ENV 593:ENV 593:Session IISession II

October 14, 2004October 14, 2004

Genomics and Public Genomics and Public

Health PolicyHealth Policy

Genomic InformationGenomic Information

DNADNA

RNARNA

proteinsproteins

metabolitesmetabolites

ProteomicsProteomics

ToxicogenomicsToxicogenomics

PharmacogenomicsPharmacogenomics

MetabolomicsMetabolomics

EcogeneticsEcogenetics Genetic variability and Genetic variability and Susceptible populationsSusceptible populations

Gene expression patterns Gene expression patterns in response to drugs in response to drugs

and toxinsand toxins

Protein expression profilesProtein expression profilesin response to toxins/drugsin response to toxins/drugs

Metabolite expression Metabolite expression patterns in response to patterns in response to

toxins/drugstoxins/drugs

Major Chemical Laws in Major Chemical Laws in USUS

EPAEPA Air pollutantsAir pollutants Clean Air Act, 1970Clean Air Act, 1970

Water pollutantsWater pollutants Federal Water Pollution Control Act Federal Water Pollution Control Act 19721972

Drinking waterDrinking water Safe Drinking Water Act Safe Drinking Water Act 19721972

PesticidesPesticides Fungicide, Insecticides and Fungicide, Insecticides and Rodenticides Rodenticides Act (FIFRA), 1972; Food Act (FIFRA), 1972; Food Quality Protection Quality Protection Act (FGPA) 1996Act (FGPA) 1996

Toxic ChemicalsToxic Chemicals Toxic Substance Control Act (TSCA) Toxic Substance Control Act (TSCA) 19761976

Hazardous WasteHazardous Waste Resource conservation and Resource conservation and Recovery Act Recovery Act (RCRA) 1976(RCRA) 1976

OSHAOSHA WorkplaceWorkplace Occupational Safety and Health Occupational Safety and Health (OSH) Act (OSH) Act 19701970

FDAFDA Foods, Drugs and CosmeticsFoods, Drugs and CosmeticsFDC Acts 1906, 1938, 1962, 1977FDC Acts 1906, 1938, 1962, 1977FDA modernization Act 1997FDA modernization Act 1997

GenomicsGenomics

How are the regulatory How are the regulatory agencies addressing agencies addressing

and incorporating into and incorporating into practices and policies practices and policies

the information the information generated by genomic generated by genomic

methods?methods?

Genomics and Genomics and Public Health Policy Public Health Policy

FDA-U.S. Food and Drug AdministrationFDA-U.S. Food and Drug Administration Drug and food safetyDrug and food safety Changes in FDA approval consideration to Changes in FDA approval consideration to

address address pharmacogenomicpharmacogenomic data? data? EPA-Environmental Protection AgencyEPA-Environmental Protection Agency

Protect human health and the environment Protect human health and the environment Develop and enforce regulationsDevelop and enforce regulations Exposure standardsExposure standards Alterations in regulations or standards due to Alterations in regulations or standards due to

toxicogenomictoxicogenomic data? data?

Genomics and the FDAGenomics and the FDA

““Pharmacogenomics is a new field but we Pharmacogenomics is a new field but we intend to do all we can to use it to promote intend to do all we can to use it to promote

the development of medicine….it holds the development of medicine….it holds great promise to shed scientific light on the great promise to shed scientific light on the

often risky and costly process of drug often risky and costly process of drug development, and to provide greater development, and to provide greater

confidence about the risks and benefits of confidence about the risks and benefits of drugs.” drugs.”

FDA Commissioner Mark B McClellan, FDA Commissioner Mark B McClellan,

when releasing the new when releasing the new

pharmacogenomic draft guidelines for the FDA.pharmacogenomic draft guidelines for the FDA.

FDA and Genomics:FDA and Genomics:Pharmacogenomic DataPharmacogenomic Data

Recognizes the potential ability to identify Recognizes the potential ability to identify sources of inter-individual variability in sources of inter-individual variability in drug response (both efficacy and toxicity)drug response (both efficacy and toxicity)

Considers the field in the early Considers the field in the early developmental stagedevelopmental stage

Genomic data in isolation, not enough to Genomic data in isolation, not enough to determine regulationsdetermine regulations

Use of genomics must demonstrate a well-Use of genomics must demonstrate a well-accepted mechanistic and clinical accepted mechanistic and clinical significancesignificance

Genomics and the EPA:Genomics and the EPA:Interim PolicyInterim Policy

Encourages and supports continued Encourages and supports continued genomic research.genomic research.

Limited use of genomics while the Agency Limited use of genomics while the Agency gains experience in assessing quality, gains experience in assessing quality, accuracy and reproducibility and accuracy and reproducibility and relevance of the data.relevance of the data.

