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The Application of Single Nucleotide The Application of Single Nucleotide Polymorphisms (SNPs) Polymorphisms (SNPs) and Lung Cancer Riskand Lung Cancer Risk
Zuo-Feng Zhang, MD, PhD
Epidemiology of Lung CancerEpidemiology of Lung Cancer
Worldwide statistics (2002)– Incidence: ranked #1 (1.35 million cases)– Mortality: ranked #1 (1.18 million deaths)– 5-year survival rate: around 10% in Europe; 8.9% in de
veloping countries
U.S. statistics (2006)– Incidence: ranked #3 (174,470 cases)– Mortality: ranked #1 (162, 460 deaths)– 5-year survival rate: 15%
Risk FactorsRisk Factors for Lung Cancer for Lung Cancer
– Tobacco smoking– ETS– Asbestos– Radon exposure– Occupational exposures– Air pollution– Other radiation– Recurring inflammation– Family history of cancer– Insufficient diet and poor nutritional factors
If DNA damage not repaired
DNA damage repaired
If loose cell cycle control
Defected DNA repair gene
G1
S
G2
M
P53
Cyclin D1
P16
Environmental Carcinogens / Procarcinogens Exposures
Nitrosemins, Xenobiotics, Diet/nutrient
Active carcinogens Detoxified carcinogens
DNA Damage Normal cell
Carcinogenesis Programmed cell death
Tobacco/alcohol infection
Diet and nutritional factors
CYP2E1
GSTP1
mEH mEHNQO1
XRCC3
GSTM1
Theoretical model of gene-environmental interaction pathway for lung cancer Theoretical model of gene-environmental interaction pathway for lung cancer susceptibilitysusceptibility
Ile105Val Ala114Val
Tyr113HisHis139Arg
Tyr113HisHis139Arg
Pro187Ser
Null
Ala146ThrArg72Pro
G870A
G0
Diet/nutrient
Free radicalsOxidative Stress
DNA Repair PathwaysDNA Repair PathwaysDirect Reversal (DR)
Mismatch Repair (MMR)
Base Excision Repair (BER)
Nucleotide Excision Repair (NER)
Double Strand Break Repair (DSBR)
BER PathwayBER Pathway
BER PathwayBER Pathway
Polymorphisms in the BER pathway may alter the repairing capacity of this pathway and modify the risk of lung and head-and-neck cancers.
To examine the individual associations of the – hOGG1 Ser326Cys, – APEX1 Asp148Glu, – PCNA C T (intron 2), – XRCC1 Arg194His and Arg280His, – LIG1 T C (exon 25), A C (exon 6), C T (exon 2), and A G (intr
on 1), – and LIG3 C T (exon 21) polymorphisms – with the risk of lung and head-and-neck cancer, and to investigate whet
her these polymorphisms alter the effects of environmental risk factors, including active and passive cigarette smoking and alcohol drinking, on the development of lung and head-and-neck cancer in the population of Los Angeles County.
Study DesignStudy Design Study design: A population-based case-control study in
Los Angeles County
Subjects Selection Criteria– Patients must be newly diagnosed – Both genders– Ages 18-65 years– Residents of Los Angeles County during the observation period
(1999-2004)– In stable medical condition as determined by their physician
Epidemiology data collection– Interviewed by trained interviewers; 30 ml of buccal cell samples
were collected during the time of interviews
Data sourcesData sources
Data from cancer surveillance program
Questionnaire data Buccal cells were collected
– About 90% of subjects donated buccal cells.
Dietsys USDA food composition data Continuing survey of food intake
for individuals (CSFII)
sociodemographic characteristics
history of tobacco smoking
environmental tobacco smoking
drug use
alcohol use
occupational exposures
environmental exposures
selected clinical factors
food frequency questionnaire
RESPONSE RATES OF THE PARTICIPANTS
Eligible Interviewed (%) Buccal Biospecimen (%)
Control 1540 1040 (67.5) 928 (89.2)
Lung 1577 611 (38.7) 544 (89.0)
Oral 584 303 (51.9) 195 (64.4)
Esophageal 316 108 (34.2) 97 (89.8)
Pharynx 238 100 (42.0) 77 (77.0)
Larynx 226 90 (39.8) 79 (87.8)
Laboratory AssaysLaboratory Assays DNA Extraction and Genotyping
– Genomic DNA was isolated using a modified phenol-chloroform protocol.
– Genotyping of the SNPs was assayed by SNPlexTM techniques.
– PCR-RFLP was used for validation
Confounding VariablesConfounding Variables
Age – <35, 35-36, 37-38, 39-40, 41-42, 43-44, 45-46, 47-48,
49-50, 51-52, 53-54, 55-56, 57-58, and 59-62 Gender Race/ethnicity
– white, Mexican American, African American, Asian American, and other
Education level – years of schooling
Pack-years of smoking Alcohol consumption (for head-and-neck cancer
only) – alcohol drink-years
Logistic Regression Model for Logistic Regression Model for Individual AssociationsIndividual Associations
Logit (R)= α + β1(PCNA) + β2(pack-years) + β3(age) + β4 (gender) + β5(education level) + β6(ethnicity)
Interaction AssessmentInteraction Assessment
To assess a potential gene-environment interaction, a product term is added that allows the effect estimate for one variable to vary within levels of another, and vice versa.
Logit (R)= α + β1(PCNA) + β2(smokingY/N) + β3(age) + β4 (gender) + β5(education level) + β6(ethnicity) + 12 (PCNAsmokingY/N)
False Positive AssessmentFalse Positive Assessment
FPRP = (1-)/[(1-)+(1-)] = 1/{1+[/(1- )][(1- )/]}
: prior probability
: statistical size 1- : probability of rejecting when alternative hypothesis
is true
Wacholder et al., 2004
Haplotype MethodHaplotype Method
SNPs in one gene may have linkage disequilibrium and may be associated with cancer risk as haplotype or linked with unmeasured candidate genes.
