At the crossroads of genomics and ecology: The potential for a canary on a chip

1. At the crossroads of genomics and ecology: The potential for a canary on a chip

2. Genomics and Environmental Protection • The new age of genomics

3. Genomics and Environmental Protection • The new age of genomics • Applications of genomics data to human health

4. Genomics and Environmental Protection • What is genomics? • Applications of genomics data to human health • Applications of genomics data to environmental health

5. 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

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8. Cluster Analysis of Genome-Wide Expression Patterns

9. cDNAMechanism Enzyme YJR159W sorbitol metabolism sorbitol dehydrogenase YGL017W protein synthesis tRNA transferase YEL008W unknown unknown YFL013C unknown unknown; similar Ifh1p,Nab3p YOL014W unknown unknown YGR144W thiamine biosyn unknown enzyme YGL177W unknown unknown YDR372C unknown unknown YMR019W transcription Sin3-bind. protein YNR071C unknown UDPglucose 4-epimerase YLR054C unknown unknown YAR002C-A membrane traffic secretious enzyme-unknown YMR273C cell cycle plasma membrane protein

10. 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

12. 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

13. Toxicogenomics • Determine mechanism of action • Genes associated with particular pathways • Create toxic signature • Don’t necessarily need to know genes

14. 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

15. Genomics and Human Health • Drug discovery and drug safety • Genetics and disease • Genetics x Environment link • Environmental monitoring for exposure • Sensitive populations

16. Ecology and Genomics • Human health and model species focus of field • Ecological data-what can we learn about non-model organisms?

17. 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

20. Ecological Risk Assessment Genomics and Risk Assessment Problem Formulation Planning Characterization of Analysis As Needed: Get Data, Iterate, Monitor Exposure Ecological Effects Risk Characterization Communicate Results Risk Management

21. 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

22. 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

23. 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

24. Example Assessment Endpoints • Bird survival • Eelgrass habitat distribution • Forest community structure • Fish survival, growth, reproduction

25. Types of measures • Exposure • Effects • Ecosystem Receptor Characteristics

27. Exposure Analysis • Describe stressor sources • Describe stressor distribution • Describe contact or co-occurance • Prepare exposure profile

28. Ecological Response Analysis • Stressor-response analysis • Establish causality • Link measures to assessment endpoints • Prepare stressor-response profile

29. Linking expression to exposure in vivo Xenopus tadpoles Jelaso et al. 2002

31. Linking exposure to changes in development and changes in expression Fathead minnow Pimephales promelas Cincinnati – NERL Duluth-NHEERL

32. Male fathead minnow Normal female Female with male characters (treated with trembolone)

33. Pimephales oocytes from fish exposed to Fadrozole Normal oocyte Fadrozole treated oocyte Gary Ankley

34. Currently only 12 protein- coding • DNA sequences availablein 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

35. fathead minnow gene homologs Metabolic 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 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 Structural 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 Endocrine inhibin/activin Pit-1 estrogen receptor beta insulin receptor 2 Neural pentraxin presenilin Immunological integrin beta-2 chain myeloid protein C3-Q2 C3-H1 C3-H2 Developmental retinol binding protein fatty acid binding protein retinoic acid receptor alpha retinoic acid receptor gamma Apoptotic Tradd Ann Miracle

36. Linking in vivo expression data to in situ exposure Sheepshead MinnowCyprinodon variegatus Michael Hemmer Gulf Breeze-NHEERL • Well documented life history • Sexually dimorphic • Eurythermal / Euryhaline • Fractional spawners • Primary consumer

37. Ongoing EPA ResearchField 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

38. 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

39. 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

40. 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

43. x x x x x x x x x x x x x x Phenotype similarity x x x Genetic similarity Heritability of secondary chemical production in plants

44. Acipenser fulvescens

45. 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)

46. Ecological Genomics • Use genomics as a tool answer ecological questions • Genomics data as a major part of ecological risk assessment