Genomics data alone are currently Genomics data alone are currently insufficient as a basis for risk assessment insufficient as a basis for risk assessment and management decisions. and management decisions.

May be used in a “weight-of-evidence” May be used in a “weight-of-evidence” approach.approach.

Use of Genomics Within Use of Genomics Within the FDA and EPAthe FDA and EPA

Identification of susceptible populations Identification of susceptible populations Development of disease; drug and toxic Development of disease; drug and toxic

responseresponse Development of biomarkersDevelopment of biomarkers

Disease and drug safety; toxic exposure/effectDisease and drug safety; toxic exposure/effect Mode of action informationMode of action information

Gene expression profiles/fingerprintingGene expression profiles/fingerprinting Drug therapy; toxic exposure and responseDrug therapy; toxic exposure and response

Use of Genomics Within Use of Genomics Within the FDA and EPAthe FDA and EPA

Identification of susceptible populations Identification of susceptible populations Development of disease; drug and toxic Development of disease; drug and toxic

responseresponse Development of biomarkersDevelopment of biomarkers

Disease and drug safety; toxic exposure/effectDisease and drug safety; toxic exposure/effect Mode of action informationMode of action information

Gene expression profiles/fingerprintingGene expression profiles/fingerprinting Drug therapy; toxic exposure and responseDrug therapy; toxic exposure and response

Susceptible PopulationsSusceptible Populations Arises from human genetic variabilityArises from human genetic variability Human Genome Project Human Genome Project

found variations at approx. 1/1000 base pairsfound variations at approx. 1/1000 base pairs >1 million genetic differences between any two >1 million genetic differences between any two

individualsindividuals Genetic PolymorphismsGenetic Polymorphisms

Single nucleotide polymorphism (SNP)Single nucleotide polymorphism (SNP) A variant in the sequence of DNA found in >1% of the A variant in the sequence of DNA found in >1% of the

populationpopulation >3 million candidate SNPs identified to date>3 million candidate SNPs identified to date estimated that there are ~11 million SNPsestimated that there are ~11 million SNPs Prevalence is often found to differ between ethnic Prevalence is often found to differ between ethnic

groupsgroups

Genotypes to PhenotypesGenotypes to Phenotypes

Gene variant

Subtle change in protein function

Change in biological response

Human VariabilityHuman Variability

adapted from Eaton, 2004

Genetics is one factor contributing to overall variability between individuals

Nu

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f In

div

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General Population

Sensitive Subpopulation

Adverse Response

* Genetics, Age, Health Status, Exposure History

*

Variability & Drug Variability & Drug DevelopmentDevelopment

Genotype specific DrugsGenotype specific Drugs FDA has approved several drugs designed for FDA has approved several drugs designed for

individuals with a specific genotype or protein individuals with a specific genotype or protein expression level.expression level.

GleevecGleevecTMTM

‘‘targeted’ drug treatment of chronic myeloid leukemia targeted’ drug treatment of chronic myeloid leukemia (CML) and gastrointestinal stromal tumor (GIST) .(CML) and gastrointestinal stromal tumor (GIST) .

Most of these patients express a Bcr–Abl fusion protein Most of these patients express a Bcr–Abl fusion protein tyrosine kinase that is the basis of disease development and tyrosine kinase that is the basis of disease development and progression. progression.

GleevecGleevecTMTM targets this mutation and acts to block targets this mutation and acts to block progression.progression.

Drug development is due to advancement of the Drug development is due to advancement of the understanding of signaling and regulatory pathways of understanding of signaling and regulatory pathways of cancer through genomics.cancer through genomics.

-MacGregor, J; Tox Sci 2003-MacGregor, J; Tox Sci 2003

Variability & Toxic Variability & Toxic Response:Response:

GST and Tobacco SmokeGST and Tobacco Smoke Glutathione S-transferase (GST) Glutathione S-transferase (GST)

Metabolic enzymeMetabolic enzyme Participates in metabolic detoxification of Participates in metabolic detoxification of

benzo(a)pyrenebenzo(a)pyrene GST null donors are more sensitive to the GST null donors are more sensitive to the

induction of chromosomal aberrations due to induction of chromosomal aberrations due to tobacco smoketobacco smoke

GST null also has been linked to increased risk GST null also has been linked to increased risk of lung and bladder cancer in smokers.of lung and bladder cancer in smokers.

