National Institute of Environmental Health Sciences 04_2172 Gene-Environment Interactions in the Development of Complex Phenotypes Kenneth Olden, Ph.D.,

National Institute of Environmental Health SciencesNational Institute of Environmental Health Sciences

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Gene-Environment Interactions in the Gene-Environment Interactions in the Development of Complex PhenotypesDevelopment of Complex Phenotypes

Kenneth Olden, Ph.D., Sc.D.Kenneth Olden, Ph.D., Sc.D.

Principal Investigator Principal Investigator

Laboratory of Molecular CarcinogenesisLaboratory of Molecular Carcinogenesis

Cell Adhesion and Metastasis SectionCell Adhesion and Metastasis Section


National Institutes of Health, DHHSNational Institutes of Health, DHHS


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Dramatic change in scale and complexity of medical Dramatic change in scale and complexity of medical research.research.

Simplistic models/reductionist approaches versus holistic Simplistic models/reductionist approaches versus holistic or systems biology approaches.or systems biology approaches.

Genocentric versus gene-environment view of disease.Genocentric versus gene-environment view of disease.

Investments in pursuit of the genocentric view of disease Investments in pursuit of the genocentric view of disease has led to the development of powerful new technologies has led to the development of powerful new technologies and database resources.and database resources.


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The major challenge facing biomedical The major challenge facing biomedical researchers is to elucidate the interactive researchers is to elucidate the interactive relationship between genes and between relationship between genes and between genes and the environment.genes and the environment.

We have to go beyond descriptive studies by We have to go beyond descriptive studies by toxicologists and epidemiologists. toxicologists and epidemiologists.

The Human Genome and Haplotype Mapping Projects The Human Genome and Haplotype Mapping Projects have led to the development of powerful new tools to have led to the development of powerful new tools to conduct the kind of studies necessary to untangle conduct the kind of studies necessary to untangle complex interactions between genes and complex interactions between genes and environmental factors. environmental factors.


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The concept of gene-gene and gene-The concept of gene-gene and gene-environment interaction is not new. environment interaction is not new. About 74 years ago, Wright emphasized About 74 years ago, Wright emphasized such a relationship between biological such a relationship between biological endpoints and networks of genes and endpoints and networks of genes and environmental factors.environmental factors.


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Progress in science depends on new techniques, new Progress in science depends on new techniques, new discoveries and new ideas, probably in that order. discoveries and new ideas, probably in that order.

Sydney Brenner, 1980Sydney Brenner, 1980

The development and application of new technologies The development and application of new technologies in genomics, proteomics and metabolomics to in genomics, proteomics and metabolomics to environmental health research will dramatically environmental health research will dramatically improve our capacity to identify environmental improve our capacity to identify environmental agents that play a role in the development of breast agents that play a role in the development of breast cancer and other chronic diseases. cancer and other chronic diseases.


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Post-Genomic Post-Genomic EraEra


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EnvironmentalEnvironmentalExposuresExposures

HumanHumanHealth/DiseaseHealth/Disease

IntrinsicIntrinsicGeneticGenetic

SusceptibilitySusceptibility

Behavior/Age/Stage of DevelopmentBehavior/Age/Stage of Development


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““Genetics Loads the Gun, Genetics Loads the Gun, but Environment Pulls the but Environment Pulls the

Trigger”Trigger”

Judith SternJudith SternProfessor of Nutrition and Internal Professor of Nutrition and Internal MedicineMedicineUniversity of California at DavisUniversity of California at Davis


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““ENVIRONMENT” ENVIRONMENT”

includes:includes: Industrial Industrial

chemicalschemicals Agricultural Agricultural

chemicalschemicals Physical agents Physical agents

(e.g., heat, (e.g., heat, radiation)radiation)

By-products of By-products of combustion and combustion and industrial industrial processes (e. g. processes (e. g. dioxin)dioxin)

Foods and nutrientsFoods and nutrients Prescription drugsPrescription drugs Lifestyle choices Lifestyle choices

and substance and substance abuseabuse

Social and Social and economic factorseconomic factors

Biological agentsBiological agents


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Studies are now being reported that “blow Studies are now being reported that “blow away” the myth that “bad” genes are away” the myth that “bad” genes are responsible for the majority of human responsible for the majority of human morbidity and mortality.morbidity and mortality.

