Transcript Document
At the crossroads of genomics and ecology: The potential for a canary on a chip Genomics and Environmental Protection • The new age of genomics Genomics and Environmental Protection • The new age of genomics • Applications of genomics data to human health Genomics and Environmental Protection • What is genomics? • Applications of genomics data to human health • Applications of genomics data to environmental health The new age of genomics – A genome is the sum total of all an individual organism’s genes. – Thus, genomics analysis is the study of all the genes of a cell or tissue, at the DNA (genotype), mRNA (transcriptome), or protein (proteome) levels and can aid in understanding normal, adaptive, and abnormal cellular functions. EPA definition 2002 A B Cluster Analysis of Genome-Wide Expression Patterns cDNA Mechanism YJR159W YGL017W sorbitol metabolism sorbitol dehydrogenase protein synthesis tRNA transferase YEL008W YFL013C YOL014W YGR144W unknown unknown unknown thiamine biosyn unknown unknown; similar Ifh1p,Nab3p unknown unknown enzyme YGL177W YDR372C YMR019W YNR071C unknown unknown transcription unknown unknown unknown Sin3-bind. protein UDPglucose 4-epimerase YLR054C unknown YAR002C-A membrane traffic YMR273C cell cycle Enzyme unknown secretious enzyme-unknown plasma membrane protein Other promising field: Proteomics • Proteomics- identifies and quantifies proteins, determines the localization, modifications, interactions, activities, and, ultimately, the function of proteins. • Limited use due to need for sequence information and expense Toxicogenomics • Gene expression may be altered during toxicity or as a result of a disease • Measure associated changes in gene expression • More sensitive, characteristic and measureable endpoint than toxicity itself • Compliments existing methods Toxicogenomics • Determine mechanism of action – Genes associated with particular pathways • Create toxic signature – Don’t necessarily need to know genes Expression is not Enough • Changes in mRNA, protein or metabolic levels may also be nonspecific indicators of exposure to any stress without ties to a negative outcome. • To be meaningful toxicogenomics indicators, gene or protein expression must be linked to pathways as well as the overall phenotypic effects • Expression can be affected by diet, health, behavior, environment Genomics and Human Health • • • • • Drug discovery and drug safety Genetics and disease Genetics x Environment link Environmental monitoring for exposure Sensitive populations Ecology and Genomics • Human health and model species focus of field • Ecological data-what can we learn about nonmodel organisms? Genomics and Ecology • More precise measurement than traditional biochemical descriptions of behavior, physiology, population genetics • Large quantity of data • Comparable among species • Method to detail changes in response to environment What is Ecological Risk Assessment? • A process that evaluates the likelihood that adverse ecological effects may occur as a result of exposure to a stressor. Planning • Example Management Goal – Entity: scallop population in Waquoit Bay, MA – Attribute: abundance – Desired State: population that can support a fishery Genomics and Risk Assessment Problem Formulation Planning Characterization of Exposure Ecological Effects Risk Characterization Communicate Results Risk Management As Needed: Get Data, Iterate, Monitor Ecological Risk Assessment Genomics and Ecological Risk Assessments • Separate exposure and effects of multiple stressors • Describe effects of toxins-mechanism of action • Group compounds by mechanism of action • Measure exposure to and effects of stressors before damage occurs Traditional Assessment of Environmental Exposure • Biomarkers of exposure – Peripheral blood levels of hepatic NZ’s or DNA adducts – Measure tissue toxin level or surrogate markers • Ecological risk assessments – Changes in community – Link to stressors after change Assessment Endpoint • An explicit expression of the environmental value to be protected • Measurable entity • Based on: – Ecological relevance – Susceptibility to a stressor – Relevance to a management goal Example Assessment Endpoints • • • • Bird survival Eelgrass habitat distribution Forest community structure Fish survival, growth, reproduction Types of measures • Exposure • Effects • Ecosystem Receptor Characteristics Problem Formulation Analysis Measures of Exposure Measures of Ecosystem