Knowledge of genotype may impact behavior.Knowledge of genotype may impact behavior. Biomarker of susceptibilityBiomarker of susceptibility

-Norppa, H. ; Mut Res, 2003-Norppa, H. ; Mut Res, 2003

Use of Genomics Within Use of Genomics Within the FDA and EPAthe FDA and EPA

Identification of susceptible populations Identification of susceptible populations Development of disease; drug and toxic responseDevelopment of disease; drug and toxic response

Development of biomarkersDevelopment of biomarkers Disease and drug safety; toxic exposure/effectDisease and drug safety; toxic exposure/effect

Mode of action informationMode of action information Gene expression profiles/fingerprintingGene expression profiles/fingerprinting Drug therapy; toxic exposure and responseDrug therapy; toxic exposure and response

BiomarkerBiomarker

“…“….a xenobiotically-induced variation .a xenobiotically-induced variation in cellular or biochemical in cellular or biochemical components or processes, components or processes, structures, or functions that is structures, or functions that is measurable in a biological system.”measurable in a biological system.”

--National Academy of National Academy of ScienceScience

The Exposure/Disease The Exposure/Disease PathwayPathway

Exposure Internal Dose

Biological Effective Dose

Early Biological

Effects

Clinical Disease

Altered Structure/Function

Exposure Biomarkers

Susceptibility Biomarkers

Effect Biomarkers

Source: Committee of Biological Markers, NRC 1987

FDA Pharmacogenomic FDA Pharmacogenomic Draft GuidelinesDraft Guidelines

Valid Biomarker if:Valid Biomarker if: It is measured in an analytical test with It is measured in an analytical test with

well established performance well established performance characteristics.characteristics.

An established scientific framework or An established scientific framework or body of evidence that elucidates the body of evidence that elucidates the physiologic, pharmacologic, toxicologic, physiologic, pharmacologic, toxicologic, or clinical significance of the test or clinical significance of the test results.results.

Example of valid biomarker: CYP450 Example of valid biomarker: CYP450

Cytochrome p450Cytochrome p450 Metabolizing enzymeMetabolizing enzyme Highly polymorphic-over 70 different alleles Highly polymorphic-over 70 different alleles

identifiedidentified Different alleles have different metabolizing Different alleles have different metabolizing

capabilitiescapabilities Impacts drug metabolism leading to differences in Impacts drug metabolism leading to differences in

effective dose, side effects and drug interactionseffective dose, side effects and drug interactions P450 2D6 P450 2D6

Activity is reduced in 7-10% of the Caucasian Activity is reduced in 7-10% of the Caucasian population, resulting in higher plasma concentration of population, resulting in higher plasma concentration of p450 2D6 metabolized drugs (e.g. some classes of p450 2D6 metabolized drugs (e.g. some classes of antidepressants)antidepressants)

Genomic screening can identify biomarker for Genomic screening can identify biomarker for individualized drug therapy.individualized drug therapy.

Use of Genomics Within Use of Genomics Within the FDA and EPAthe FDA and EPA

Identification of susceptible populations Identification of susceptible populations Development of disease; drug and toxic Development of disease; drug and toxic

responseresponse Development of biomarkersDevelopment of biomarkers

Disease and drug safety; toxic exposure/effectDisease and drug safety; toxic exposure/effect Mode of action informationMode of action information

Gene expression profiles/fingerprintingGene expression profiles/fingerprinting Drug therapy; toxic exposure and responseDrug therapy; toxic exposure and response

Mode of ActionMode of Action

The series of key events The series of key events that occurs during the that occurs during the

development of an development of an adverse toxicological adverse toxicological response, following response, following

exposure to a toxicant, exposure to a toxicant, which provides a which provides a

biologically plausible biologically plausible explanation of causality explanation of causality

for that toxic effect.for that toxic effect.

- - IPCS, 1999; NRC, IPCS, 1999; NRC, 20002000

ObservedObservedToxicityToxicity

Characteristic profileCharacteristic profileof gene of gene

expression/protein/expression/protein/metabolitemetabolite

Characterization and Characterization and elucidation of elucidation of mechanismmechanism

Gene Expression and Gene Expression and Mode of ActionMode of Action

Toxins/drugs can impact expression of Toxins/drugs can impact expression of genesgenes Alterations to normal function of cellular Alterations to normal function of cellular

pathways leads to toxicitypathways leads to toxicity ““fingerprints” of expression reflect fingerprints” of expression reflect

commonalities within mode of action: commonalities within mode of action: Classification through clustering (NIEHS Classification through clustering (NIEHS

‘toxchip’)‘toxchip’) Gene expression changes are a sensitive Gene expression changes are a sensitive

way to evaluate responseway to evaluate response Potential biomarkers of exposure/diseasePotential biomarkers of exposure/disease Drug discoveryDrug discovery