Cancer: about 2/3 is non-genetic Cancer: about 2/3 is non-genetic (NEJM 343(2):78-85, 2000(NEJM 343(2):78-85, 2000; ; Lichtenstein, et al; Int J Cancer 83:743-749, 1999; Verkasalo et al)Lichtenstein, et al; Int J Cancer 83:743-749, 1999; Verkasalo et al)

Parkinson’s Disease: about 85% is non-genetic Parkinson’s Disease: about 85% is non-genetic (JAMA 281(4):(JAMA 281(4):

341-346, 1999; Tanner, et al)341-346, 1999; Tanner, et al)

Cardiovascular Disease: about 90% of patients with heartCardiovascular Disease: about 90% of patients with heart

disease have at least one or more of the major risk factorsdisease have at least one or more of the major risk factors(JAMA, Aug 20, 2003; Greenland et al)(JAMA, Aug 20, 2003; Greenland et al)

Autoimmune Diseases: about 2/3 is non-genetic Autoimmune Diseases: about 2/3 is non-genetic (EHP 107:(EHP 107:

667-672, 1999; Bishop et al)667-672, 1999; Bishop et al)


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““Genes are only a small part of our make-up; Genes are only a small part of our make-up; the the

environment has a spectacular impact”environment has a spectacular impact”

Eric LanderEric Lander Director, MIT Center for Genome ResearchDirector, MIT Center for Genome Research

Washington Fax Washington Fax

9/25/01 9/25/01


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Evolution of the Concept of Evolution of the Concept of Gene-Environment InteractionGene-Environment Interaction

Garrod, 1902Garrod, 1902 Wright, 1932Wright, 1932 Olden, 1993; Olden & Guthrie, 2000; Olden, 1993; Olden & Guthrie, 2000;

Olden Olden etet al.al., 2001, 2001


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Evidence for the role of the environment in the Evidence for the role of the environment in the development of complex diseases is so compelling development of complex diseases is so compelling that the following quotes have been reported in the that the following quotes have been reported in the scientific literature.scientific literature.

““The epidemiological evidence accumulated to date The epidemiological evidence accumulated to date indicates that environmental exposures, broadly indicates that environmental exposures, broadly defined to include lifestyle factors, are responsible for defined to include lifestyle factors, are responsible for most cancers.”most cancers.”

Rothman Rothman etet alal. (2001), . (2001), Biochem Biophys ActaBiochem Biophys Acta 1471:C1-C10 1471:C1-C10

““New data now being reported “blow away” the myth New data now being reported “blow away” the myth that “bad genes” are responsible for the majority of that “bad genes” are responsible for the majority of human morbidity and mortality.” human morbidity and mortality.”

Olden (2004), Olden (2004), Current GenomicsCurrent Genomics 5:1-6 5:1-6


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Genes are relevant to the Genes are relevant to the development of most chronic development of most chronic diseases, but are not determinant…diseases, but are not determinant…they load the gunthey load the gun!!


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Studies on environmental risk factors for Studies on environmental risk factors for disease is confounded by gene-environment disease is confounded by gene-environment interactions.interactions.

Such interactions imply that at the molecular Such interactions imply that at the molecular level, there is synergy between a gene product level, there is synergy between a gene product and the environmental insult, resulting in a and the environmental insult, resulting in a greater than additive-effect on risk. greater than additive-effect on risk.


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Challenges presented by complex diseases Challenges presented by complex diseases versus infectious diseasesversus infectious diseases

Infectious diseases are characterized by relatively short Infectious diseases are characterized by relatively short latency periods between exposure and onset of illness.latency periods between exposure and onset of illness.

Complex diseases are characterized by long latency Complex diseases are characterized by long latency periods between exposure and disease development.periods between exposure and disease development.

