DNA repair gene polymorphisms and tobacco smoking in the risk for colorectal adenomas

Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-7236, USA.
Carcinogenesis (Impact Factor: 5.33). 06/2011; 32(6):882-7. DOI: 10.1093/carcin/bgr071
Source: PubMed
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) (Pinteraction = 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) (Pinteraction = 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.


Available from: Neil Caporaso, Aug 21, 2014
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;
Email: gaoying@mail.nih.gov
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) 5 1.30,
95% confidence interval (CI) 5 1.11–1.51, P 5 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 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) (P
5 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 association was restricted to never smokers (OR 5 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) (P
5 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.
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
been linked to the risk of colorectal cancers with microsatellite instability
(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
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.
Ó The Author 2011. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
Page 1
Cancer Institute in Bethesda, MD, USA, and all participants provided
informed consent.
Study population
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 SNPs from 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.
Tag SNPs were selected for each gene, including the region 20 kb upstream and
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 r
threshold of 0.8 and minor allele frequency 5%. SNPs with known or putative
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
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%.
Statistical analysis
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 r
) 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 with risk among 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,
FAN C C 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
5 1503
Cases (%) N
5 1338
White 1370 (91) 1241 (93)
Black 66 (4) 50 (4)
Other 67 (5) 47 (3)
Male 950 (63) 853 (64)
Female 553 (37) 485 (36)
55–59 498 (33) 390 (29)
60–64 460 (31) 419 (31)
65–69 344 (23) 333 (25)
70–75 201 (13) 196 (15)
Smoking status
Never 650 (43) 451 (34)
Former cigarette smoker 679 (45) 627 (47)
Current cigarette smoker 105 (7) 197 (15)
Cigar or pipe smoker 69 (5) 62 (5)
Family history of colorectal cancer
Yes 141 (9) 162 (12)
No 1362 (91) 1176 (88)
Body mass index (BMI)
,25 451 (30) 369 (28)
25–29.9 680 (46) 594 (45)
30 354 (24) 364 (27)
,12 years 439 (29) 470 (35)
Post high school 489 (33) 479 (36)
College graduate or postgraduate 574 (38) 389 (29)
Regular non-steroidal
anti-inflammatory drug use
Yes 935 (62) 776 (58)
No 565 (38) 559 (42)
DNA repair gene and colorectal adenoma
Page 2
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 (P
5 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)
5 0.002). A stronger increased risk was also observed among
individuals with longer smoking duration (24 years: OR 5 1.59; 95%
CI: 1.20–2.10) compared with shorter duration (,24 years: OR 5 1.48;
95% CI: 1.09–1.99) (P
5 0.02), as well as individuals who quit
more recently (,20 years: OR 5 1.64;95%CI:1.242.18)(P
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,
rs4658535, also showed a monotonically increasing pattern of risk from
never, former, to current smokers (P
5 0.002). These two SNPs in
EXO1 were strongly correlated (r
5 0.82), making it difficult to dif-
ferentiate the associations of one from the other statistically. When both
SNPs were put in the same model, neither of them remained signifi-
cantly associated with adenoma risk (P . 0.05 for both) due to the 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 (P
5 0.02) with
the T allele 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
Caucasian subjects
All subjects
SNP Gene Risk allele RAF
OR 95% CI P OR 95% CI P
rs9350 T/C EXO1 C 0.82 1.30 1.11–1.51 0.001 1.24 1.07–1.44 0.003