ToxChipToxChip

2,100 human genes2,100 human genes Involved in basic Involved in basic

cellular responsecellular response Involved in different Involved in different

types of toxic injurytypes of toxic injury Cellular pathways Cellular pathways

included:included:

Apoptosis Cell cycle control Cytochromes DNA replication and repair Estrogen responsive Heat shock proteins Kinases Oncogenes and tumor

suppressor genes Oxidative stress and redox

homeostasis P450’s Peroxisome proliferator

responsive Phosphatases Transcription Factors

Clustering and Toxicant IdentificationClustering and Toxicant Identification

MatchMatch

No Match

Group AGroup A

Group BGroup B

Group CGroup C

Known Agents

ToxicantSignature

PeroxisomePeroxisomeProliferatorsProliferators

Polycyclic AromaticPolycyclic AromaticHydrocarbonsHydrocarbonsOxidant StressorsOxidant Stressors

SuspectedToxicant

RawData

No Match

Identification of toxicologically Identification of toxicologically predictive gene sets using cDNA predictive gene sets using cDNA

microarraysmicroarrays

Russell S. Thomas, David R. Rank, Sharron G. Russell S. Thomas, David R. Rank, Sharron G. Penn, Gina M. Zastrow, Kevin R. Hayes, Kalyan Penn, Gina M. Zastrow, Kevin R. Hayes, Kalyan Pande, Edward Glover, Tomi Silander, Mark W. Pande, Edward Glover, Tomi Silander, Mark W. Craven, Janardan K. Reddy, Stevan B. Jovanovich Craven, Janardan K. Reddy, Stevan B. Jovanovich and Christopher A. Bradfieldand Christopher A. Bradfield

Molecular Pharmacology, 60:1189, 2001.Molecular Pharmacology, 60:1189, 2001.

Example mechanisms evaluated:Example mechanisms evaluated:

• Peroxisome proliferationPeroxisome proliferation

• Aryl hydrocarbon receptive agonistsAryl hydrocarbon receptive agonists

• Noncoplanar polychlorinated biphenylsNoncoplanar polychlorinated biphenyls

• InflammationInflammation

• HypoxiaHypoxia

Variation in expression of approximately 500 transcripts in 24 Variation in expression of approximately 500 transcripts in 24 experimental treatmentsexperimental treatments

From Thomas et al., Molecular From Thomas et al., Molecular Pharmacology, 2001Pharmacology, 2001

ConclusionsConclusions

• A diagnostic set of 12 liver gene transcript changes was A diagnostic set of 12 liver gene transcript changes was

identified to predict the five mechanisms.identified to predict the five mechanisms.

• The 12 transcripts included:The 12 transcripts included:

CYP1A2CYP1A2 FM05FM05 CYP4A14CYP4A14

IL-18IL-18 CUYP2B10CUYP2B10 CYP4A10CYP4A10

UnknownUnknown BHMTBHMT CYP2C29CYP2C29

CYP1A1CYP1A1 UnknownUnknown SAA1/2SAA1/2

• Only half of the changes in the diagnostic set were Only half of the changes in the diagnostic set were

previously described.previously described.

How does Genomics How does Genomics impact public policy?impact public policy?

Genomics may change who is “at risk” Genomics may change who is “at risk” by defining susceptible populationsby defining susceptible populations Identifying genetic polymorphismsIdentifying genetic polymorphisms Tightening of standards?Tightening of standards? Raises issue of ethical and legal Raises issue of ethical and legal

implicationsimplications

Language of RiskLanguage of RiskSignificant versus Negligible RiskSignificant versus Negligible Risk

StatuteStatute Risk MandateRisk Mandate

FIFRAFIFRA ““risks being less than benefits”risks being less than benefits”Balance risks, benefits, social and economic costsBalance risks, benefits, social and economic costsEfficacious, yet without “unreasonable risk to man or Efficacious, yet without “unreasonable risk to man or the environment”the environment”

FQPAFQPA ““reasonable certainty of no harm”reasonable certainty of no harm”Requires that tolerances be “safe” defined as Requires that tolerances be “safe” defined as “reasonable certainty that no harm will result from “reasonable certainty that no harm will result from aggregate exposure”aggregate exposure”Sets a uniform health based standard for riskSets a uniform health based standard for risk

Commission on Risk Assessment and Risk Management, 1996; EPA, 2002

Interpreting Statutory Risk Interpreting Statutory Risk LanguageLanguage

Legal Cases:Legal Cases: Ober v. Whitman, 2000Ober v. Whitman, 2000 ALA v. EPA, 1998ALA v. EPA, 1998 Lead Industries v. EPA, 1980Lead Industries v. EPA, 19801970 Senate Report: 1970 Senate Report: ““particularly sensitive citizens such as particularly sensitive citizens such as

bronchial asthmatics and bronchial asthmatics and emphysematics”emphysematics”

““ambient standard necessary to ambient standard necessary to protect…sensitive group rather than a protect…sensitive group rather than a single person in such a group.” single person in such a group.”

