Download Genomics and Environmental Protection

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
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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
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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
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Describe stressor sources
Describe stressor distribution
Describe contact or co-occurance
Prepare exposure profile
Ecological Response Analysis
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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