DNA repair gene polymorphisms and tobacco smoking in the risk for colorectal adenomas.
ABSTRACT DNA damage is thought to play a critical role in the development of colorectal adenoma. Variation in DNA repair genes may alter their capacity to correct endogenous and exogenous DNA damage. We explored the association between common single-nucleotide polymorphisms (SNPs) in DNA repair genes and adenoma risk with a case-control study nested in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. A total of 1338 left sided, advanced colorectal adenoma cases and 1503 matched controls free of left-sided polyps were included in the study. Using DNA extracted from blood, 3144 tag SNPs in 149 DNA repair genes were successfully genotyped. Among Caucasians, 30 SNPs were associated with adenoma risk at P < 0.01, with four SNPs remaining significant after gene-based adjustment for multiple testing. The most significant finding was for a non-synonymous SNP (rs9350) in Exonuclease-1 (EXO1) [odds ratio (OR) = 1.30, 95% confidence interval (CI) = 1.11-1.51, P = 0.001)], which was predicted to be damaging using bioinformatics methods. However, the association was limited to smokers with a strong risk for current smokers (OR = 2.15, 95% CI = 1.27-3.65) and an intermediate risk for former smokers (OR = 1.45, 95% CI = 1.14-1.82) and no association for never smokers (OR = 0.98, 95% CI = 0.76-1.25) (P(interaction) = 0.002). Among the top findings, an SNP (rs17503908) in ataxia telangiectasia mutated (ATM) was inversely related to adenoma risk (OR = 0.75, 95% CI = 0.63-0.91). The association was restricted to never smokers (OR = 0.55, 95% CI = 0.40-0.76) with no increased risk observed among smokers (OR = 0.89, 95% CI = 0.70-1.13) (P(interaction) = 0.006). This large comprehensive study, which evaluated all presently known DNA repair genes, suggests that polymorphisms in EXO1 and ATM may be associated with risk for advanced colorectal adenoma with the associations modified by tobacco-smoking status.
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ABSTRACT: Background Although numerous studies have investigated the association between DNA repair gene variants and lung cancer risk, the results remain inconclusive and incomplete.Methods We examined variants in seven nucleotide excision repair (NER) and RRM1 genes in association with primary lung cancer risk among 385 patients with newly diagnosed primary non-small cell lung cancer and 208 cancer-free controls collected from 2007 to 2009 in east China. The relationship between single nucleotide polymorphisms and risk of lung cancer was assessed by logistic regression and stratification analysis.Results The rs17655GG (ERCC5) and rs5744751CT (POLE) were associated with increased risk of lung cancer (adjusted odds ratio [OR], 2.32, 95% confidence interval [CI], 1.41–3.83; adjusted OR, 2.84, 95% CI, 1.70–4.74]. In stratification analysis, we found the increased effect of rs17655GG on the risk of lung cancer was observed among female, older subjects, or non-smokers. The heterozygote computed tomography (CT) of rs5744751 had a stronger unprotective effect on lung cancer among male, older subjects, or heavy smokers.Conclusion These results suggest that rs17655GG and rs5744751CT may be associated with lung cancer susceptibility in the Chinese population. However, these findings still need to be verified in larger confirmatory studies.Thoracic Cancer. 08/2012; 3(3).
- Biotechnology & Biotechnological Equipment 06/2014; 28(1):2-7. · 0.38 Impact Factor
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ABSTRACT: The capacity for repair of damage in DNA may vary between clinically healthy people and in patients with different diseases and conditions, contributing to the risk for development of late-onset multifactorial disease, eligibility for different therapies and various therapy-related complications. At present, the effects of individual variance in DNA repair capacity in human disease are best studied in cancer. The first part of this paper briefly reviews the history of the field and the currently available biomarkers of individual repair capacity associated with the risk for development of cancer and other late-onset multifactorial diseases and conditions.Biotechnology & Biotechnological Equipment 04/2014; 27(6):4208-4216. · 0.38 Impact Factor
Carcinogenesis vol.32 no.6 pp.882–887, 2011
Advance Access publication April 18, 2011
DNA repair gene polymorphisms and tobacco smoking in the risk for colorectal
Ying Gao?, Richard B.Hayes, Wen-Yi Huang,
Neil E.Caporaso, Laurie Burdette, Meredith Yeager,
Stephen J.Chanock and Sonja I.Berndt
Division of Cancer Epidemiology and Genetics, National Cancer Institute,
National Institutes of Health, Bethesda, MD 20892-7236, USA
?To whom correspondence should be addressed. Genetic Epidemiology
Branch, Division of Cancer Epidemiology and Genetics, National Cancer
Institute, National Institutes of Health, 6120 Executive Boulevard, Building
EPS/Room 7110, Bethesda, MD 20892-7236, USA. Tel: þ1 301 496 9249;
Fax: þ1 301 402 4489;
DNA damage is thought to play a critical role in the development
of colorectal adenoma. Variation in DNA repair genes may alter
theircapacity to correct endogenous andexogenous DNAdamage.
