ENV 593: Session II October 14, 2004

ENV 593:Session IIOctober 14, 2004 Genomics and Public Health Policy

Genomic Information Genetic variability and Susceptible populations Ecogenetics DNA Pharmacogenomics Gene expression patterns in response to drugs and toxins RNA Toxicogenomics Protein expression profiles in response to toxins/drugs Proteomics proteins Metabolite expression patterns in response to toxins/drugs Metabolomics metabolites

Major Chemical Laws in US EPA Air pollutants Clean Air Act, 1970 Water pollutants Federal Water Pollution Control Act 1972 Drinking water Safe Drinking Water Act 1972 Pesticides Fungicide, Insecticides and Rodenticides Act (FIFRA), 1972; Food Quality Protection Act (FGPA) 1996 Toxic Chemicals Toxic Substance Control Act (TSCA) 1976 Hazardous Waste Resource conservation and Recovery Act (RCRA) 1976 OSHA Workplace Occupational Safety and Health (OSH) Act 1970 FDA Foods, Drugs and Cosmetics FDC Acts 1906, 1938, 1962, 1977 FDA modernization Act 1997

Genomics How are the regulatory agencies addressing and incorporating into practices and policies the information generated by genomic methods?

Genomics and Public Health Policy • FDA-U.S. Food and Drug Administration • Drug and food safety • Changes in FDA approval consideration to address pharmacogenomic data? • EPA-Environmental Protection Agency • Protect human health and the environment • Develop and enforce regulations • Exposure standards • Alterations in regulations or standards due to toxicogenomic data?

Genomics and the FDA “Pharmacogenomics is a new field but we intend to do all we can to use it to promote the development of medicine….it holds great promise to shed scientific light on the often risky and costly process of drug development, and to provide greater confidence about the risks and benefits of drugs.” FDA Commissioner Mark B McClellan, when releasing the new pharmacogenomic draft guidelines for the FDA.

FDA and Genomics:Pharmacogenomic Data • Recognizes the potential ability to identify sources of inter-individual variability in drug response (both efficacy and toxicity) • Considers the field in the early developmental stage • Genomic data in isolation, not enough to determine regulations • Use of genomics must demonstrate a well-accepted mechanistic and clinical significance

Genomics and the EPA:Interim Policy • Encourages and supports continued genomic research. • Limited use of genomics while the Agency gains experience in assessing quality, accuracy and reproducibility and relevance of the data. • Genomics data alone are currently insufficient as a basis for risk assessment and management decisions. • May be used in a “weight-of-evidence” approach.

Use of Genomics Within the FDA and EPA • Identification of susceptible populations • Development of disease; drug and toxic response • Development of biomarkers • Disease and drug safety; toxic exposure/effect • Mode of action information • Gene expression profiles/fingerprinting • Drug therapy; toxic exposure and response

Susceptible Populations • Arises from human genetic variability • Human Genome Project • found variations at approx. 1/1000 base pairs • >1 million genetic differences between any two individuals • Genetic Polymorphisms • Single nucleotide polymorphism (SNP) • A variant in the sequence of DNA found in >1% of the population • >3 million candidate SNPs identified to date • estimated that there are ~11 million SNPs • Prevalence is often found to differ between ethnic groups

Genotypes to Phenotypes Gene variant Subtle change in protein function Change in biological response

* Genetics, Age, Health Status, Exposure History General Population * Sensitive Subpopulation Number of Individuals Adverse Response Human Variability Genetics is one factor contributing to overall variability between individuals adapted from Eaton, 2004

Variability & Drug Development • Genotype specific Drugs • FDA has approved several drugs designed for individuals with a specific genotype or protein expression level. • GleevecTM • ‘targeted’ drug treatment of chronic myeloid leukemia (CML) and gastrointestinal stromal tumor (GIST) . • Most of these patients express a Bcr–Abl fusion protein tyrosine kinase that is the basis of disease development and progression. • GleevecTM targets this mutation and acts to block progression. • Drug development is due to advancement of the understanding of signaling and regulatory pathways of cancer through genomics. -MacGregor, J; Tox Sci 2003

Variability & Toxic Response:GST and Tobacco Smoke • Glutathione S-transferase (GST) • Metabolic enzyme • Participates in metabolic detoxification of benzo(a)pyrene • GST null donors are more sensitive to the induction of chromosomal aberrations due to tobacco smoke • GST null also has been linked to increased risk of lung and bladder cancer in smokers. • Knowledge of genotype may impact behavior. • Biomarker of susceptibility -Norppa, H. ; Mut Res, 2003

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

Early Biological Effects Altered Structure/Function Internal Dose Biological Effective Dose Clinical Disease Exposure ExposureBiomarkers Susceptibility Biomarkers Effect Biomarkers The Exposure/Disease Pathway Source: Committee of Biological Markers, NRC 1987

FDA Pharmacogenomic Draft Guidelines • Valid Biomarker if: • It is measured in an analytical test with well established performance characteristics. • An established scientific framework or body of evidence that elucidates the physiologic, pharmacologic, toxicologic, or clinical significance of the test results. • Example of valid biomarker: CYP450

Cytochrome p450 • Metabolizing enzyme • Highly polymorphic-over 70 different alleles identified • Different alleles have different metabolizing capabilities • Impacts drug metabolism leading to differences in effective dose, side effects and drug interactions • P450 2D6 • Activity is reduced in 7-10% of the Caucasian population, resulting in higher plasma concentration of p450 2D6 metabolized drugs (e.g. some classes of antidepressants) • Genomic screening can identify biomarker for individualized drug therapy.