Haplotypes were reconstructed using the PHASE version 2.
Statistical AnalysisStatistical Analysis We used SAS 9.1 software to perform data
analyses.
Primarily, unconditional logistic regression was employed to obtain odds ratios and 95% confidence limits.
Stratified analysis was used to assess effect modification.
Demographic characteristics for lung cancer cases and population controlsDemographic characteristics for lung cancer cases and population controlsVariables Lung Cancer Cases (n = 611)
N (%)Controls (n = 1029)
N (%)
With DNA(551)
Without DNA(60)
With DNA(939)
Without DNA(90)
Mean Age (years)(Age range)
52.2 (32 – 59)
52.3(41 – 59)
50.2 (29 – 62)
49.5(30 – 60)
P-value = 0.90 P-value = 0.37
Age (years) < 35 35-44 45-54 55
4 (0.73) 51 (9.3)273 (50)223 (40)
0 (0.0)6 (10)
28 (47)26 (43)
38 (4.1)155 (17)452 (48)294 (31)
3 (3.3)16 (18)47 (52)24 (27)
P-value = 0.88 P-value = 0.79
Race/Ethnicity Caucasian Mexican American African American Asian American Other Missing
320 (58)50 (9.1)90 (16)59 (11)31 (5.6)
1
39 (65)3 (5.0)6 (10)
11 (18)1 (1.7)
0
583 (62)140 (15)79 (8.4)53 (5.7)83 (8.9)
1
45 (50)8 (8.9)23 (25)7 (7.8)7 (7.8)
0
P-value = 0.13 P-value < 0.0001
Gender Male Female
278 (50)273 (50)
25 (42)35 (58)
575 (61)364 (39)
41 (46)49 (54)
P-value = 0.20 P-value = 0.004
Education Level 12 years >12 - 16 years > 16 years Missing
248 (45)248 (45)55 (10)
0
17 (28)27 (45)16 (27)
0
276 (29)422 (45)240 (26)
1
23 (26)49 (54)18 (20)
0
P-value = 0.0003 P-value = 0.22
Association between tobacco smoking and alcohol consumption and lung cancer riskAssociation between tobacco smoking and alcohol consumption and lung cancer risk
Tobacco Smoking
Cases Controls Adjusted OR (95% CL)
Pack-Years*
0 110 484 1.0
>0-20 102 350 1.4 (0.99, 1.9)
>20-40 202 136 8.3 (6.0, 12)
>40 197 58 22 (15, 33)
Trends Ptrend < .0001
Alcohol(drinks/day)**
0 - <2 446 870 1.0
2 164 156 1.1 (0.80, 1.5)
*Adjusted for age, gender, ethnicity, and education.**Adjusted for age, gender, ethnicity, education and pack-years of smoking.
THE ASSOCIATION BETWEEN THE ASSOCIATION BETWEEN PCNAPCNA (C (C T) (rs25406) IN INTRON 2 AND LUNG CANCER RISK T) (rs25406) IN INTRON 2 AND LUNG CANCER RISK
Stratified by Cases N (%)
Controls N (%)
Crude OR(95% CL)
Adjusted OR(95% CL)
PCNA genotypesa
CC 128 (33.3) 259 (36.3) 1.0 1.0
CT 177 (46.1) 357 (50.1) 1.0 (0.76, 1.3) 0.90 (0.65, 1.2)
TT 79 (20.6) 97 (13.6) 1.6 (1.1, 2.4) 1.4 (0.89, 2.1)
Ptrend = 0.0228 Ptrend = 0.3060
CC + CT 305 (79.4) 616 (86.4) 1.0 1.0
TT 79 (20.6) 97 (13.6) 1.6 (1.2, 2.3) 1.5 (0.99, 2.1)
Pack-years of Smokingb
0
CC + CT 55 (85.9) 289 (86.8) 1.0 1.0
TT 9 (14.1) 44 (13.2) 1.1 (0.50, 2.3) 0.89 (0.38, 2.0)
>0 – 20
CC + CT 49 (84.5) 211 (85.4) 1.0 1.0
TT 9 (15.5) 36 (14.6) 1.1 (0.49, 2.4) 0.97 (0.43, 2.2)
>20
CC + CT 201 (76.7) 116 (87.2) 1.0 1.0
TT 61 (23.3) 17 (12.8) 2.1 (1.2, 3.7) 2.4 (1.3, 4.5)a Adjusted for gender, age, education, ethnicity, and tobacco smoking (pack-years).b Adjusted for gender, age, education, and ethnicity.
THE ASSOCIATION BETWEEN THE ASSOCIATION BETWEEN PCNAPCNA (C (C T) (rs25406) IN INTRON 2 T) (rs25406) IN INTRON 2 AND LUNG CANCER RISKAND LUNG CANCER RISK
Stratified by Cases N (%)
Controls N (%)
Crude OR(95% CL)
Adjusted OR(95% CL)
Alcohol Drinking (Drinks/Day)a
0 - <2
CC + CT 227 (82.2) 517 (86.6) 1.0 1.0
TT 49 (17.8) 80 (13.4) 1.4 (0.95, 2.1) 1.3 (0.80, 2.0)
2
CC + CT 77 (72.0) 98 (85.2) 1.0 1.0
TT 30 (28.0) 17 (14.8) 2.2 (1.2, 4.4) 2.2 (0.99, 4.9)
a Adjusted for gender, age, education, ethnicity, and tobacco smoking (pack-years).