We explored the association between common single-nucleotide
polymorphisms (SNPs) in DNA repair genes and adenoma risk
with a case–control study nested in the Prostate, Lung, Colorectal
and Ovarian Cancer Screening Trial. A total of 1338 left sided,
advanced colorectal adenoma cases and 1503 matched controls
free of left-sided polyps were included in the study. Using DNA
extracted from blood, 3144 tag SNPs in 149 DNA repair genes
were successfully genotyped. Among Caucasians, 30 SNPs were
associated with adenoma risk at P < 0.01, with four SNPs
remaining significant after gene-based adjustment for multiple
testing. The most significant finding was for a non-synonymous
SNP (rs9350) in Exonuclease-1 (EXO1) [odds ratio (OR) 5 1.30,
95% confidence interval (CI) 5 1.11–1.51, P 5 0.001)], which was
predictedto bedamaging using bioinformatics methods.
However, the association was limited to smokers with a strong
risk for current smokers (OR 5 2.15, 95% CI 5 1.27–3.65) and
an intermediate risk for former smokers (OR 5 1.45, 95% CI 5
1.14–1.82) and no association for never smokers (OR 5 0.98, 95%
CI 5 0.76–1.25) (Pinteraction5 0.002). Among the top findings, an
SNP (rs17503908) in ataxia telangiectasia mutated (ATM) was
inversely related to adenoma risk (OR 5 0.75, 95% CI 5 0.63–
0.91). The associationwas restricted to neversmokers (OR5 0.55,
95% CI 5 0.40–0.76) with no increased risk observed among
smokers (OR 5 0.89, 95% CI 5 0.70–1.13) (Pinteraction5 0.006).
This large comprehensive study, which evaluated all presently
known DNA repair genes, suggests that polymorphisms in
EXO1 and ATM may be associated with risk for advanced
colorectal adenoma with the associations modified by tobacco-
Colorectal cancer is the third most common cancer in the USA for
both men and women (1). Epidemiological studies have shown that
non-steroidal anti-inflammatory drugs, exogenous hormones and se-
lect dietary factors are risk factors of colorectal neoplasia (2,3). Ge-
netic factors also contribute to risk with the heritability of colorectal
cancer estimated to be 35% from a large twin study (4). Genome-wide
association studies have identified at least 14 loci associated with the
risk of colorectal cancer (5,6); however, additional loci are predicted
to exist (7). Although there have been no genome-wide association
studies exclusively of colorectal adenoma, a known precursor to
colorectal cancer, studying genetic susceptibility to colorectal
adenoma may give insight into the etiology of colorectal cancer.
Smoking has been consistently associated with an increased risk of
colorectal adenoma (8,9). A recent meta-analysis found the risk
estimate of adenoma for ever smokers to be 1.82 [95% confidence
interval (CI) 5 1.65–2.00] (8). Generally, the risk was stronger for
current [odds ratio (OR) 5 2.14, 95% CI 5 1.86–2.46] as opposed to
former smokers (OR 5 1.47, 95% CI 5 1.29–1.67) (8). Carcinogens
generated from tobacco smoking interact with DNA to form DNA
adducts, which can interfere with cell replication and if not repaired
correctly, can cause somatic mutations leading eventually to cancer.
Emerging evidence has also shown that tobacco smoking may interact
with genetic factors, predisposing certain individuals to greater polyp
susceptibility (10). However, the studies focused on limited number of
candidate genes to date have only provided limited evidence for
gene–environmental interactions (10).
