6, Antreas Afantitis 4 and Dario Greco 1,2,7,* 1 Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; angela.serra@tuni.fi (A.S.); michele.fratello@tuni.fi (M.F.); luca.cattelani@tuni.fi (L.C.); antonio.federico@tuni.fi (A.F.); pia.kinaret@helsinki.fi (P.A.S.K.) 2 BioMediTech Institute, Tampere University, FI-33014 Tampere, Finland 3 School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece; [email protected] (I.L.); [email protected] (H.S.) 4 Nanoinformatics Department, NovaMechanics Ltd., Nicosia 1065, Cyprus; [email protected] (G.M.); [email protected] (A.A.) 5 Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; [email protected] (P.K.); [email protected] (P.N.); [email protected] (R.G.); 6 Division of Toxicology, Misvik Biology, 20520 Turku, Finland 7 Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland 8 QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland; [email protected] -
Genomics and Toxic Substances: Part I—Toxicogenomics by Gary E
Copyright © 2003 Environmental Law Institute®, Washington, DC. reprinted with permission from ELR®, http://www.eli.org, 1-800-433-5120. 1-2003 ELR 33 ELR 10071 NEWS&ANALYSIS Genomics and Toxic Substances: Part I—Toxicogenomics by Gary E. Marchant dvances in genomics, the study of the structure and ticle will address the application of toxicogenomics to Afunction of our genetic make-up, are fundamentally toxic torts and environmental regulation; a subsequent transforming toxicology, the science of how toxic sub- companion article will address toxicogenetic applications. stances affect our bodies. These changes will inevitably spill After first describing the scientific background of toxico- over into the legal regimes that frequently rely on toxicolog- genomics, this Article explores some potential uses of ical data, including toxic torts and environmental regula- toxicogenomic data in regulation and litigation involving tion.1 Genomic data, and the techniques with which they are toxic substances. generated, have the potential to make toxic torts and envi- ronmental regulation more effective, efficient, and fair, but Scientific Background at the same time will present many new doctrinal, eviden- tiary, and ethical challenges. Toxicogenomics is defined “as the study of the relationship Two key applications of genomic data for toxic torts and between the structure and activity of the genome (the cellu- environmental regulation are2: (i) the study of the expres- lar complement of genes) and the adverse biological effects sion of genes in -
Review TOXICITY STUDIES of DRUGS AND
Bulgarian Journal of Veterinary Medicine, 2016 ONLINE FIRST ISSN 1311-1477; DOI: 10.15547/bjvm.983 Review TOXICITY STUDIES OF DRUGS AND CHEMICALS IN ANIMALS: AN OVERVIEW S. A. SAGANUWAN Department of Veterinary Physiology, Pharmacology and Biochemistry, College of Veterinary Medicine, University of Agriculture, Makurdi, Benue State, Nigeria Summary Saganuwan, S. A., 2016. Toxicity studies of drugs and chemicals in animals: An overview. Bulg. J. Vet. Med. (online first). Toxicity study is the investigation of either short or long-term toxic effects of a drug or chemical on animals. The toxicity is dose-dependent as asserted by Paracelsus over 500 years ago. However, short-term toxic effect is determined using median lethal dose (LD50) first introduced by Trevan in 1927 and revised many times. Presently there is a growing preponderance of rejection of scientific papers on acute toxicity study, simply because of the belief that in the current hazard and safety as- sessment of drugs and chemicals, LD50 values are no longer used. In view of this, literature search was carried out with a view to investigating the relevance of LD50 in development and assessment of drugs and chemicals. The findings revealed that in the past, many animals had been used for LD50 determination. OECD has reduced the number of test animals to 5–15 and presently it is further re- duced to 2–6. Acute toxicity study is being carried out in medicinal plants research and in the study of patent medicine. Although the application of LD50 has been drastically reduced, it is still applied and accepted in some parts of the world. -
Public Data Sources to Support Systems Toxicology Applications Allan Peter Davis1, Jolene Wiegers1, Thomas C
Available online at www.sciencedirect.com Current Opinion in ScienceDirect Toxicology Public data sources to support systems toxicology applications Allan Peter Davis1, Jolene Wiegers1, Thomas C. Wiegers1 and Carolyn J. Mattingly1,2 Abstract metabolic pathways, interaction networks, and/or bio- Public databases provide a wealth of freely available infor- logical processes; and the outcome can be the perturbed mation about chemicals, genes, proteins, biological networks, biological system trying to return back to a normal state phenotypes, diseases, and exposure science that can be in- (resilience) or a new, and potentially, adverse state due tegrated to construct pathways for systems toxicology appli- to toxicity [2]. The toxicant may trigger multiple cations. Relating this disparate information