and Receptor Characteristics Exposure Analysis Exposure Profile Measures of Effects Ecological Response Analysis StressorResponse Profile Risk Characterization As Needed: Get Data, Iterate, Monitor Characterization of Exposure Effects Exposure Analysis • • • • Describe stressor sources Describe stressor distribution Describe contact or co-occurance Prepare exposure profile Ecological Response Analysis • • • • Stressor-response analysis Establish causality Link measures to assessment endpoints Prepare stressor-response profile Linking expression to exposure in vivo Xenopus tadpoles Jelaso et al. 2002 Linking exposure to changes in development and changes in expression Fathead minnow Pimephales promelas Cincinnati – NERL Duluth-NHEERL Male fathead minnow Normal female Female with male characters (treated with trembolone) Pimephales oocytes from fish exposed to Fadrozole Normal oocyte Fadrozole treated oocyte Gary Ankley Currently only 12 protein- coding DNA sequences available in GenBank -12S ribosomal RNA -androgen receptor -vitellogenin -P450 aromatase (CYP19) -peroxisome proliferator activated receptor isoform b -P4501A (CYP1A) -P450 17alpha-hydroxylase,17,20-lyase (cyp17 gene) -aromatase -natural resistance associated macrophage protein -G6P1D -glutathione S-transferase -zona pellucida glycoprotein 3 fathead minnow gene homologs Structural Metabolic 18S 60S 28S alpha-globin matrix metalloproteinase 9 myosin regulatory light chain beta-actin beta-globin Desmoglein keratin lamin B1 lamin B2 dynein heavy chain delta-6 fatty acyl desaturase glucose transporter 1 lactate dehydrongenase I mt ATP synthase gamma unit mt cytochrome c oxidase subunit II mt cytochrome c oxidase subunit III mt cytochrome b mt NADH ubiquinone oxidoreductase subunit 4 taurine transporter apolipoprotein ITIH2 diamine oxidase Na, K ATPase adh 3 ada UDP-glucose dehydrogenase GAD 65 GAD 67 GTPase activating protein Endocrine inhibin/activin Pit-1 estrogen receptor beta insulin receptor 2 Immunological integrin beta-2 chain myeloid protein C3-Q2 C3-H1 C3-H2 Neural pentraxin presenilin Developmental retinol binding protein fatty acid binding protein retinoic acid receptor alpha retinoic acid receptor gamma Signal Transduction/Cell Cycle Regulation/Transcription MAP kinase G protein-coupled receptor kinase 7 janus kinase 3 MAP kinase kinase 6 jnk b creatine kinase 1 creatine kinase 2 creatine kinase 3 mef 2c mef2a myo D heat shock protein 90 beta K-ras Rap1b Cyclin A2 Cyclin B EF1 alpha EF1 gamma heat shock 90 alpha cmos Traf2 heat shock factor 2 smad 2 hexokinase Apoptotic Tradd Ann Miracle Linking in vivo expression data to in situ exposure Michael Hemmer Gulf Breeze-NHEERL Well documented life history Sexually dimorphic Eurythermal / Euryhaline Fractional spawners Sheepshead Minnow Primary consumer Cyprinodon variegatus Ongoing EPA Research Field Studies Adult SHM collected over two years from six sites in Pensacola Bay system Bayou sites: Texar (urban runoff), Chico (urban, industrial), Grande (Superfund sites) Male SHM from several locations contained moderate to high levels of plasma Vtg Courtesy of Michael Hemmer NHEERL-Gulf Breeze Challenges • Linking gene expression change to toxic endpoint or reproductive endpoint • Linking changes in gene expression to population or community level effect (ecological risk assessments) • Lack of genomic information on useful ecological species Toxicogenomics and ecology: the potential for a canary on a chip • What is toxicogenomics? • Applications of genomic data to human health • Applications to ecological health – EPA research and others • Applications for toxicology and beyond Applications for toxicology and beyond • Predict community wide effects toxins and other stressors – ecological monitoring • Interspecies comparisions- sensitive species, competition among species • Elucidate mechanisms of complex traits • Identify importance of biological diversity Heritability of secondary chemical production in plants x x xx x x x x x x x x x x Genetic similarity x x x Acipenser fulvescens Questions for the Great Lakes • What types of factors are affecting reproduction of sturgeon in the Great Lakes region? • How similar are sturgeon to model fish species (zebrafish, fathead minnow)? • Develop a comparable invertebrate model species (Daphnia, Chironomids, Dragonfly) • Use genomics as a tool answer ecological questions • Genomics data as a major part of ecological risk assessment Ecological Genomics