THE ASSOCIATION BETWEEN THE ASSOCIATION BETWEEN PCNAPCNA (C (C T) (rs25406) IN INTRON 2 T) (rs25406) IN INTRON 2 AND LUNG CANCER RISKAND LUNG CANCER RISK
Stratified by Cases N (%)
Controls N (%)
Crude OR(95% CL)
Adjusted OR(95% CL)
Histologya
Large cell
CC + CT 50 (73.5) 616 (86.4) 1.0 1.0
TT 18 (26.5) 97 (13.6) 2.3 (1.3, 4.1) 2.1 (1.1, 4.1)
Small cell
CC + CT 38 (80.8) 616 (86.4) 1.0 1.0
TT 9 (19.2) 97 (13.6) 1.5 (0.71, 3.2) 1.6 (0.67, 3.9)
Squamous cell
CC + CT 45 (83.3) 616 (86.4) 1.0 1.0
TT 9 (16.7) 97 (13.6) 1.3 (0.60, 2.7) 1.2 (0.51, 2.9)
Adenocarcinoma
CC + CT 156 (78.8) 616 (86.4) 1.0 1.0
TT 42 (21.2) 97 (13.6) 1.7 (1.1, 2.6) 1.7 (1.1, 2.6)a Adjusted for gender, age, education, ethnicity, and tobacco smoking (pack-years).
THE ASSOCIATION BETWEEN THE ASSOCIATION BETWEEN PCNAPCNA (C (C T) (rs25406) IN INTRON 2 AND T) (rs25406) IN INTRON 2 AND LUNG CANCER RISKLUNG CANCER RISK
Stratified by Cases N (%)
Controls N (%)
Crude OR(95% CL)
Adjusted OR(95% CL)
Ethnicityc
Caucasian
CC + CT 174 (76.0) 386 (86.3) 1.0 1.0
TT 55 (24.0) 61 (13.7) 2.0 (1.3, 3.0) 1.9 (1.1, 3.2)
Mexican/Hispanic
CC + CT 27 (93.1) 101 (91.8) 1.0 1.0
TT 2 (6.9) 9 (8.2) 0.83 (0.17, 4.1) 0.64 (0.11, 3.9)
African American
CC + CT 50 (84.7) 48 (81.4) 1.0 1.0
TT 9 (15.3) 11 (18.6) 0.79 (0.30, 2.1) 0.66 (0.20, 2.2)
Asian
CC + CT 38 (86.4) 28 (80.0) 1.0 1.0
TT 6 (13.6) 7 (20.0) 0.63 (0.19, 2.1) 0.48 (0.12, 1.8)
Other**
CC + CT 16 (72.7) 53 (85.5) 1.0 1.0
TT 6 (27.3) 9 (14.5) 2.2 (0.68, 7.1) 2.7 (0.72, 10)c Adjusted for age, gender, education, and tobacco smoking (pack-years).
Gene SNP
Stratum OR(95%CL)
Power under recessive modela
Reported P value
Prior Probabilityb
.5 .25 .1 .01 .001
PCNA All (TT vs. CC+CT)
1.5 (0.99, 2.1) 0.79 0.018 .022 .065 .172 .695 .958
Heavy smokers 2.4 (1.3, 4.5) 0.25 0.006 .025 .071 .186 .715 .962
Heavy drinkers 2.2 (0.99, 4.9) 0.21 0.054 .203 .434 .697 .962 .996
Large cell 2.1 (1.1, 4.1) 0.26 0.030 .103 .255 .507 .919 .991
Adenocarcinoma 1.7 (1.1, 2.6) 0.49 0.014 .028 .081 .209 .744 .967
Caucasian 1.9 (1.1, 3.2) 0.46 0.016 .033 .093 .236 .773 .972
FALSE POSITIVE REPORT PROBABILITY FOR MAJOR LUNG CANCER FALSE POSITIVE REPORT PROBABILITY FOR MAJOR LUNG CANCER RESULTS RESULTS
a Estimation of the statistical power to detect an OR of 1.5 with level of 0.05.b False-positive report probabilities for the observed odds ratios.
ASSOCIATIONS OF THE ASSOCIATIONS OF THE LIG1 LIG1 HAPLOTYPES OF THE FOUR SNPS HAPLOTYPES OF THE FOUR SNPS AND LUNG CANCERAND LUNG CANCER
TCCA CACA CATA CCCG CCCA CCTA TACA All Others
Overall, n (case/control)
346/695 325/582 112/169 51/65 11/25 18/28 3/8 10/6
Crude OR1.0 1.1
(0.93, 1.4)1.3
(1.0, 1.4)1.6
(1.1, 2.3)0.88
(0.43, 1.8)1.3
(0.70, 2.4)0.75
(0.20, 2.9)3.3
(1.2, 9.3)
Adj ORa
1.0 1.2 (0.95, 1.5)
1.4 (1.0, 1.9)
1.8 (1.1, 2.8)
0.81 (0.35, 1.9)
1.6 (0.78, 3.1)
1.3 (0.31, 5.9)
3.2 (0.99, 11)
* Adjusted for gender, age, education, ethnicity, and tobacco smoking (pack-years).
ASSOCIATIONS OF THE ASSOCIATIONS OF THE LIG1 LIG1 HAPLOTYPES AND LUNG CANCERHAPLOTYPES AND LUNG CANCER
TCCA CACA CATA CCCG CCCA CCTA TACA All Others
Stratified by Smoking status
Never 55/322 68/272 15/71 13/30 1/15 1/15 0/5 1/2
Crude OR 1.01.5
(1.0, 2.2)1.2
(0.66, 2.3)2.5
(1.2, 5.2)0.39
(0.051, 3.0) 0.39
(0.051, 3.0)- 2.9
(0.26, 33)
Adj Orb 1.01.4
(0.94, 2.1)1.2
(0.62, 2.2)2.3
(1.1, 4.8)0.34
(0.043, 2.6)0.40
(0.051, 3.1)- 2.6
(0.22, 30)
Former 209/252 180/208 63/63 27/18 7/9 12/8 2/2 8/4
Crude OR 1.01.0
(0.80, 1.4)1.2
(0.81, 1.8) 1.8
(0.97, 3.4)0.94
(0.34, 2.6)1.8
(0.73, 4.5)1.2
(0.17, 8.6)2.4
(0.72, 8.1)
Adj ORb 1.01.0
(0.79, 1.4)1.2
(0.78, 1.8)1.5
(0.78, 2.8)0.84
(0.30, 2.3)2.1
(0.84, 5.3)1.3
(0.18, 9.1)2.9
(0.84, 9.8)
Current 82/121 77/102 34/35 11/17 3/1 5/5 1/1 1/0
Crude OR 1.01.1
(0.74, 1.7)1.4
(0.83, 2.5)0.96
(0.43, 2.1)4.4
(0.45, 43)1.5
(0.41, 5.3)1.5
(0.091, 24)-
Adj ORb 1.01.1
(0.74, 1.7)1.5
(0.85, 2.6)0.94
(0.41, 2.2)4.4
(0.44, 44)1.3
(0.35, 4.6)1.5
(0.088, 26)-
b Adjusted for gender age, education, and ethnicity.