Damage caused by smoking and other environmental exposures
activates several different DNA repair pathways, including base
excision repair, mismatch repair (MMR), nucleotide excision repair
and double-strand break repair pathways (11). Rare germ line
mutations in MMR have been shown to lead to hereditary non-polyposis
colorectal cancer (HNPCC) (12) and mutations in the base excision
repair gene, MUTYH, have been linked to a familial polyposis syndrome
(13). Some significant associations have also been reported between
common DNA repair gene polymorphisms and colorectal neoplasia risk
(14–17). In particular, a common variant in the MLH1 gene region has
(18–21). However, most studies examined only small sets of single--
nucleotide polymorphisms (SNPs) (14–17), and the associations remain
to be confirmed. As a complex disease, multiple genetic variants with
minor to moderate effects probably contribute to colorectal adenoma
development, which makes scanning a large number of genes simulta-
neously rather than a small set of individual SNPs attractive.
Studies of genetic susceptibility to colorectal adenoma may give
insight into the etiology of colorectal carcinogenesis. To examine
the relationship between polymorphisms in DNA repair genes and
colorectal adenoma risk as well as potential effect modification by
tobacco smoking, we conducted a nested case–control study within
the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screen-
ing Trial. As most DNA repair genes have not been well charac-
terized with regard to disease susceptibility, we decided to
undertake a comprehensive approach including all DNA repair
genes known to our knowledge to date (11). For each gene, we
selected tag SNPs to thoroughly capture the common genetic
variation in the region.
The PLCO Cancer Screening Trial
The PLCO is a clinical trial, designed to assess the efficacy of screening
tests to reduce death from cancers of prostate, lung, colon and rectum and
ovary. As described previously (22,23), 154 938 cancer-free men and
women aged 55–74 were recruited from 10 sites in the USA between
1993 and 2001. Participants were randomly assigned to the control group
or the intervention group (screening arm), where they underwent a 60 cm
flexible sigmoidoscopy examination at study entry (T0) and year 3 (T3) or
year 5 (T5) of the study. Those found to have a suspicious lesion were
referred to their personal physician for subsequent diagnostic follow-up.
Among the 64 658 men and women who underwent sigmoidoscopy at T0 in
the PLCO Cancer Screening Trial, 8.8% were found to have adenoma (24).
Cases of colorectal adenoma were pathologically verified according to
medical records. Information on demographics, personal and family
medical history and lifestyle factors (e.g. smoking and dietary intake) were
collected by standard questionnaire at baseline. This trial was approved by
the institutional review boards of the 10 screening centers and the National
Abbreviations: ATM, ataxia telangiectasia mutated; CI, confidence interval;
EXO1, Exonuclease-1; HNPCC, hereditary non-polyposis colorectal cancer;
MMR, mismatch repair; OR, odds ratio; PLCO, Prostate, Lung, Colorectal and
Ovarian; SNP, single-nucleotide polymorphism.
? The Author 2011. Published by Oxford University Press. All rights reserved. For Permissions, please email: email@example.com
Cancer Institute in Bethesda, MD, USA, and all participants provided
A nested case–control study was conducted among the PLCO participants
randomized to the screening arm, who consented to participate in etiologic
studies of cancer and related diseases, completed a risk factor questionnaire,
provided a blood specimen and had no previous history of inflammatory bowel
disease, colorectal polyps, Gardner’s syndrome, familial polyposis or cancer
other than basal or squamous cell skin cancer. For this study, cases were
participants found to have advanced colorectal adenoma (?1 cm in size,
containing villous/tubulovillous characteristics, or had severe dysplasia) of
the distal colon or rectum at the T0 exam. Carcinoma in situ was classified
as severe dysplasia. Controls were participants, who had successful
sigmoidoscopy at T0 and were negative for polyps in the distal colon and
rectum. Controls were frequency matched to cases on self-reported ethnicity
(non-Hispanic Caucasian, non-Hispanic Black, Asian, Hispanic, Pacific
Islander, American Indian or Alaskan Native or Unknown), gender and for
a subset on age (55–59, 60–64, 65–69 and 70–74 years). Over 90% of the
subjects were non-Hispanic Caucasians.