Infectious diseases are usually caused by single agents Infectious diseases are usually caused by single agents that can be identified, isolated, mechanism of action that can be identified, isolated, mechanism of action elucidated, and effective prevention or treatment elucidated, and effective prevention or treatment strategies developed.strategies developed.

Complex diseases are caused by multiple interactive Complex diseases are caused by multiple interactive agents that are difficult to identify, isolate, and agents that are difficult to identify, isolate, and elucidate mechanisms. elucidate mechanisms.


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What are some of the practical problems What are some of the practical problems related to the conduct of studies to related to the conduct of studies to elucidate interactions between genes and elucidate interactions between genes and the environment? the environment?

Development of a standard definition of the Development of a standard definition of the environment. environment.

Development of standard metrics and more Development of standard metrics and more accurate methodologies to assess exposure. accurate methodologies to assess exposure.

Development of statistical approaches to Development of statistical approaches to model multiple interactive components that model multiple interactive components that make modest contributions to the phenotype. make modest contributions to the phenotype.


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Evolution of Toxicology and EnvironmentalEvolution of Toxicology and Environmental

Health Sciences Health Sciences

Historically, Historically, the effort to understand the interplay the effort to understand the interplay between the environmentbetween the environment and human health has and human health has been considered primarily the domain of toxicology.been considered primarily the domain of toxicology.

Toxicologists have relied heavily on relatively well-Toxicologists have relied heavily on relatively well-established approachesestablished approaches, especially long-term rodent , especially long-term rodent bioassays that detect endpoints of late disease (e.g., bioassays that detect endpoints of late disease (e.g., tumor development) or clinical signs of toxicity.tumor development) or clinical signs of toxicity.

However, However, the field of toxicology has recently begun the field of toxicology has recently begun the process of reinventing itselfthe process of reinventing itself, in light of the rapid , in light of the rapid state of technological and conceptual change in state of technological and conceptual change in molecular biology and genomics. molecular biology and genomics.

Toxicology is now truly an interdisciplinary science. Toxicology is now truly an interdisciplinary science.


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Modified from the Herald Sun, Feb 17, 2001

This represents the use of This represents the use of genes as a bait to “fish-out” genes as a bait to “fish-out” environmental risk factors.environmental risk factors.


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Vision of environmental health research:Vision of environmental health research:

To sort out the way that genes and the environment To sort out the way that genes and the environment interact to cause common diseases over the next 10 interact to cause common diseases over the next 10 to 20 years. to 20 years.


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To achieve the vision of Environmental Health To achieve the vision of Environmental Health Research, the following databases will have to be Research, the following databases will have to be

developed:developed:

A DNA database to determine A DNA database to determine Genetic DiversityGenetic Diversity in the in the population…the EGP, the population…the EGP, the International SNPs Consortium International SNPs Consortium and and Hap Map ProjectHap Map Project..

A database on the A database on the Chemical Effects on Biological Systems Chemical Effects on Biological Systems (NCT).(NCT).

A prospective A prospective database of environmental exposuredatabase of environmental exposure (e.g., (e.g., dietary behavior, occupation, etc.)…the NIH Family Study.dietary behavior, occupation, etc.)…the NIH Family Study.

A database identifying A database identifying all the metabolitesall the metabolites (the (the so-called so-called “parts“parts listlist;” e.g., fatty acids, sugars, amino acids) ;” e.g., fatty acids, sugars, amino acids) generated by the generated by the cell…NIH Road Map Initiative. cell…NIH Road Map Initiative.


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The Environmental Genome ProjectThe Environmental Genome Project

Kaiser, 1997 (Kaiser, 1997 (ScienceScience 298:569-570) 298:569-570) Brown & Hartwell, 1998 (Brown & Hartwell, 1998 (Nature GeneticsNature Genetics

18:91-93)18:91-93) Olden & Wilson, 2000 (Olden & Wilson, 2000 (Nature Review Nature Review

GeneticsGenetics

1:149-153)1:149-153)


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The Key Objective of the The Key Objective of the Environmental Genome Project Environmental Genome Project is to Identify Alleles that is to Identify Alleles that Confer Susceptibility to Confer Susceptibility to Environmental Agents Environmental Agents


