Predicting Environmental Disease Susceptibility
with Genetic Polymorphism Data: Are We There Yet ?
Jun-Yan Hong
University of Medicine and Dentistry of New Jersey
hongju@umdnj.edu
5th ICOEM, Dujiangyan, April 6-10, 2010
The Environment Genome Project (NIEHS, NIH, 1997)

Advancement of molecular biology and human genome
project provide new opportunities to understand the
genetic basis for individual difference in susceptibility to
environmental exposure.

Human disease is the consequence of both genetic
susceptibility and environmental exposure.

By identifying the genes and allelic variants that affect
individual response to environmental toxins, we can
better predict health risks and develop environmental
policies to protect the most vulnerable subgroups of the
population.
Two Major Problems in Early Genetic
Susceptibility Studies

Small sample size, including low allelic distribution
frequenies of given SNPs in certain ethnic groups
(statistical power)

While the functions of candidate gene(s) were well
known, there was little considerations on the
functionality of the related SNPs.
CYP2A6 Gene Deletion and Lung Cancer Risk
CYP2A6 Healthy controls Lung cancer cases
genotype
(%)
(%)
OR
95% CI
wild-type
27 (13.4)
59 (24.0)
1.00
wild/del
27 (15.9)
20 (8.1)
0.29
0.14-0.59*
del/del
9 (4.5)
5 (2.0)
0.25
0.08-0.83*
There were 246 cases and 201 controls, in total. Information on smoking history was not
provided.
*significantly different from healthy controls (p<0.05)
Miyamoto et al., Biochem. Biophys. Res. Comm., 1999
Frequency Distribution among Esophageal Cancer
Cases and Controls and Relative Risks Associated
with Genotype Variants of CYP2E1
CYP2E1
Frequency
Cases
Controls
RR
95% CI
Dral
Homozygous Wild-type
Heterozygous
Homozygous Variant
25
15
8
31
17
2
1. 0
1. 1
5. 0
[0.45,2.7]
[0.95,16]
Rsal
Homozygous Wild-type
Heterozygous
Homozygous Variant
30
11
7
33
16
1
1. 0
0. 76
7. 7
[0.30,1.9]
[0.87,68]
Hildesheim et al 1995
Environmental Health Perspectives, 105 (Suppl. 4)
759-762, 1997
International Symposium on Environmental
Genomics and Pharmacogenetics, May1417,2001, Shanghai, China, Sponsored by NIEHS
and NCI

He XY, Shen J, Hu WY, Ding X, Lu AY, Hong JY.
Identification of Val117 and Arg372 as critical amino acid residues for the activity
difference between human CYP2A6 and CYP2A13 in coumarin 7-hydroxylation.
Arch Biochem Biophys. 2004;427:143.

He XY, Shen J, Ding X, Lu AY, Hong JY.
Identification of critical amino acid residues of human CYP2A13 for the metabolic
activation of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, a tobacco-specific
carcinogen. Drug Metab Dispos. 2004;32:1516.

He XY, Tang L, Wang SL, Cai QS, Wang JS, Hong JY.
Efficient activation of aflatoxin B1 by cytochrome P450 2A13, an enzyme
predominantly expressed in human respiratory tract. Int J Cancer. 2006;118:2665.

Wang SL, He XY, Shen J, Wang JS, Hong JY.
The missense genetic polymorphisms of human CYP2A13: functional
significance in carcinogen activation and identification of a null allelic variant.
Toxicol Sci. 2006;94:38.

Han JF, He XY, Herrington JS, White LA, Zhang J, and Hong JY.
Metabolism of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) by
Human CYP1B1 Genetic Variants. Drug Metab Dispos. 2008;36:745.

Han JF, Wang SL, He XY, Liu CY, Hong JY.
Effect of genetic variation on human cytochrome p450 reductase-mediated
paraquat cytotoxicity. Toxicol Sci. 2006;91:42.

Wang SL, Han JF, He XY, Wang XR, Hong JY.
Genetic variation of human cytochrome p450 reductase as a potential
biomarker for mitomycin C-induced cytotoxicity. Drug Metab Dispos.
2007;35:176.