A total of 3338 tag SNPsfrom 149 genes (supplementary Table 1 is available at
Carcinogenesis Online) involved in DNA repair pathways (11) were selected
to comprehensively interrogate genetic variations across the candidate genes.
TagSNPs wereselected foreach gene,includingthe region 20 kbupstreamand
10 kb downstream of the gene, using the CEU, JPT, CHB and YRI HapMap
populations and the Carlson method (25) as implemented in Tagzilla with a r2
thresholdof0.8 and minorallele frequency ?5%. SNPswith known orputative
functional significance (i.e. non-synonymous, promoter, intron–exon splice
sites) were also included whenever possible. The SNPs were genotyped on
a custom iSelect panel utilizing Illumina’s GoldenGate platform.
Whole blood or buffy coat DNA was extracted with QIAamp DNA Blood
Midi or Maxi Kits. For this study, sufficient DNA was available from 1342
cases and 1507 controls for genotyping. For quality control purposes, replicate
samples from 195 individuals (?7% of the population) were interspersed
randomly within the plates. Genotyping was conducted at the National Cancer
Institute Core Genotyping Facility, NIH. A total of 1338 cases and 1503
controls were successfully genotyped with over 90% of the genotypes for each
subject having valid calls, and the overall concordance rate was .99% for
replicated samples. After excluding the SNPs with call rate ,90%, minor
allele frequency ,1%, or Hardy–Weinberg Equilibrium P-value ,1 ? 10?6
among Caucasian controls, 3144 SNPs of 3401 selected (92%) remained for
analysis. For each gene, the percentage of tagSNPs passing our quality control
criteria varied from 67 to 100% with an average of 93%.
The initial analyses were conducted using Plink, a whole genome association
analysis toolset (26). Logistic regression was used to estimate the OR and
95% CI for the association between each SNP and colorectal adenoma risk
assuming a log-additive model for the genotype, adjusting for age (55–59,
60–64, 65–69, 70–74 years), gender and ethnicity (non-Hispanic Caucasian,
non-Hispanic Black and other). Another set of analysis was conducted among
non-Hispanic Caucasians only.
For SNPs with main association P , 0.01, we tested if the SNP associa-
tions differed by smoking status (ever versus never) using the Breslow–Day
test of homogeneity. The SNPs with evidence of heterogeneity (P , 0.05
between ever versus never smoker) among Caucasians were further tested for
interaction with smoking status (never, former and current smoking) using
a likelihood ratio test. The P-value for trend was generated by treating the
smoking status (never 5 0, former 5 1 and current 5 2) as a continuous
variable in the interaction model, and the P-value for interaction was gener-
ated by treating the smoking status as categorical variable in the interaction
model. Similarly, we also conducted analyses to examine the effect modifi-
cation by smoking duration (,24 years, ?24 years) and years since quitting
smoking (,20 years, ?20 years). These additional analyses were conducted
with SAS 9.1.
Pairwise linkage disequilibrium measures (D# and r2) were inferred from
the Caucasian controls using the program Haploview (27). Haplotypes
among Caucasians were estimated using an expectation–maximization
algorithm for SNPs within the gene Exonuclease-1 (EXO1), which carried
the SNP with lowest P-value in the current study, and risks for individual
haplotypes were calculated assuming a log-additive model and using the
generalized linear model implemented in R Haplostats package, adjusted
for age and gender (28). For consistency with the SNP results, we used the
haplotype containing the T allele at rs9350 as the reference haplotype.
To evaluate the potential for false-positive findings due to multiple testing,
we adjusted the P values using a Bonferroni correction for the total number of
(a) tag SNPs for each individual gene (gene based) as well as (b) all the SNPs
tested in the current analysis, using the R multtest package.
A total of 1338 colorectal adenoma cases and 1503 frequency-
matched controls were included in the current analyses (Table I). Over
90% of the study subjects were Caucasian and ,10% were African-
American or other ethnicity. Compared with controls, cases were
more probably to be current smokers, have a family history of co-
lorectal cancer and be less educated.