MULTIGENETIC ASSOCIATION WITH LUNG CANCER MULTIGENETIC ASSOCIATION WITH LUNG CANCER
# of Potential Risk Genotypes
Cases Control Crude OR Adjusted OR*
0 50 (24.5) 157 (34.3) 1.0 1.0
1-2 122 (59.8) 237 (51.7) 1.6 (1.1, 2.4) 1.7 (1.1, 2.7)
3-5 32 (15.7) 64 (14.0) 1.6 (0.92, 2.7) 2.2 (1.1, 4.1)
Ptrend = 0.038 Ptrend = 0.0104
Continuous 1.1 (0.98, 1.3) 1.2 (1.0, 1.5)
* Adjusted for age, gender, education, race/ethnicity and pack-years of smoking.
Discussion on BER ResultsDiscussion on BER Results We observed an overall association of PCNA (C T) SNP with lun
g cancer risk, and the smoking status in pack-years and alcohol drinking status seemed to modify the association of PCNA SNP with lung cancer.
We did not detect any consistent association between individual LIG1 polymorphisms and lung cancer.
When we considered all the SNPs together as haplotypes, we observed the associations between the LIG1 haplotypes and the cancer risks.
The dose-response association of these SNPs in the BER pathway suggested the possible interaction among these SNPs since they are the components involved in this pathway. This also explained why we could not detect the individual SNP association. The SNPs in the same pathway work together to maintain the genome stability.
NER Pathway
Costa RM, 2003
OR (95% CL) XPG Cases N (%)
Controls N (%) Crude Adjusted1
All lung cancer cases
His/His 244 (49.1) 468 (51.9) 1.0 1.0 His/Asp 212 (42.7) 356 (39.5) 1.1 (0.91, 1.4) 1.1 (0.80, 1.4) Asp/Asp 41 (8.2) 78 (8.6) 1.0 (0.67, 1.5) 0.65 (0.39, 1.1) Ptrend=0.51 Ptrend=0.36 His/His+His/Asp 456 (91.8) 824 (91.4) 1.0 1.0 Asp/Asp 41 (8.2) 78 (8.6) 0.95 (0.64, 1.4) 0.62 (0.38, 1.0)
Histology-specific
Adenocarcinoma His/His+His/Asp 221 (91.3) 824 (91.4) 1.0 1.0 Asp/Asp 21 (8.7) 78 (8.6) 1.0 (0.61, 1.7) 0.69 (0.39, 1.2) Squamous cell carcinoma His/His+His/Asp 68 (86.1) 824 (91.4) 1.0 1.0 Asp/Asp 11 (13.9) 78 (8.6) 1.7 (0.87, 3.4) 1.0 (0.45, 2.3) Small-cell lung cancer His/His+His/Asp 60 (93.7) 824 (91.4) 1.0 1.0 Asp/Asp 4 (6.3) 78 (8.6) 0.70 (0.25, 2.0) 0.55 (0.18, 1.7) Large-cell lung cancer His/His+His/Asp 85 (95.5) 824 (91.4) 1.0 1.0 Asp/Asp 4 (4.5) 78 (8.6) 0.50 (0.18, 1.4) 0.31 (0.10, 0.92)
XPG polymorphism and the risk of lung cancer
1Adjusted for age, sex, race-ethnicity, educational level, and tobacco smoking.
Joint effect of tobacco smoking and XPG polymorphism on lung cancer risk
0
5
10
15
20
25
Pack-years: Never 1-20 >20 Never 1-20 >20
XPG: Asp/Asp Asp/Asp Asp/Asp His/His +His/Asp His/His +His/Asp His/His +His/Asp
Departure from additivity:
23-13-1.9+1=9.1, 95% CL=-2.9, 21.7
Joint effect of tobacco, alcohol, and XPG polymorphism on SCCUAT
0
2
4
6
8
10
12
14
16
18
Drinks per day: 1-2 1-2 >=3 >=3 1-2 1-2 >=3 >=3
Packyears: <=20 <=20 <=20 <=20 >20 >20 >20 >20
XPG: Asp/Asp His/His +His/Asp Asp/Asp His/His +His/Asp Asp/Asp His/His +His/Asp Asp/Asp His/His +His/Asp