Current Standards: children, the Current Standards: children, the elderly, and pre-existing elderly, and pre-existing diseasedisease

PM Staff Paper Risk Assessment, 2003:PM Staff Paper Risk Assessment, 2003: Mortality: Non-accidental total, Mortality: Non-accidental total,

cardiovascular and respiratorycardiovascular and respiratory Morbidity: Hospital Admissions Morbidity: Hospital Admissions

for Cardiovascular and for Cardiovascular and Respiratory causesRespiratory causes

Symptomatic: increased Symptomatic: increased respiratory symptomsrespiratory symptoms

“Adverse Health Effects”“Sensitive or Susceptible Individuals or Groups”

Toxicogenomics and Toxicogenomics and Clean Air StandardsClean Air Standards

EPA sets ambient air quality EPA sets ambient air quality standards to protect from “adverse standards to protect from “adverse effects” in susceptible subpopulations effects” in susceptible subpopulations with an adequate margin of safety.with an adequate margin of safety.

Are gene expression changes Are gene expression changes “adverse effects”?“adverse effects”?

Do gene expression changes trigger Do gene expression changes trigger “adequate margin of safety”?“adequate margin of safety”?

Adopted from Marchant, G; 2003

Federal Clean Air Act Federal Clean Air Act (CAA)(CAA)

Clean Air Act -- Title I

Research, investigation, training, and other activities (§103)

Criteria Pollutants, “may reasonably be anticipated to endanger public health or

welfare” (§108)PM, SOx, NO2, CO, O3, and Lead

Hazardous Air Pollutants189 List established by Congress

(§112(b)(1))

• Promulgate primary and secondary air quality standards (§109)• Primary: “adequate margin of safety” (§109)• “sensitive or susceptible individuals or groups” from “adverse effects” (§108)

• coordinate and accelerate research, investigations…• cooperate with public and private agencies, institutions…• conduct investigations and research• establish technical advisory committees

• Health Effects Institute (NEI)• National Environmental Respiratory Center (NERC)• PM Research Centers• Advisory Committees

• “present…a threat of adverse human health effects” (§112(b))•Maximum Achievable Control Technology (MACT)• Feasible on technical and economic grounds

• Assessment of “residual risk” at a future time •Maximally Exposed Individual• 1/1,000,000 increased cancer (§112(f)(2)(A))

Human Health Risk Assessment Technology-Based Control Standard

Human Health Risk AssessmentAnnual Daily

PM10 50 µg/m3 150 µg/m3

PM2.5 15 µg/m3 65 µg/m3

National Ambient Air Quality Standard

National Research and Development

Benefits and future….Benefits and future….

Improve understanding of mechanism of Improve understanding of mechanism of action; pinpoint molecular targetaction; pinpoint molecular target Drug discovery and treatmentDrug discovery and treatment Regulatory standardsRegulatory standards

Predictive toxicology using databases; Predictive toxicology using databases; prioritize chemicals for testingprioritize chemicals for testing

Identification of quantification of Identification of quantification of susceptible populationssusceptible populations

Identification of biomarkers of chemical Identification of biomarkers of chemical exposure and effect.exposure and effect.

Challenges and Challenges and LimitationsLimitations

Assays must be reliable, rapid, accurateAssays must be reliable, rapid, accurate Need to recognize that gene expression is not equal to Need to recognize that gene expression is not equal to

functional or protein changes.functional or protein changes. Need to distinguish between normal gene response and Need to distinguish between normal gene response and

toxic response….are these methods predictive of toxicity?toxic response….are these methods predictive of toxicity? Standardization needed for genotype information and Standardization needed for genotype information and

database construction; sharing across agencies and database construction; sharing across agencies and research groupsresearch groups

Privacy, discrimination, stigma and psychological stress Privacy, discrimination, stigma and psychological stress issuesissues

Ethical, social and legal issues require active Ethical, social and legal issues require active involvement of stakeholdersinvolvement of stakeholders

““omics” is a powerful tool but should be considered on omics” is a powerful tool but should be considered on conjunction with traditional risk assessment practices.conjunction with traditional risk assessment practices.

Next time….Next time….

Review of the current risk Review of the current risk assessment processassessment process

How is genomics is influencing this How is genomics is influencing this process and key considerationsprocess and key considerations