Of the 3144 SNPs analyzed, 129 SNPs (supplementary Table 2 is
available at Carcinogenesis Online) were associated with adenoma risk
among all subjects and 127 SNPs withriskamong Caucasians only at P
, 0.05. The SNPs associated with colorectal adenoma risk at P ? 0.01
level among Caucasians and are shown in Table II. After adjusting for
multiple testing for all the SNPs tested in the analysis, none of these 30
SNPs remained statistically significant. However, six SNPs remained
associated with adenoma risk among Caucasians at P ? 0.05 level
after a gene-based multiple testing correction: EXO1 rs9350,
FANCC rs400727, ERCC1 rs10412761, DCLRE1A rs2301180,
RAD54B rs3762053 and POLE rs11614717. Further adjustment
for smoking status did not substantially alter the results in Table II
(results not shown). The most statistically significant SNP associated
with risk was EXO1 rs9350 with heterozygotes displaying a 1.95-
fold risk (95% CI 5 1.05–3.62) and CC homozygotes displaying
a 2.39-fold risk (95% CI 5 1.30–4.38) comparing with TT homo-
Given the importance of smoking as a risk factor for adenoma, we
examined the heterogeneity in risk by smoking status (ever versus
Table I. Demographic characteristics of cases and controls, PLCO Cancer
Screening Trial baseline exam 1993–2001
Controls (%) N
Cases (%) N
Former cigarette smoker
Current cigarette smoker
Cigar or pipe smoker
Family history of colorectal cancer
Body mass index (BMI)
Post high school
College graduate or postgraduate
anti-inflammatory drug use
DNA repair gene and colorectal adenoma
never). Of the SNPs with a P , 0.01 for their main association, three
SNPs displayed significant heterogeneity in risk by smoking status (P
, 0.05) and were selected for further analyses stratified by cigarette
smoking status (never, former and current) (Table III). The risk of co-
lorectal adenoma at EXO1 rs9350 was significantly modified by smok-
ing status (Pinteraction5 0.006) with a 2-fold increased risk among
current smokers (OR 5 2.15; 95% CI: 1.27–3.65), a modest increased
risk among former smokers (OR 5 1.45; 95% CI: 1.14–1.82), and no
association among never smokers (OR 5 0.98; 95% CI: 0.76–1.25)
(Ptrend5 0.002). A stronger increased risk was also observed among
individuals with longer smoking duration (?24 years: OR5 1.59; 95%
95% CI: 1.09–1.99) (Pinteraction5 0.02), as well as individuals who quit
more recently (,20 years: OR 5 1.64; 95% CI: 1.24–2.18) (Pinteraction
5 0.02) compared with those who quit a longer time ago (?20 years:
OR 5 1.42; 95% CI: 1.0–1.99). Similarly, another SNP in EXO1,
never, former, to current smokers (Ptrend5 0.002). These two SNPs in
EXO1 were strongly correlated (r25 0.82), making it difficult to dif-
ferentiate the associations ofone fromthe otherstatistically.Whenboth
SNPs were put in the same model, neither of them remained signifi-
cantlyassociatedwithadenoma risk(P . 0.05 for both) due tothe high
correlation. Combining former and current smokers, the C allele at
rs9350 and G allele at rs4658535 were associated with increased risk
among ever smokers with ORs of 1.54 (95% CI 5 1.26–1.89) and 1.46
(95% CI 5 1.21–1.77) for the two SNPs, respectively.
The risk of adenoma at rs17503908 in ataxia telangiectasia mutated
(ATM) was also modified by smoking status (Pinteraction5 0.02) with
the Tallele displaying a decreased risk for adenoma only among never
smokers (OR 5 0.55, 95% CI 5 0.40–0.76) (Table III) but not among
ever smokers (OR 5 0.89, 95% CI 5 0.70–1.13). Notably,
rs17503908 showed an intermediate risk for adenoma also among
former smokers (OR 5 0.84, 95% CI 5 0.64–1.11) compared with
never smokers (OR 5 0.55, 95% CI 5 0.40–0.76) and current
Table II. OR of colorectal adenoma for polymorphisms in DNA repair genes with P , 0.01, PLCO Cancer Screening Trial baseline exam 1993–2001
SNPGene Risk alleleRAFc
OR 95% CIPOR95% CIP
aOR per risk allele assuming a log-additive model, adjusted for age and sex.
bOR per risk allele assuming a log-additive model, adjusted for age, sex and race.
cRAF, risk allele frequency among Caucasian controls.