NER Cases (%) Controls (%) Crude OR Adjusted OR*
All Lung Cancer Cases
ERCC6 Q1413R
Q/Q 251 (62.0%) 451 (61.4) 1.0 1.0
Q/R 125 (30.9%) 254 (34.6%) 0.88 (0.68, 1.15) 1.23 (0.89, 1.70)
R/R 29 (7.2%) 29 (4.0%) 1.80 (1.05, 3.08) 2.10 (1.09, 4.03)
Ptrend=0.02
Q/Q + Q/R 376 (92.8%) 705 (96.1%) 1.0 1.0
R/R 29 (7.2%) 29 (4.0%) 1.88 (1.10, 3.19) 1.94 (1.02, 3.68)
Total 405 (100%) 734 (100%)
ERCC6 R1230P
R/R 420 (85.4%) 756 (86.7%) 1.0 1.0
P/R 67 (13.6%) 107 (12.3%) 1.13 (0.81, 1.56) 1.13 (0.76, 1.69)
P/P 5 (1.0%) 9 (1.0%) 1.00 (0.33, 3.00) 1.37 (0.36, 5.26)
Ptrend=0.46
P/R + P/P 72 (14.6%) 116 (13.3%) 1.0 1.0
R/R 420 (85.4%) 756 (86.7%) 0.90 (0.65, 1.23) 0.87 (0.59, 1.29)
Total 492 (100%) 872 (100%)
TABLE III – ASSOCIATION BETWEEN THE NER POLYMORPHISM AND THE RISK OF LUNG CANCER STRATIFIED BY PATHOLOGICAL DIAGNOSIS
Gene / SNP Cases (%) Controls (%) Crude OR Adjusted OR*
RCC6 Q1413R
Adenocarcinoma
Q/Q + Q/R 184 (92.5%) 705 (96.1%) 1.0 1.0
R/R 15 (7.5%) 29 (4.0%) 1.98 (1.04, 3.77) 2.19 (1.05, 4.59)
Total 199 (100%) 734 (100%)
Squamous
Q/Q + Q/R 59 (95.2%) 705 (96.1%) 1.0 1.0
R/R 3 (4.8%) 29 (4.0%) 1.24 (0.37, 4.18) 1.66 (0.38, 7.19)
Total 62 (100%) 734 (100%)
Small Cell
Q/Q + Q/R 46 (90.2) 705 (96.1%) 1.0 1.0
R/R 5 (9.8%) 29 (4.0%) 2.64 (0.98, 7.15) 2.18 (0.63, 7.47)
Total 51 (100%) 734 (100%)
Large Cell
Q/Q + Q/R 72 (93.5%) 705 (96.1%) 1.0 1.0
R/R 5 (6.5%) 29 (4.0%) 1.69 (0.63, 4.50) 2.19 (0.71, 6.78)
Total 77 (100%) 734 (100%)
SmokerERCC6 Q1413R Cases Controls Adjusted OR*
No Q/Q + Q/R 64 324 1.0
No R/R 2 18 0.59 (0.12, 2.82)
Yes Q/Q + Q/R 312 381 4.41 (3.18, 6.14)
Yes R/R 27 11 19.44 (8.33, 45.35)
OR interaction = 5.82 (1.08, 31.38)
Smoker ERCC6 R1230P Cases Controls Adjusted OR*
No R/R 41 202 1.0
No P/R + P/P 25 140 2.87 (1.28, 6.40)
Yes R/R 210 249 4.29 (3.12, 5.92)
Yes P/R + P/P 129 143 5.63 (3.43, 9.24)
OR interaction = 0.56 (0.25, 1.27)
TABLE III – ASSOCIATION BETWEEN THE NER POLYMORPHISM AND THE RISK OF LUNG CANCER STRATIFIED BY PATHOLOGICAL DIAGNOSIS
Gene / SNP Cases (%) Controls (%) Crude OR Adjusted OR*
RCC6 Q1413R
Adenocarcinoma
Q/Q + Q/R 184 (92.5%) 705 (96.1%) 1.0 1.0
R/R 15 (7.5%) 29 (4.0%) 1.98 (1.04, 3.77) 2.19 (1.05, 4.59)
Total 199 (100%) 734 (100%)
Squamous
Q/Q + Q/R 59 (95.2%) 705 (96.1%) 1.0 1.0
R/R 3 (4.8%) 29 (4.0%) 1.24 (0.37, 4.18) 1.66 (0.38, 7.19)
Total 62 (100%) 734 (100%)
Small Cell
Q/Q + Q/R 46 (90.2) 705 (96.1%) 1.0 1.0
R/R 5 (9.8%) 29 (4.0%) 2.64 (0.98, 7.15) 2.18 (0.63, 7.47)
Total 51 (100%) 734 (100%)
Large Cell
Q/Q + Q/R 72 (93.5%) 705 (96.1%) 1.0 1.0
R/R 5 (6.5%) 29 (4.0%) 1.69 (0.63, 4.50) 2.19 (0.71, 6.78)
Total 77 (100%) 734 (100%)
Double Strand Break RepairDouble Strand Break Repair
NBS1 protein (Nibrin or p95)NBS1 protein (Nibrin or p95)Has 3 known functional regions:N-terminus (1-196 a.a.)Central region (278-343 a.a.)C-terminus (665-693 a.a.)