The series of key events that occurs during the development of an adverse toxicological response, following exposure to a toxicant, which provides a biologically plausible explanation of causality for that toxic effect. - IPCS, 1999; NRC, 2000 Mode of Action Observed Toxicity Characteristic profile of gene expression/protein/ metabolite Characterization and elucidation of mechanism

Gene Expression and Mode of Action • Toxins/drugs can impact expression of genes • Alterations to normal function of cellular pathways leads to toxicity • “fingerprints” of expression reflect commonalities within mode of action: • Classification through clustering (NIEHS ‘toxchip’) • Gene expression changes are a sensitive way to evaluate response • Potential biomarkers of exposure/disease • Drug discovery

2,100 human genes Involved in basic cellular response Involved in different types of toxic injury Cellular pathways 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 ToxChip

Clustering and Toxicant Identification Known Agents Suspected Toxicant Polycyclic Aromatic Hydrocarbons Peroxisome Proliferators Oxidant Stressors Raw Data Group A Toxicant Signature Group B Group C No Match No Match Match

Identification of toxicologically predictive gene sets using cDNA microarrays Russell S. Thomas, David R. Rank, Sharron G. Penn, Gina M. Zastrow, Kevin R. Hayes, Kalyan Pande, Edward Glover, Tomi Silander, Mark W. Craven, Janardan K. Reddy, Stevan B. Jovanovich and Christopher A. Bradfield Molecular Pharmacology, 60:1189, 2001.

Example mechanisms evaluated: • Peroxisome proliferation • Aryl hydrocarbon receptive agonists • Noncoplanar polychlorinated biphenyls • Inflammation • Hypoxia

Variation in expression of approximately 500 transcripts in 24 experimental treatments From Thomas et al., Molecular Pharmacology, 2001

Conclusions • A diagnostic set of 12 liver gene transcript changes was identified to predict the five mechanisms. • The 12 transcripts included:CYP1A2 FM05 CYP4A14 IL-18 CUYP2B10 CYP4A10 Unknown BHMT CYP2C29 CYP1A1 Unknown SAA1/2 • Only half of the changes in the diagnostic set were previously described.

How does Genomics impact public policy? • Genomics may change who is “at risk” by defining susceptible populations • Identifying genetic polymorphisms • Tightening of standards? • Raises issue of ethical and legal implications

Language of RiskSignificant versus Negligible Risk Commission on Risk Assessment and Risk Management, 1996; EPA, 2002

Interpreting Statutory Risk Language “Sensitive or Susceptible Individuals or Groups” Legal Cases: • Ober v. Whitman, 2000 • ALA v. EPA, 1998 • Lead Industries v. EPA, 1980 1970 Senate Report: • “particularly sensitive citizens such as bronchial asthmatics and emphysematics” • “ambient standard necessary to protect…sensitive group rather than a single person in such a group.” Current Standards: children, the elderly, and pre-existing disease PM Staff Paper Risk Assessment, 2003: • Mortality: Non-accidental total, cardiovascular and respiratory • Morbidity: Hospital Admissions for Cardiovascular and Respiratory causes • Symptomatic: increased respiratory symptoms “Adverse Health Effects”

Toxicogenomics and Clean Air Standards • EPA sets ambient air quality standards to protect from “adverse effects” in susceptible subpopulations with an adequate margin of safety. • Are gene expression changes “adverse effects”? • Do gene expression changes trigger “adequate margin of safety”? Adopted from Marchant, G; 2003

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 Pollutants 189 List established by Congress (§112(b)(1)) • coordinate and accelerate research, investigations… • cooperate with public and private agencies, institutions… • conduct investigations and research • establish technical advisory committees National Research and Development • Promulgate primary and secondary air quality standards (§109) • Primary: “adequate margin of safety” (§109) • “sensitive or susceptible individuals or groups” from “adverse effects” (§108) Human Health Risk Assessment • “present…a threat of adverse human health effects” (§112(b)) • Maximum Achievable Control Technology (MACT) • Feasible on technical and economic grounds Technology-Based Control Standard • Health Effects Institute (NEI) • National Environmental Respiratory Center (NERC) • PM Research Centers • Advisory Committees AnnualDaily PM10 50 µg/m3 150 µg/m3 PM2.5 15 µg/m3 65 µg/m3 National Ambient Air Quality Standard • 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 Federal Clean Air Act (CAA)

Benefits and future…. • Improve understanding of mechanism of action; pinpoint molecular target • Drug discovery and treatment • Regulatory standards • Predictive toxicology using databases; prioritize chemicals for testing • Identification of quantification of susceptible populations • Identification of biomarkers of chemical exposure and effect.

Challenges and Limitations • Assays must be reliable, rapid, accurate • Need to recognize that gene expression is not equal to functional or protein changes. • Need to distinguish between normal gene response and toxic response….are these methods predictive of toxicity? • Standardization needed for genotype information and database construction; sharing across agencies and research groups • Privacy, discrimination, stigma and psychological stress issues • Ethical, social and legal issues require active involvement of stakeholders • “omics” is a powerful tool but should be considered on conjunction with traditional risk assessment practices.

Next time…. • Review of the current risk assessment process • How is genomics is influencing this process and key considerations

ENV 593: Session II October 14, 2004