Table III. OR of colorectal adenoma for select DNA repair SNPs stratified by smoking status among Caucasiansa, PLCO Cancer Screening Trial baseline exam
Never Former CurrentP trendb
GeneRisk alleleOR POR POR P
aSNPs selected here were those with significant main effect (adjusted for age, sex) (P , 0.01) and gene–smoking (ever versus never smoking) interaction (P , 0.05).
bP-value for trend was calculated assuming smoking status (never 5 0, former 5 1 and current 5 2) as continuous variable in the interaction model.
cP-value for interaction was calculated assuming smoking status (never 5 0, former 5 1 and current 5 2) as categorical variable in the interaction model.
Y.Gao et al.
smokers (OR 5 1.25, 95% CI 5 0.71–2.22) (Ptrend5 0.008). Similar
patterns were also observed when the results were stratified by smok-
ing duration and time since quitting (data not shown).
Given that the associations of two SNPs in EXO1 appeared to be
modified by smoking status, we explored this region in greater detail.
A total of 25 SNPs were genotyped in EXO1. Seven SNPs (rs9350,
rs1635488, rs4408133, rs1635484, rs4150018, rs4150027 and
rs4658535), including the two SNPs significantly associated with risk,
were in strong linkage disequilibrium as measured by D# (Figure 1)
and mildly to strongly correlated (r2range: 0.23–0.84). The five most
frequent haplotypes comprised of these seven SNPs were analyzed in
association with adenoma risk by smoking status (never and ever
smoking, but not never, former and current smoking status due to
limited power) (supplementary Table 3 is available at Carcinogenesis
Online). Compared with the haplotype containing the T allele at
rs4150027-rs4658535: TCGCGTA), three haplotypes, each containing
the risk alleles at rs9350 and rs4658535, were significantly associated
with an increased risk of adenoma with risk estimates ranging from
1.23 to 1.30. The associations were stronger among smokers (40–60%
increased risk) compared with never smokers for which none of the
ing interaction was marginally significant (P 5 0.06).
DNA repair has long been implicated in colorectal cancer with the
discovery that germ line mutations in MMR genes lead to HNPCC
(29) and mutations in the base excision repair gene, MUTYH, lead to
a familial polyposis syndrome. However, the etiological role of com-
mon genetic variation in DNA repair genes in colorectal adenoma and
cancer has not been comprehensively studied in the context of epide-
miological studies. Although some common SNPs in DNA repair
genes have been reported to be associated with colorectal cancer
and/or adenoma (18–21,30,31), with the exception of the MHL1-
93G . A variant with microsatellite instable tumors (18–21), most
associations have not been replicated (30,31). Furthermore, data on
effect modifications by important environmental factors are sparse.
In our study, .3000 SNPs from 153 DNA repair genes were eval-
uated simultaneously among 2841 study subjects, which is the largest
and most comprehensive study for colorectal adenoma risk focusing
on DNA repair genes to date. Among the SNPs associated with risk,
we found that genetic polymorphisms in EXO1 and ATM significantly
modified the effectof cigarette smoking on risk,predisposing smokers
to greater adenoma susceptibility. When stratified by genotype, smok-
ing was only significantly associated with increased adenoma risk
among individuals homozygous for the risk allele at EXO1 rs9350
(OR 5 1.80, 95% CI 5 1.47–2.19 for ever smokers with the CC
genotype) and ATM rs17503908 (OR 5 1.69, 95% CI 5 1.40–2.03
for ever smokers with the GG genotype).
EXO1, located at chromosome 1q42–q43, encodes a protein with
5#/ 3# and 3#/ 5# double-stranded DNA exonuclease activity. It
also exhibits some endonuclease activity correcting 5#-overhanging
flap structures. EXO1 is involved in DNA MMR, recombination, rep-
lication and telomere stabilization (32). EXO1-mutant cells showed
increased microsatellite instability and incomplete MMR capability
(33). Mice with EXO1 knockout were found to have lower survival
rates and higher mutation rates as well as higher susceptibility to
lymphomas (33). EXO1 has been implicated in hereditary HNPCC
due to its role in DNA MMR; however, studies investigatingrare germ
line variants in EXO1 have not shown consistent findings as reviewed
by Liberti et.al. (34).