– Believed to bind site to the MRN complex
Variable Controls (%)HWE p-value
Cases (%) HWE p-value
Crude OR (95% CI)
ORadj (95% CI)*
Ex16+1785 T>C
T/T 369 (45.95) 211 (46.68) 1.0 1.0
C/T 363 (45.21) 0.19 188 (41.59) 0.28 0.91 (0.71, 1.16) 0.85 (0.63, 1.13)
C/C 71 (8.84) 53 (11.73) 1.31 (0.88, 1.94) 1.12 (0.69, 1.80)
Missing 226 159 p-trend= 0.5974
Ex16+572 C>G
C/C 397 (45.74) 223 (45.70) 1.0 1.0
C/G 397 (45.74) 0.83 208 (42.62) 0.41 0.93 (0.74, 1.18) 0.88 (0.67, 1.17)
G/G 74 (8.53) 57 (11.68) 1.37 (0.94, 2.01) 1.35 (0.85, 2.14)
Missing 161 123 p-trend=0.628
Pro672Pro
A/A 356 (44.33) 233 (50.76) 1.0 1.0
A/G 366 (45.58) 0.40 169 (36.82) 0.0043a 0.71 (0.55, 0.90) 0.71 (0.53, 0.95)
G/G 81 (10.09) 57 (12.42) 1.08 (0.74, 1.57) 1.25 (0.80, 1.96)
Missing 226 152 p-trend=0.7126
Table III. Association of Pro672Pro and lung cancer (smoking and Table III. Association of Pro672Pro and lung cancer (smoking and passive smoking exposure)passive smoking exposure)
Pro672Pro Controls (%) Cases (%) Crude OR (95% CI) ORadj (95% CI)*
Never-smokers
wt/wt 170 (45.3) 32 (39.5) 1.0 1.0
wt/var 165 (44) 34 (42.0) 1.10 (0.65, 1.86) 1.27 (0.71, 2.26)
var/var 40 (10.7) 15 (18.5) 1.99 (0.99, 4.03) 1.92 (0.85, 4.36)
Ever-smokers
wt/wt 186 (43.5) 201 (53.2) 1.0 1.0
wt/var 201 (47.0) 135 (35.7) 0.62 (0.46, 0.84) 0.66 (0.48, 0.90)
var/var 41 (9.6) 42 (11.1) 0.95 (0.59, 1.52) 1.22 (0.73, 2.05)
Passive no exposure
wt/wt 40 (46.5) 10 (40.0) 1.0 1.0
wt/var 39 (45.4) 10 (40.0) 1.03 (0.38, 2.74) 1.57 (0.47, 5.23)
var/var 7 (8.1) 5 (20.0) 2.86 (0.75, 10.92) 5.42 (0.88, 33.54)
Yes exposure
wt/wt 130 (45.1) 22 (39.3) 1.0 1.0
wt/var 126 (43.8) 24 (42.9) 1.13 (0.60, 2.11) 1.29 (0.65, 2.55)
var/var 32 (11.1) 10 (17.9) 1.85 (0.80, 4.28) 1.59 (0.61, 4.13)
Table IV. Associations of NBS1 polymorphisms and lung cancer, Table IV. Associations of NBS1 polymorphisms and lung cancer, stratified by smoking and passive smokingstratified by smoking and passive smoking
Variables Ex16+1785 T>C Ex16+572 C>G
Controls Cases ORadj (95% CI)* controls Cases ORadj (95% CI)*
Stratify by smoking
No
wt/wt + wt/var 345 68 1.0 376 75 1.0
var/var 28 10 2.05 (0.86, 4.87) 34 13 1.82 (0.83, 3.99)
Yes
wt/wt + wt/var 387 331 1.0 418 356 1.0
var/var 43 43 1.19 (0.74, 1.92) 40 44 1.35 (0.84, 2.19)
Stratified by passive smoking
No
wt/wt + wt/var 80 24 1.0 90 28 1.0
var/var 6 1 0.61 (0.04, 9.31) 7 1 0.40 (0.03, 5.38)
Yes
wt/wt + wt/var 265 44 1.0 286 47 1.0
var/var 21 9 2.84 (1.11, 7.28) 26 12 2.74 (1.16, 6.47)
DNA Methylation and Risk of DNA Methylation and Risk of Lung CancerLung Cancer
Source: Sharp 2004.
THF cycle
Methionine cycle
DNA Methylation and Lung Cancer DNA Methylation and Lung Cancer RiskRisk
Controls Small Cell Lung Cancer Non-Small Cell Lung Cancer Methylation N (%) N (%) Crude OR
(95% CI) Adjusted OR1
(95% CI) N (%) Crude OR
(95% CI) Adjusted OR1
(95% CI) P16
No 769 (84) 54 (79) 1.00 1.00 379 (82) 1.00 1.00 Yes 146 (16) 14 (21) 1.37 (0.74-2.52) 1.43 (0.69-3.00) 86 (18) 1.20 (0.89-1.60) 1.27 (0.90-1.80)
MGMT
No 721 (82) 50 (81) 1.00 1.00 330 (77) 1.00 1.00 Yes 157 (18) 12 (19) 1.10 (0.57-2.12) 0.99 (0.47-2.10) 100 (23) 1.39 (1.05-1.85) 1.22 (0.87-1.70)
GSTP1
No 675 (88) 44 (85) 1.00 1.00 310 (85) 1.00 1.00 Yes 96 (12) 8 (15) 1.18 (0.52-2.71) 1.35 (0.55-3.31) 53 (15) 1.20 (0.84, 1.73) 1.12 (0.73-1.70)
Number of
0 590 (64) 41 (60) 1.00 1.00 272 (58) 1.00 1.00 1 262 (29) 21 (31) 1.08 (0.60-1.93) 0.94 (0.49-1.78) 150 (32) 1.24 (0.97-1.59) 1.18 (0.88-1.58)
2-3 64 (7) 6 (9) 1.44 (0.59-3.55) 1.81 (0.67-4.91) 43 (9) 1.46 (0.97-2.20) 1.38 (0.85-2.24)
continuous 1.15 (0.81-1.65) 1.16 (0.76-1.76) 1.19 (1.01-1.41) 1.15 (0.95-1.39) Adjusted for age (continuous), sex, race, and pack-year of smoking
P16 hypermethylation and Lung Cancer P16 hypermethylation and Lung Cancer Risk by smoking, drinking, and folate Risk by smoking, drinking, and folate
intakeintakeControls Lung P16
methylation N (%) N (%) Crude OR (95% CI)
Adjusted OR (95% CI)
Smoking (pack-year)
1