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The Search for Susceptibility GenesThe Search for Susceptibility Genes Environmental Genome Project (candidate gene Environmental Genome Project (candidate gene

approach) approach) ScienceScience 278:569-570, 1997 278:569-570, 1997Nature GeneticsNature Genetics 18:91-93, 1998 18:91-93, 1998Nature Reviews GeneticsNature Reviews Genetics 1:149-153, 2000 1:149-153, 2000Science 300Science 300:563, 2003 :563, 2003 Molecular InterventionMolecular Intervention 4:147-156, 2004 4:147-156, 2004Genome ResearchGenome Research 14:1821-1831, 2004 14:1821-1831, 2004

Single Nucleotide Polymorphism Project Single Nucleotide Polymorphism Project ScienceScience 278:1580-1581, 1997 278:1580-1581, 1997


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The Specific Goals of the The Specific Goals of the Environmental Genome Project Environmental Genome Project

are:are: To To develop a repository of DNA sequencesdevelop a repository of DNA sequences that that

represent the U.S. population.represent the U.S. population. To To identify various polymorphismsidentify various polymorphisms (i.e. genetic (i.e. genetic

alterations) in specific genes.alterations) in specific genes. To determine which of the various To determine which of the various

polymorphisms are functionally important.polymorphisms are functionally important. To determine which of the various To determine which of the various

polymorphisms are associated with specific polymorphisms are associated with specific diseases based on molecular epidemiology diseases based on molecular epidemiology studies.studies.


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The key objectives of the The key objectives of the Mouse Genomics Centers are Mouse Genomics Centers are

to: to:

Create polymorphic variations in Create polymorphic variations in candidate genes similar to those candidate genes similar to those discovered in the EGPdiscovered in the EGP

Provide the transgenic mice to Provide the transgenic mice to researchers upon request. researchers upon request.


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Use of Transgenic Approaches for Use of Transgenic Approaches for Modeling of Gene-Environment Modeling of Gene-Environment

InteractionsInteractions

As disease susceptibility genes are As disease susceptibility genes are discovered, one can create genetically discovered, one can create genetically manipulatable mouse models responsive to manipulatable mouse models responsive to specific environmental agents. specific environmental agents.

The consequences of the inappropriate The consequences of the inappropriate expression or inactivation of candidate expression or inactivation of candidate susceptibility genes can be functionally susceptibility genes can be functionally validated in vivo using the mouse as a model validated in vivo using the mouse as a model system. system.


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Mouse Haplotype Mouse Haplotype Mapping ProjectMapping Project

Create genetic variation maps of the Create genetic variation maps of the

15 most commonly used mouse strains.15 most commonly used mouse strains.


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National Center for National Center for ToxicogenomicsToxicogenomics

The National Center was developed to make toxicity The National Center was developed to make toxicity testing faster, cheaper, more informative, and less testing faster, cheaper, more informative, and less dependent on the use of animals.dependent on the use of animals.

Logic: exposure to a toxic substance should alter the Logic: exposure to a toxic substance should alter the expression of specific genes, proteins, and or expression of specific genes, proteins, and or metabolites that play a role in the development of the metabolites that play a role in the development of the toxic response.toxic response.

Gene, protein, and metabolite profiles reveal much Gene, protein, and metabolite profiles reveal much about the cell. If a drug or environmental agent is about the cell. If a drug or environmental agent is toxic to the cell or tissue, metabolism will be affected. toxic to the cell or tissue, metabolism will be affected.


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Toxicogenomics is a “systems toxicology” Toxicogenomics is a “systems toxicology” approach that combines the following approach that combines the following

features to elucidate gene-environment features to elucidate gene-environment interaction:interaction:

Genome-scale analysis of RNA expression Genome-scale analysis of RNA expression (transcriptomics)(transcriptomics)

Cell and tissue-wide analysis of protein Cell and tissue-wide analysis of protein expression, expression,

structure and function (proteomics)structure and function (proteomics) Metabolite profiling (metabolomics)Metabolite profiling (metabolomics) InformaticsInformatics Conventional toxicology/pathology Conventional toxicology/pathology


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Definition of Systems Definition of Systems Biology:Biology:

Systems Biology is the study of complex Systems Biology is the study of complex biological interactions using approaches biological interactions using approaches appropriate for monitoring all relevant appropriate for monitoring all relevant biological reactions (events) biological reactions (events) simultaneously. simultaneously.