We observed an increased colorectal adenoma risk among individ-
uals carrying a C allele at rs9350 and a G allele at rs4658535 in EXO1.
Fig. 1. Linkage disequilibrium plot of EXO1 among Caucasian controls from the PLCO Cancer Screening Trial baseline exam 1993–2001. The colors represent
the extent of pairwise linkage disequilibrium as measured by D# with red indicating D# 5 1.0 and shades of pink to white indicating D# ,1.0. The numeric values
are the pairwise r2values.
DNA repair gene and colorectal adenoma
The SNPs were highly correlated (r25 0.82), making it impossible to
differentiate the associations of each statistically. Using the PolyPhen
database, we found that rs9350 was predicted to be ‘probably dam-
aging’ (position-specific independent counts score difference 5 2.17)
with the C to T substitution causing a non-synonymous amino acid
change by replacing proline with leucine (35), suggesting that rs9350
may be a causal variant. The substitution was also predicted to be
‘deleterious’ using the SIFT database. Several studies have examined
the association between common polymorphisms in EXO1 and the
risk of lung, oral, brain and colorectal cancer (36–42); however, data
are limited and inconclusive due to the small sample size and differ-
ences in the SNPs genotyped in the studies (36–42). No studies have
examined the association between this polymorphism and adenoma.
Consistent with our findings, two case–control studies of colorectal
cancer found a decreased cancer risk for individuals carrying T allele
at EXO1 rs9350 compared with C allele (40,43). No association was
observed with rs9350 in two studies of lung cancer (37,38), one study
of oral cancer (39) and one study of breast cancer (44), suggesting that
the association of C allele at rs9350 may be organ/tissue specific. In
addition, the previous studies in other cancers (37–39) were relatively
small (N ? 680 cases each) and conducted in Asian populations,
where differences in environmental exposures may modify the
association of rs9350 and cancer risk compared with Caucasians.
Smoking is an important risk factor for adenoma with current
smokers having an 1.8-fold increased risk (95% CI 5 1.5–2.1) in
the full PLCO cohort (45). We observed a stronger association
between adenoma risk and rs9350 in EXO1 among smokers compared
with non-smokers and hypothesize that the C allele at EXO1 rs9350
may increase risk among smokers by reducing the protein’s capacity
or efficiency to repair the damage caused by smoking exposure. Tsai
et al. also reported an increased risk of oral cancer among smokers
who carried the A allele at rs1047840 (r25 0.18 with rs9350 in our
study) in EXO1 but not among non-smokers (39). The haplotype
results further confirmed the strong association between the EXO1
region encompassing rs9350 and adenoma risk.
We observed a significant decreased risk among never smokers for
the T allele at rs17503908 in ATM. ATM, located at chromosome
11q22.3, encodes a cell cyclecheckpoint kinasewhich regulates many
downstream proteins, includingthe tumor suppressor proteinsp53 and
BRCA1, the checkpoint kinase CHK2, checkpoint proteins RAD17
and RAD9 and the DNA repair protein NBS1. ATM is thought to be
a master controller of the cell cycle checkpoint-signaling pathways
and functions to repair DNA damage and maintain genome stability.
Persons with ataxia telangiectasia, an autosomal recessive diseased
caused by rare missense or truncating mutations in ATM, have an
increased sensitivity to ionizing radiation and an increased risk of
cancer (46). Heterozygous carriers of these rare ATM mutations have
an increased risk of several cancers including colorectal cancer (47).