rs400727 T/G FANCC G 0.91 1.44 1.15–1.80 0.002 1.40 1.14–1.72 0.001
rs3762053 G/T RAD54B G 0.16 1.25 1.09–1.44 0.002 1.23 1.07–1.41 0.004
rs11614717 T/G POLE T 0.14 1.27 1.09–1.49 0.002 1.24 1.07–1.44 0.005
rs4703564 T/C XRCC4 C 0.89 1.42 1.13–1.78 0.002 1.31 1.09–1.59 0.005
rs242448 A/T FANCC T 0.92 1.42 1.13–1.78 0.002 1.41 1.14–1.75 0.002
rs4658535 A/G EXO1 G 0.79 1.26 1.08–1.45 0.002 1.25 1.09–1.42 0.002
rs1699499 C/T FANCC T 0.97 1.70 1.20–2.40 0.003 1.67 1.19–2.35 0.003
rs17503908 G/T ATM G 0.08 1.34 1.11–1.62 0.003 1.33 1.10–1.60 0.003
rs10412761 G/A ERCC1 A 0.57 1.19 1.06–1.33 0.003 1.19 1.07–1.33 0.001
rs3885676 C/T XRCC4 T 0.87 1.36 1.11–1.66 0.003 1.31 1.10–1.56 0.003
rs4465523 A/G APEX1 A 0.33 1.18 1.05–1.32 0.006 1.20 1.08–1.34 0.001
rs17277375 T/C APEX1 T 0.32 1.18 1.05–1.33 0.006 1.19 1.06–1.33 0.003
rs2301180 C/T DCLRE1A T 0.71 1.18 1.05–1.34 0.006 1.16 1.03–1.30 0.01
rs6864054 G/A XRCC4 A 0.94 1.44 1.11–1.87 0.006 1.33 1.05–1.70 0.02
rs5744990 A/G POLE A 0.13 1.24 1.06–1.45 0.006 1.23 1.06–1.43 0.007
rs6573333 T/G MNAT1 G 0.98 2.36 1.26–4.40 0.007 1.18 0.80–1.74 0.39
rs3102854 G/A RAD54B G 0.24 1.19 1.05–1.35 0.007 1.18 1.04–1.33 0.009
rs7829886 A/T RAD54B T 0.73 1.19 1.05–1.35 0.008 1.16 1.03–1.31 0.02
rs12050102 T/G APEX1 T 0.33 1.17 1.04–1.32 0.008 1.19 1.06–1.33 0.002
rs4150628 G/A GTF2H1 G 0.44 1.16 1.04–1.23 0.008 1.14 1.03–1.27 0.02
rs228606 T/G ATM T 0.39 1.16 1.04–1.30 0.008 1.15 1.04–1.28 0.009
rs3212986 A/C ERCC1 C 0.74 1.19 1.04–1.35 0.008 1.19 1.05–1.34 0.006
rs10838192 C/T ALKBH3 C 0.21 1.19 1.05–1.36 0.009 1.19 1.04–1.35 0.008
rs828918 G/C XRCC5 G 0.13 1.24 1.06–1.45 0.009 1.19 1.02–1.38 0.03
rs3131382 T/C MSH5 C 0.93 1.36 1.08–1.71 0.009 1.37 1.09–1.72 0.007
rs1150793 G/A MSH5 G 0.06 1.34 1.08–1.67 0.009 1.26 1.02–1.55 0.03
rs707915 A/T MSH5 A 0.06 1.34 1.08–1.67 0.009 1.26 1.02–1.55 0.03
rs11615 G/A ERCC1 A 0.58 1.16 1.04–1.31 0.009 1.15 1.02–1.28 0.02
rs5744903 T/C POLE T 0.06 1.32 1.07–1.62 0.01 1.28 1.04–1.57 0.02
OR per risk allele assuming a log-additive model, adjusted for age and sex.
OR per risk allele assuming a log-additive model, adjusted for age, sex and race.
RAF, risk allele frequency among Caucasian controls.
Table III. OR of colorectal adenoma for select DNA repair SNPs stratified by smoking status among Caucasians
, PLCO Cancer Screening Trial baseline exam
Never Former Current P trend
P interaction
Gene Risk allele OR P OR P OR P
rs9350 EXO1 C 0.98 (0.76–1.25) 0.86 1.45 (1.14–1.82) 0.002 2.15 (1.27–3.65) 0.004 0.002 0.006
rs4658535 EXO1 G 0.98 (0.77–1.23) 0.84 1.34 (1.08–1.68) 0.008 2.13 (1.30–3.49) 0.003 0.002 0.006
rs17503908 ATM T 0.55 (0.40–0.76) 0.0003 0.84 (0.64–1.11) 0.22 1.25 (0.71–2.22) 0.44 0.008 0.02
SNPs 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).
P-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.
P-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.
Page 3
smokers (OR 5 1.25, 95% CI 5 0.71–2.22) (P
5 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 (r
range: 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
rs9350 (rs9350-rs1635488-rs4408133-rs1635484-rs4150018-
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
haplotypes were associated with risk. The test for the haplotype–smok-
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 effect of 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 investigating rare 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 r
DNA repair gene and colorectal adenoma
Page 4
The SNPs were highly correlated (r
5 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 (r
5 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 cycle checkpoint kinase which regulates many
downstream proteins, including the tumor suppressor proteins p53 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 T allele 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
intobaccosmoke,hasbeenshowntobindtoATM (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.
Supplementary material
Supplementary Tables 1–3 can be found at http://carcin.oxfordjournals.org/
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.
Y.Gao et al.
