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 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

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 non-model 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

PlanningProblem Formulation

Ecological Risk Assessment

Risk Characterization

Ana

lysi

s Characterization of

Exposure Ecological Effects

Communicate Results

Risk Management

As N

eeded: Get D

ata, Iterate, Monitor

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

As N

eeded: Get D

ata, Iterate, Monitor

Exposure Ecological ResponseAnalysis Analysis

Problem Formulation

Risk Characterization

Stressor-Response

Profile

ExposureProfile

Characterization ofExposure Effects

Measures of Ecosystem andReceptor Characteristics

Measuresof Effects

Measures ofExposure

An

alys

is

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 vivoXenopus tadpoles

Jelaso et al. 2002

Pimephales promelasCincinnati – NERLDuluth-NHEERL

Fathead minnow

Linking exposure to changes in development and changes in expression

Male fathead minnow

Normal female

Female with male characters(treated with trembolone)

Normal oocyte

Fadrozoletreated oocyte

Pimephales oocytes from fish exposed to Fadrozole

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 homologsStructural18S60S28Salpha-globinmatrix metalloproteinase 9myosin regulatory light chainbeta-actinbeta-globinDesmogleinkeratinlamin B1lamin B2dynein heavy chain

Metabolicdelta-6 fatty acyl desaturaseglucose transporter 1lactate dehydrongenase Imt ATP synthase gamma unitmt cytochrome c oxidase subunit IImt cytochrome c oxidase subunit IIImt cytochrome bmt NADH ubiquinone oxidoreductase subunit 4taurine transporterapolipoproteinITIH2diamine oxidaseNa, K ATPaseadh 3adaUDP-glucose dehydrogenaseGAD 65GAD 67GTPase activating protein

Signal Transduction/Cell Cycle Regulation/TranscriptionMAP kinaseG protein-coupled receptor kinase 7janus kinase 3MAP kinase kinase 6jnk bcreatine kinase 1creatine kinase 2creatine kinase 3mef 2cmef2amyo Dheat shock protein 90 betaK-rasRap1bCyclin A2Cyclin BEF1 alphaEF1 gammaheat shock 90 alphacmosTraf2heat shock factor 2smad 2hexokinaseApoptoticTradd

Neuralpentraxinpresenilin

Developmentalretinol binding proteinfatty acid binding proteinretinoic acid receptor alpharetinoic acid receptor gamma

Immunologicalintegrin beta-2 chainmyeloid proteinC3-Q2C3-H1C3-H2

Endocrineinhibin/activinPit-1estrogen receptor betainsulin receptor 2

Ann Miracle

Sheepshead MinnowCyprinodon variegatus

Well documented life history

Sexually dimorphic

Eurythermal / Euryhaline

Fractional spawners

Primary consumer

Michael HemmerGulf Breeze-NHEERL

Linking in vivo expression data to in situ exposure

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 HemmerNHEERL-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

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Genetic similarity

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xx

x

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Heritability of secondary chemical production in plants

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)

Ecological Genomics• Use genomics as a

tool answer ecological questions

• Genomics data as a major part of ecological risk assessment