Several lines of evidence have suggested the etiological role for
ATM in colorectal carcinogenesis (47,48). Polymorphisms at
rs1800056 and rs1800057 in ATM have been associated with colo-
rectal cancer risk (49) and although the results were not replicated in
a follow-up study (50), rs1801516 has been associated with disease
penetrance among HNPCC carriers (51). In our study, the Tallele at
ATM rs1801516 was also marginally associated with adenoma risk
(P 5 0.011 for Caucasians and P 5 0.016 for all subjects), but no
association was observed with rs1800056 (P 5 0.22). To date, no
study has reported an association between ATM rs17503908 and
colorectal adenoma, which is located in an intronic region of
ATM. We observed an inverse association for the T allele at
rs17503908. Differences in sensitivity to DNA damage or higher
expression levels of ATM could reduce risk for neoplastic transfor-
mation or subsequent proliferation by activating p53 (52). In strat-
ified analyses, this inverse association was restricted to never
smokers. It is possible that smokers do not benefit from carrying
this allele due to an antagonistic effect between the SNP and smok-
ing exposure. An in vitro study observed that smoking exposure
activated ATM in human pulmonary adenocarcinoma cells through
phosphorylation in a dose-dependent manner (53). Similarly, ben-
zo[a]pyrene diol epoxide, a polycyclic aromatic hydrocarbon found
in tobacco smoke, has been shown to bind to ATM (54) and induce
ATM expression in esophageal cancer cell lines (55), suggesting that
ATM plays an active role in responding to tobacco smoke exposure.
We speculate that the kinase encoded by the ATM may be saturated
by smoking exposure, which may prevent its protective effect.
Our study has several advantages and limitations. First, it is the
largest study to date to investigate a broad range of DNA repair gene
polymorphisms for colorectal adenoma risk. Although still somewhat
underpowered to examine gene–environment interactions for the
SNPs of moderate association, our findings provide promising leads
for replication in future pooled analyses. Future analyses exploring
these interactions with regard to colorectal cancer may lead to
additional insight into colorectal neoplasm progression. Our study
included only advanced adenoma cases and so the results may not
be generalizable to non-advanced adenomatous polyps; however,
advanced adenomas are more to progress to colorectal cancer and
therefore clinically more relevant. Moreover, our study only included
left-sided adenomas in the distal colon and rectum. Thus, the results
of our study may not be generalizable to adenomas observed in the
proximal colon, which may be more probably to occur as the result
deficiencies in MMR. In addition, our study population came from
a cancer prevention screening trial in which participants were
generally more probably to be Caucasian, more educated, less
probably to smoke and more physically active than the general
population (56). Thus, our results may not be broadly generalizable
to the entire population or to other ethnicities. However, since our
case–control study was nested within a randomized population-based
colorectal cancer screening trial, this reduces the potential for selec-
tion bias often inherited in clinic-based case–control studies of
adenoma, where persons may undergo endoscopy for reasons other
than routine screening, such as gastrointestinal symptoms, blood in
their stools, diagnostic follow-up or because they have a family
history of colorectal cancer.
In summary, in this large comprehensive study of DNA repair gene
polymorphisms and colorectal adenoma risk, we found that an SNP in
EXO1 predicted to deleteriously alter function was associated with
increased adenoma risk. The association was restricted to ever smok-
ers and stronger in current smokers than former smokers. Although
additional studies are needed to confirm our findings, this intriguing
result suggests that genetic variation in EXO1 may modify suscepti-
bility to colorectal adenoma, particularly among smokers.
Intramural Research Program of the Division of Cancer Epidemi-
ology and Genetics, National Cancer Institute, National Institutes
of Health (NIH).
The authors thank Drs Christine Berg and Philip Prorok, Division of Cancer
Prevention, NCI, the screening center investigators and staff of the PLCO
Cancer Screening Trial, Mr Thomas Riley and staff at Information Manage-
ment Services and Ms Barbara O’Brien and staff at Westat for their contribu-
tions to the PLCO Cancer Screening Trial. Finally, we acknowledge the study
participants for donating their time and making this study possible.
Author contributions: Y.G., S.B., R.H. and W.-Y.H. designed the study. Y.G.
and S.B. also analyzed data and wrote the manuscript. L.B., M.Y. and S.C.
were instrumental in the genotyping for this project. All authors read, gave
comments and approved the final version of the manuscript. All authors had
full access to all of the data in the study and take responsibility for the integrity
of the data and the accuracy of the data analysis.
Conflict of Interest Statement: None declared.
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Received October 27, 2010; revised March 17, 2011; accepted March 25, 2011
DNA repair gene and colorectal adenoma