The NIEHS Environmental Genome Project: Enabling Studies of Gene-Environment Interaction. Douglas A. Bell, Ph.D. Environmental Genomics Section National Institute of Environmental Health Sciences Professor, Dept of Epidemiology UNC School of Public Health.
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Douglas A. Bell, Ph.D.
Environmental Genomics Section
National Institute of Environmental Health Sciences
Professor, Dept of Epidemiology
UNC School of Public Health
Modulation of Response to Exposure
Genetic Modulation of Exposure, Damage, and Biological Response
Genetic Modulation of Exposure Risk
1- 50 Packyears Smoking
Bell et al, JNCI 85:1559,1993
Phenotypic variation in response due to:
Timing of Exposure
Range of Enzyme Activity in Human Populations
No Phenotypic Polymorphism
Examples: N-Acetyltransferase 2, GSTM1, CYP2D6
Human Genetic Susceptibility
(Extrapolation to humans)
Animal toxicology (dose/response)
Effects in Humans ?
Risk Assessment Process
Replace default assumptions about variability
Cancer - Yes/No
Extrapolate to Humans
Susceptible human subgroup?
Thus, a protective allele for one chemical may convey risk for a different chemical. Similarly one organ system may be protected at the risk of another; e.g. immune system response could increase DNA damage or neurotoxicity.
GST Theta 1 (GSTT1) - One gene with 2 effects
(also Methyl chloride)
Effects of polymorphism dependent on chemical and toxicity pathway:
The Effect of GSTT1 Genotype on Metabolism of Methyl Chloride
T1 Null No Metabolism
Measure exhaled methyl chloride
T1 + Metabolism to DNA reactive forms
From Lof, A. et al, Pharmacogenetics 10:645, 2000.
Background: Ethylene oxide –hemoglobin adducts are a good measure of smoking exposure in blood.
Experiment: To test if GST genotypes modulated effects of smoking in erythrocytes, we measured ethylene oxide hemoglobin adducts in freshly collected human erythrocytes from nonsmokers and smokers.
Fennel et al CEBP 9:705,2000
Disease Risk Characterization
Effects in Populations
Coding region changes:
aa subs, deletions, stops.
Regulatory polymorphisms alter transcription factor binding and mRNA/protein level.
Polymorphism and Function
Gene Deletions, Duplications
e.g. GSTM1, CYP2D6
Phenotype—Directed Approach to Find SNPs That Alter Gene Expression Level
TGGGCCCCGCCCCCTTATGTAGGGTATAAAGCCC …. CCCGTCACC ATG
Liu, X. et al
Resequencing Projects: Describing candidate gene polymorphisms in diverse populations.
~9 million SNPs in dbSNP now,
by 2006, expect ~20 million human SNPs.
Haplotype Map: Describing which SNPs occur together on chromosomes in populations (haplotypes).
SNP data is entered into the NCBI dbSNP database
Bioinformatic Tools Available For Picking Haplotype Tagging SNPs
Resequencing of candidate environmental disease genes
2. High resolution candidate gene studies.
Bioinformatic Identification of SNPs That Affect Gene Expression
p53 inducible genes contain p53
Following UV exposure
p53 binds RE of target gene.
Using bioinformatic methods, identify SNPs that disrupt p53 response elements.
Test SNPs Against p53 Response Element Consensus
Build Table of
All Promoter SNPs
DNA ambiguity code
R = A or G
Y = C or T
W = A or T
Mismatch with consensus
Do SNPs in putative p53 response elements affect p53 induced expression in Saos2 cells?
Saos2 Osteosarcoma Cells (p53 null)
Mike Resnick, Alberto Inga, Daniel Menendez
Douglas A. Bell
Gary S. Pittman
Merrill ‘Chip’ Miller, III
Daniel J. Tomso
Michelle R. Campbell
Phylogenetic Footprinting of NRF2/ARE Genes
~4000 Mouse ARE containing genes
~4000 Human ARE containing genes
~2100 Rat ARE containing genes