You WC, Hong JY, Zhang L, Pan KF, Pee D, Li JY, Ma JL, Rothman N,
Caporaso N, Fraumeni JF Jr, Xu GW, Gail MH.
Genetic polymorphisms of CYP2E1, GSTT1, GSTP1, GSTM1, ALDH2, and
ODC and the risk of advanced precancerous gastric lesions in a Chinese
population. Cancer Epidemiol Biomarkers Prev. 2005;14:451.

Misra A, Hong JY, Kim S.
Multiplex genotyping of cytochrome P450 single-nucleotide polymorphisms
by use of MALDI-TOF mass spectrometry. Clin Chem. 2007;53:933.
NNK-induced cytotoxicity in CHO cells
expressing CYP2A13 and its genetic variants
100
80
Viability (%)
vect or
wt
60
Arg25Gln
Arg101Gln
Asp158Glu
Arg257Cys
40
Arg25Gln/ Arg257Cys
Val323Leu
Phe453Tyr
Arg494Cys
20
0
0.0
0.1
1.0
10.0
NNK (uM)
All the cells were treated with NNK for 24 hr.
100.0
1000.0
AFB1-induced cytotoxicity in CHO cells
expressing CYP2A13 and its genetic variants
100
Viability (%)
80
60
vect or
wt
Arg25Gln
Arg101Gln
40
Asp158Glu
Arg257Cys
Arg25Gln/ Arg257Cys
Val323Leu
20
Phe453Tyr
Arg494Cys
0
0.000
0.001
0.010
0.100
AFB1 (uM)
All the cells were treated with AFB1 for 48 hr.
1.000
10.000
Number of Journal Articles Published Over Time
PubMed search using “genetic, susceptibility, and environment” identified a total
of 2460 articles (from 1968 to March 16, 2008)
Nicholas Roden, 2008, unpublished
Total Funding
Over 500 million in research dollars from Environmental Protection Agency, the National
Cancer Institute and the National Institute of Environmental Health Sciences.
Nicholas Roden, 2008, unpublished
Recent
Progress in Genetic Polymorphism
Studies
High-throughput/low-cost genotyping and DNA
sequencing, e.g. GWAS
Knock-in mouse model
Computational modeling
Arg
64
Gly
479
Lys4
76
Substrat
e
Binding
Site
Heme
160
His
The first 29 amino acids at N-terminus is not
included. The substrate binding pocket is
marked by H2O molecules (green).
Collaborated with Dr. Jian Shen (Aventis)
Remaining
Challenges
Susceptibility genes are common alleles with low penetrance.
Functional significance of most SNPs, particularly those
localized in non-coding region of the gene.
Knowledge of SNP function is always required to provide
mechanistic support to association studies, including GWAS.
Epigenetics and other non-gentic facotrs that regulate gene
expression and/or protein activity
Gene-gene interaction
Metabolic and Biochemical
Issues in the Molecular
Epidemiology of Cancer
Robert Snyder and Jun-Yan Hong
Partricia Buffer et. al., Mechanisms of
Carcinogenesis: Contributions of
Molecular Epidemiology, 2004, p51-69
For example, a small but statistically
significant changes in Km values
may have no real importance in
human studies.
Recent
Progress in Exposure Assessment
Environmental sensors
Genographic information systems
Biologic sensors
Toxicogenomics
Body burden (biologic) measurements
Remaining
Challenges
Feasibility of obtaining accurate and quantitative information on
exposure to environmental toxicants (identity, number, and
level), particularly in long-term exposure situation.
Identification and validation of highly sensive exposure-specific
biomarkers.
 Gene-Environment
Interaction
The risk is strongly dependent on exposure.
 Uncertainty
Factor in Risk Assessment
Accouting for uncertainties in applied extrapolations
-10A Experimental Animal to Human
-10S Subchronic to Chronic Duration
-10L LOAEL to NOAEL
-10D Incomplete Data Base (to account for the inability of
any single animal study to adequately address all possible
adverse outcomes in humans)
-10C Children
-10H Human to Sensitive Human
The actual range for each factor is from 1-10, with 3 and
10 the most commonly applied.
From QY Meng’slecture, 2010