Never No 358 (39) 74 (14) 1.00 1.00 Never Yes 72 (8) 21 (4) 1.41 (0.82-2.44) 1.32 (0.75-2.31) >0-40 No 367 (40) 219 (41) 1.00 1.00 >0-40 Yes 66 (7) 45 (8) 1.14 (0.76-1.73) 1.18 (0.77-1.80) >40 No 43 (5) 140 (26) 1.00 1.00 >40 Yes 8 (1) 34 (6) 1.31 (0.56-3.03) 1.36 (0.58-3.18)
Drinking (drinks/day)
2
0-2 No 648 (71) 311 (58) 1.00 1.00 0-2 Yes 122 (13) 73 (14) 1.25 (0.91-1.72) 1.42 (0.98-2.05) 2 No 118 (13) 121 (23) 1.00 1.00 2 Yes 24 (3) 27 (5) 1.10 (0.60-2.01) 0.92 (0.41-2.06)
Folate (g/day)
2
>200 No 276 (36) 156 (31) 1.00 1.00 >200 Yes 53 (7) 45 (9) 1.50 (0.96-2.34) 1.51 (0.89-2.57) 200 No 357 (47) 246 (50) 1.00 1.00 200 Yes 77 (10) 48 (10) 0.90 (0.61-1.34) 0.96 (0.60-1.54) 1. Adjusted for age (continuous), sex, and race. 2. Adjusted for age (continuous), sex, race, and pack-years of smoking
MGMT hypermethylation and Lung cancer MGMT hypermethylation and Lung cancer Risk by smoking, drinking, and folate Risk by smoking, drinking, and folate
intakeintakeControls Lung MGMT methylation
N (%) N (%) Crude OR (95% CI)
Adjusted OR (95% CI)
Smoking (pack-year)
1
Never No 341 (39) 68 (14) 1.00 1.00 Never Yes 77 (9) 17 (3) 1.11 (0.62-1.99) 1.05 (0.57-1.92) >0-40 No 337 (38) 198 (40) 1.00 1.00 >0-40 Yes 71 (8) 50 (10) 1.20 (0.80-1.79) 1.20 (0.79-1.82) >40 No 43 (5) 114 (23) 1.00 1.00 >40 Yes 9 (1) 45 (9) 1.89 (0.85-4.18) 2.05 (0.91-4.61)
Drinking (drinks/day)
2
0-2 No 607 (69) 276 (56) 1.00 1.00 0-2 Yes 132 (15) 80 (16) 1.33 (0.98-1.82) 1.19 (0.83-1.72) 2 No 112 (13) 103 (21) 1.00 1.00 2 Yes 25 (3) 32 (7) 1.39 (0.77-2.50) 1.18 (0.57-2.46)
Folate (g/day)
2
>200 No 249 (34) 132 (29) 1.00 1.00 >200 Yes 68 (9) 51 (11) 1.41 (0.93-2.15) 1.12 (0.68-1.86) 200 No 340 (47) 217 (48) 1.00 1.00 200 Yes 73 (10) 56 (12) 1.20 (0.82-1.77) 1.06 (0.66-1.69) 1. Adjusted for age (continuous), sex, and race. 2. Adjusted for age (continuous), sex, race, and pack-years of smoking
GSTP1 hypermethylation and Lung GSTP1 hypermethylation and Lung cancer Risk by smoking, drinking, and cancer Risk by smoking, drinking, and
folate intakefolate intakeControls Lung GSTP1 methylation N (%) N (%) Crude OR
(95% CI) Adjusted OR
(95% CI) Smoking
(pack-year) 1
Never No 313 (41) 62 (15) 1.00 1.00 Never Yes 47 (6) 12 (3) 1.29 (0.65-2.57) 1.24 (0.61-2.52) >0-40 No 326 (42) 171 (41) 1.00 1.00 >0-40 Yes 43 (6) 33 (8) 1.46 (0.90-2.39) 1.34 (0.81-2.22) >40 No 36 (5) 121 (29) 1.00 1.00 >40 Yes 6 (1) 16 (4) 0.79 (0.29-2.18) 0.76 (0.27-2.12)
Drinking (drinks/day)
2
0-2 No 562 (73) 251 (61) 1.00 1.00 0-2 Yes 85 (11) 48 (11) 1.26 (0.86-1.86) 1.17 (0.75-1.82) 2 No 111 (14) 102 (25) 1.00 1.00 2 Yes 11 (1) 13 (3) 1.29 (0.55-3.00) 1.19 (0.44-3.22)
Folate (g/day)
2
>200 No 235 (37) 133 (34) 1.00 1.00 >200 Yes 44 (7) 25 (6) 1.00 (0.59-1.71) 0.90 (0.48-1.69) 200 No 321 (50) 197 (51) 1.00 1.00 200 Yes 42 (6) 32 (8) 1.24 (0.76-2.03) 1.30 (0.73-2.34) 1. Adjusted for age (continuous), sex, and race. 2. Adjusted for age (continuous), sex, race, and pack-years of smoking
Number of methylated genes and lung Number of methylated genes and lung cancer Risk by smoking, drinking, and cancer Risk by smoking, drinking, and
folate intakefolate intakeControls Lung Number of
methylated genes N (%) N (%) Crude OR (95% CI)
Adjusted OR (95% CI)
Smoking (pack-year)
1
Never 0-1 398 (43) 87 (16) 1.00 1.00 Never 2-3 32 (4) 8 (2) 1.14 (0.51-2.57) 0.97 (0.43-2.23) >0-40 0-1 402 (44) 240 (45) 1.00 1.00 >0-40 2-3 31 (3) 24 (5) 1.30 (0.74-2.26) 1.30 (0.74-2.31) >40 0-1 51 (6) 157 (29) 1.00 1.00 >40 2-3 1 (0.1) 17 (3) 5.52 (0.72-42.46) 5.69 (0.73-44.22)
Drinking (drinks/day)
2
0-2 0-1 715 (78) 346 (65) 1.00 1.00 0-2 2-3 55 (6) 38 (7) 1.43 (0.93-2.20) 1.41 (0.86-2.33) 2 0-1 134 (15) 137 (26) 1.00 1.00 2 2-3 9 (1) 11 (2) 1.20 (0.48-2.98) 1.01 (0.31-3.24)
Folate (g/day)
2
>200 0-1 302 (40) 179 (36) 1.00 1.00 >200 2-3 27 (4) 22 (4) 1.37 (0.76-2.49) 1.17 (0.58-2.39) 200 0-1 402 (53) 271 (55) 1.00 1.00 200 2-3 33 (4) 23 (5) 1.03 (0.59-1.80) 1.05 (0.54-2.05) 1. Adjusted for age (continuous), sex, and race. 2. Adjusted for age (continuous), sex, race, and pack-years of smoking