from public different pathways simultaneously by interacting with repositories, however, can be challenging because databases different biological mediators, complicating under- use a variety of ways to represent, describe, and make avail- standing about the specific connectivity between indi- able their content. The use of standard vocabularies to anno- vidual events, mediators, and outcomes. As well, in the tate key data concepts, however, allows the information to be real world, humans are typically exposed simultaneously more easily exchanged and combined for discovery of new to mixtures of chemicals and drugs, further complicating findings. We explore some of the many public data sources understanding of toxic mechanisms of actions [3,4]. currently available to support systems toxicology and demon- strate the value of standardizing data to help construct The goal of systems toxicology is to discern and organize chemical information pathways. exposure and toxicogenomic events to help formalize an understanding for drug therapy, risk assessment, expo- Addresses e 1 Department of Biological Sciences, North Carolina State University, sure hazards, and toxicity to humans [5 9]. -
OECD Environment, Health and Safety Publications
OECD Environment, Health and Safety Publications Series on Testing and Assessment No. 39 DRAFT GUIDANCE DOCUMENT ON ACUTE INHALATION TOXICITY TESTING Environment Directorate Organisation for Economic Co-operation and Development 28 November 2008 1 Also published in the Series on Testing and Assessment: No. 1, Guidance Document for the Development of OECD Guidelines for Testing of Chemicals (1993; reformatted 1995, revised 2006) No. 2, Detailed Review Paper on Biodegradability Testing (1995) No. 3, Guidance Document for Aquatic Effects Assessment (1995) No. 4, Report of the OECD Workshop on Environmental Hazard/Risk Assessment (1995) No. 5, Report of the SETAC/OECD Workshop on Avian Toxicity Testing (1996) No. 6, Report of the Final Ring-test of the Daphnia magna Reproduction Test (1997) No. 7, Guidance Document on Direct Phototransformation of Chemicals in Water (1997) No. 8, Report of the OECD Workshop on Sharing Information about New Industrial Chemicals Assessment (1997) No. 9, Guidance Document for the Conduct of Studies of Occupational Exposure to Pesticides during Agricultural Application (1997) No. 10, Report of the OECD Workshop on Statistical Analysis of Aquatic Toxicity Data (1998) No. 11, Detailed Review Paper on Aquatic Testing Methods for Pesticides and industrial Chemicals (1998) No. 12, Detailed Review Document on Classification Systems for Germ Cell Mutagenicity in OECD Member Countries (1998) No. 13, Detailed Review Document on Classification Systems for Sensitising Substances in OECD Member Countries 1998) No. 14, Detailed Review Document on Classification Systems for Eye Irritation/Corrosion in OECD Member Countries (1998) No. 15, Detailed Review Document on Classification Systems for Reproductive Toxicity in OECD Member Countries (1998) 2 No. -
Prioritizing Candidate Diseases-Related Metabolites Based
Wang et al. BMC Bioinformatics 2019, 20(Suppl 18):574 https://doi.org/10.1186/s12859-019-3127-4 RESEARCH Open Access Prioritizing candidate diseases-related metabolites based on literature and functional similarity Yongtian Wang1, Liran Juan2, Jiajie Peng3, Tianyi Zang1* and Yadong Wang1* From Biological Ontologies and Knowledge bases workshop at IEEE BIBM 2018 Madrid, Spain. 3-6 December 2018 Abstract Background: As the terminal products of cellular regulatory process, functional related metabolites have a close relationship with complex diseases, and are often associated with the same or similar diseases. Therefore, identification of disease related metabolites play a critical role in understanding comprehensively pathogenesis of disease, aiming at improving the clinical medicine. Considering that a large number of metabolic markers of diseases need to be explored, we propose a computational model to identify potential disease-related metabolites based on functional relationships and scores of referred literatures between metabolites. First, obtaining associations between metabolites and diseases from the Human Metabolome database, we calculate the similarities of metabolites based on modified recommendation strategy of collaborative filtering utilizing the similarities between diseases. Next, a disease-associated metabolite network (DMN) is built with similarities between metabolites as weight. To improve the ability of identifying disease-related metabolites, we introduce scores of text mining from the existing database of chemicals and proteins into DMN and build a new disease-associated metabolite network (FLDMN) by fusing functional associations and scores of literatures. Finally, we utilize random walking with restart (RWR) in this network to predict candidate metabolites related to diseases. Results: We construct the disease-associated metabolite network and its improved network (FLDMN) with 245 diseases, 587 metabolites and 28,715 disease-metabolite associations.