Page 5
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Received October 27, 2010; revised March 17, 2011; accepted March 25, 2011
DNA repair gene and colorectal adenoma
Page 6
  • Source
    • "Both rs509360 and rs108499 are located 59-upstream of FEN1, occurring within intronic regions of C11orf9. A previous study among predominantly NHW found no associations between these FEN1 SNPs and colorectal adenoma [38] . The FEN1 endonuclease is involved in BER and DNA replication and has been reported to play important roles in genomic stability [44], chronic inflammation, autoimmunity and cancers [45,46]. "
    [Show abstract] [Hide abstract] ABSTRACT: Cigarette smoking, high alcohol intake, and low dietary folate levels are risk factors for colorectal adenomas. Oxidative damage caused by these three factors can be repaired through the base excision repair pathway (BER). We hypothesized that genetic variation in BER might modify colorectal adenoma risk. In a sigmoidoscopy-based study, we examined associations between 182 haplotype tagging SNPs in 14 BER genes, and colorectal adenoma risk, and examined their potential role as modifiers of the effect cigarette smoking, alcohol intake, and dietary folate levels. Among all individuals, no statistically significant associations between BER SNPs and adenoma risk persisted after correction for multiple comparisons. However, among Asian-Pacific Islanders we observed two SNPs in FEN1 and one in NTHL1, and among African-Americans one SNP in APEX1 that were associated with colorectal adenoma risk. Significant associations were also observed between SNPs in the NEIL2 gene and rectal adenoma risk. Three SNPS modified the effect of smoking (MUTYH interaction p = 0.002; OGG1 interaction p = 0.013); FEN1 interaction p = 0.013)), one SNP in LIG3 modified the effect of alcohol consumption (interaction p = 0.024) and two SNPs in LIG3 modified the effect of dietary folate (interaction p = 0.001 and p = 0.08) on colorectal adenoma risk. These findings support a role for genetic variants in the BER pathway as potential modifiers of colorectal adenoma risk. Our findings strengthen the role of oxidative damage induced by key lifestyle and dietary risk factors in colorectal adenoma formation.
    Full-text · Article · Aug 2013 · PLoS ONE
  • Source
    • "Caucasian US Nested case–control within screening arm of PLCO (Gao et al, 2011) Age ESCC 1027 1452 Asian China Neighborhood-based case–control from the UGI Cancer Genetics Project (Gao et al, 2009) and nested case–control from NITs (Blot et al, 1993) "
    [Show abstract] [Hide abstract] ABSTRACT: Background: The chromosome 9p21.3 region has been implicated in the pathogenesis of multiple cancers. Methods: We systematically examined up to 203 tagging SNPs of 22 genes on 9p21.3 (19.9-32.8 Mb) in eight case-control studies: thyroid cancer, endometrial cancer (EC), renal cell carcinoma, colorectal cancer (CRC), colorectal adenoma (CA), oesophageal squamous cell carcinoma (ESCC), gastric cardia adenocarcinoma and osteosarcoma (OS). We used logistic regression to perform single SNP analyses for each study separately, adjusting for study-specific covariates. We combined SNP results across studies by fixed-effect meta-analyses and a newly developed subset-based statistical approach (ASSET). Gene-based P-values were obtained by the minP method using the Adaptive Rank Truncated Product program. We adjusted for multiple comparisons by Bonferroni correction. Results: Rs3731239 in cyclin-dependent kinase inhibitors 2A (CDKN2A) was significantly associated with ESCC (P=7 × 10(-6)). The CDKN2A-ESCC association was further supported by gene-based analyses (Pgene=0.0001). In the meta-analyses by ASSET, four SNPs (rs3731239 in CDKN2A, rs615552 and rs573687 in CDKN2B and rs564398 in CDKN2BAS) showed significant associations with ESCC and EC (P<2.46 × 10(-4)). One SNP in MTAP (methylthioadenosine phosphorylase) (rs7023329) that was previously associated with melanoma and nevi in multiple genome-wide association studies was associated with CRC, CA and OS by ASSET (P=0.007). Conclusion: Our data indicate that genetic variants in CDKN2A, and possibly nearby genes, may be associated with ESCC and several other tumours, further highlighting the importance of 9p21.3 genetic variants in carcinogenesis.
    Full-text · Article · Jan 2013 · British Journal of Cancer
  • Source
    • "While cancer of the immune system is more common in the early lives of A-T patients (mostly occurring in first 15 years), older A-T patients are at a greater risk of developing a variety of solid tumours including gastric, breast, medulloblastoma and basal cell carcinoma [74]. Furthermore, the role of heterozygous carriership of defective ATM alleles has been clearly demonstrated in a proportion of familial breast cancer and colorectal cancer cases as well [39, 154]. "
    [Show abstract] [Hide abstract] ABSTRACT: The ability of a cell to conserve and maintain its native DNA sequence is fundamental for the survival and normal functioning of the whole organism and protection from cancer development. Here we review recently obtained results and current topics concerning the role of the ataxia-telangiectasia mutated (ATM) protein kinase as a damage sensor and its potential as therapeutic target for treating cancer. This monograph discusses DNA repair mechanisms activated after DNA double-strand breaks (DSBs), i.e. non-homologous end joining, homologous recombination and single strand annealing and the role of ATM in the above types of repair. In addition to DNA repair, ATM participates in a diverse set of physiological processes involving metabolic regulation, oxidative stress, transcriptional modulation, protein degradation and cell proliferation. Full understanding of the complexity of ATM functions and the design of therapeutics that modulate its activity to combat diseases such as cancer necessitates parallel theoretical and experimental efforts. This could be best addressed by employing a systems biology approach, involving mathematical modelling of cell signalling pathways.
    Full-text · Article · Nov 2012
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