Folate intake, MTHFR C677T Polymorphism Folate intake, MTHFR C677T Polymorphism on Lung Cancer Riskon Lung Cancer Risk
Control SCLC NSCLC
N (%) N (%) Adjusted OR(95% CI)
N (%) Adjusted OR(95% CI)
Folate intake(μg/day)
1 1
>300 102 (12) 4 (6) 1.00 56 (12) 1.00
200-300 265 (31) 17 (25) 1.59 (0.47-5.44) 136 (29) 1.15 (0.72-1.83)
100-200 412 (48) 34 (51) 1.52 (0.45-5.10) 214 (46) 0.83 (0.52-1.33)
≤100 78 (9) 12 (18) 2.14 (0.52-8.85) 63 (13) 0.80 (0.43-1.50)
P for trend 0.3897 0.1640
MTHFR C677T 2 2
CC 391 (42) 32 (49) 1.00 211 (49) 1.00
CT 411 (45) 26 (40) 0.89 (0.48-1.65) 171 (40) 0.78 (0.59-1.04)
TT 118 (13) 7 (11) 1.11 (0.44-2.82) 49 (11) 0.86 (0.56-1.34)
1. Adjusted for age, sex, race, pack-years of smoking, total energy intake and BMI
2. Adjusted for age, sex, race, and pack-years of smoking
Folate on Lung Cancer Risk by Smoking anFolate on Lung Cancer Risk by Smoking and Drinkingd Drinking
Control SCLC NSCLC
N N Adjusted OR(95% CI)
N Adjusted OR(95% CI)
Smoking Folate intake(μg/day)
1 1
Never >200 183 2 1.00 38 1.00
≤200 219 1 0.67 (0.05-5.81) 51 1.07 (0.66-1.74)
Former >200 120 15 1.00 111 1.00
≤200 185 29 1.29 (0.62-2.65) 165 0.92 (0.64-1.33)
Current >200 64 4 1.00 43 1.00
≤200 86 16 3.05 (0.88-10.60) 61 1.05 (0.61-1.81)
Drinking 2 2
Light >200 303 17 1.00 123 1.00
≤200 428 32 0.82 (0.39-1.72) 216 0.76 (0.55-1.06)
Heavy >200 63 4 1.00 69 1.00
≤200 61 14 4.08 (0.85-19.66) 61 0.70 (0.37-1.31)1. Adjusted for age, sex, race, total energy intake, and BMI
2. Adjusted for age, sex, race, pack-years of smoking, total energy intake, and BMI
MTHFR C677T Polymorphism on Lung MTHFR C677T Polymorphism on Lung Cancer Risk by DrinkingCancer Risk by Drinking
Control SCLC NSCLC
Drinking MTHFR
C677T
N N Adjusted OR(95% CI)
N Adjusted OR(95% CI)
Light CC 326 25 1.00 153 1.00
CT/TT 450 26 0.95 (0.50-1.81) 152 0.73 (0.54-0.98)
Heavy CC 65 7 1.00 57 1.00
CT/TT 76 7 0.87 (0.23-3.31) 58 1.20 (0.67-2.16)Adjusted for age, sex, race, and pack-years of smoking
Folate and MTHFR C677T Polymorphism on Folate and MTHFR C677T Polymorphism on Lung and Head and Neck Cancer Risks amoLung and Head and Neck Cancer Risks amo
ng Heavy Drinkersng Heavy Drinkers
Control
SCLC NSCLC SCCHN
Heavy Drinker
N N Adjusted OR(95% CI)
N Adjusted OR(95% CI)
N Adjusted OR(95% CI)
>200 CC 27 0 28 1.00 27 1.00
>200 CT/TT 31 2 1.00 33 1.12 (0.46-2.71)
29 0.78 (0.34-1.79)
≤200 CC 28 7 25 0.63 (0.24-1.66)
28 1.31 (0.52-3.28)
≤200 CT/TT 26 4 2.67 (0.20-35.60)
32 1.02 (0.40-2.65)
32 2.17 (0.86-5.45)
Adjusted for age, sex, race, pack-years of smoking, total energy intake, and BMI
IL-10IL-10 and and IFNGR1IFNGR1 Polymorphisms and Polymorphisms and Lung CancerLung Cancer
Modulation of Immune ResponseModulation of Immune Response
Achieved through balance of T-helper (Th) cells via cytokine expression – Type 1: pro-inflammatory, cellular immune response
Secrete IFNG
– Type 2: anti-inflammatory, humoral immune response Secrete IL-10
Activation of one Th-cell pathway inactivates the other
Inflammatory Anti-inflammatory
SNPsSNPs
IL-10– -7334 T→C, AKA IL-10-819– -6653 A→C, AKA IL-10-592– TA haplotype associated with low IL-10 production
IFNGR1– Associated with altered immune cell function (mice)
and respiratory disease (humans)– Ex7 +189 T→G
Table 1
Table 2
Table 3
Table 3, cont
IFNGR1 & SmokingCont Case Crude OR variance lower CL upper CL361 77 1.0
7 1 0.67 1.15861 0.08 2.51405 339 3.92 0.02118 2.95 4.95
8 17 9.96 0.19958 4.15 32.38OR-int 3.79 2.84827 0.14 11.67
Never/wNever/vEver/wEver/v
Table 4
ORint = 23.44 – 12.10 – 3.83 + 1 = 8.51
Additive Interaction
AcknowledgmentsAcknowledgmentsDr. Amy Lee
Dr. Yan Cui
Ms. Shu-Chun Chuang
Ms. Lani Park
Mr. Yiren Wang
Mr. Sam Oh
Dr. Barbara Visscher
Dr. Eric Hurwitz
Dr. Donald P. Tashkin
Dr. Jian Yu Rao
Dr. Jenny Papp
Dr. Hal Morgenstern,
Dr. Sander Greenland
Dr. Wei Cao
Dr. Wendy Cozen
Dr. Thomas M. Mack
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