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The key objective of the The key objective of the toxicogenomics effort is to develop toxicogenomics effort is to develop a database on chemical effects on a database on chemical effects on biological systems. biological systems.


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The major goals of the National The major goals of the National Center for ToxicogenomicsCenter for Toxicogenomics

To promote the development and application To promote the development and application of gene, protein and metabolite expression of gene, protein and metabolite expression technologies in environmental health technologies in environmental health research.research.

To develop a public database of the chemical To develop a public database of the chemical effects on biological systems. effects on biological systems.

To develop biomarkers of toxicity.To develop biomarkers of toxicity. To elucidate mechanisms of toxicity. To elucidate mechanisms of toxicity.


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The major goals of the National The major goals of the National Center for Toxicogenomics Center for Toxicogenomics

(continued)(continued)

Elucidate the role of genetic variation in Elucidate the role of genetic variation in susceptibility to toxic injury.susceptibility to toxic injury.

Improve computational and analytical Improve computational and analytical methods to analyze gene expression, protein methods to analyze gene expression, protein and metabolite expression, and protein and metabolite expression, and protein structure and function.structure and function.

Provide a foundation for hypothesis-driven Provide a foundation for hypothesis-driven research. research.


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One Postdoc-OneProtein-One-Pathway One Postdoc-OneProtein-One-Pathway Approach for Analysis of Molecular Approach for Analysis of Molecular

InteractionsInteractions


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Looking at single markers (e.g., mRNA or Looking at single markers (e.g., mRNA or protein) will have a limited predictive power, protein) will have a limited predictive power, which highlights the need for an approach which highlights the need for an approach based on many biomarkers; i.e., a gene or based on many biomarkers; i.e., a gene or protein signature pattern.protein signature pattern.

The functional annotation for the genes and The functional annotation for the genes and proteins expressed will provide insight into proteins expressed will provide insight into biological mechanisms and suggest possible biological mechanisms and suggest possible targets for chemoprevention. targets for chemoprevention.


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Polymorphisms in Environmental ResponsePolymorphisms in Environmental ResponseGenes Can Modify an Individual’s Risk for Genes Can Modify an Individual’s Risk for

DiseaseDisease


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Summary: Summary: Better understanding of gene-gene and gene-environment Better understanding of gene-gene and gene-environment

interactions will enable us to determine the causes of common interactions will enable us to determine the causes of common diseases, identify high risk individuals, and devleop effective diseases, identify high risk individuals, and devleop effective prevention strategies.prevention strategies.

Genes do not function in isolation; they respond to internal and Genes do not function in isolation; they respond to internal and external signals.external signals.

Most common diseases are likely caused by genes in combination Most common diseases are likely caused by genes in combination with the environment.with the environment.

The elucidation of gene-environment interactions will require the The elucidation of gene-environment interactions will require the use of a variety of complementary techniques, including in vitro use of a variety of complementary techniques, including in vitro analysis, mouse models, and human data. analysis, mouse models, and human data.


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ConclusionsConclusions

To make progress on understanding gene-gene and gene-To make progress on understanding gene-gene and gene-environment interactions, it will be important to address environment interactions, it will be important to address

thethefollowing issues:following issues: Agreement on a standard definition of the environment.Agreement on a standard definition of the environment.

Development of standard measures for the environment, Development of standard measures for the environment, particularly the social/behavioral environment.particularly the social/behavioral environment.

Development of innovative technologies to measure Development of innovative technologies to measure environmental exposure. environmental exposure.

Documents

National Institute of Environmental Health Sciences 04_2172 Gene-Environment Interactions in the Development of Complex Phenotypes Kenneth Olden, Ph.D.,