Genetic variation in DNA repair may affect the clinical response to cytotoxic therapies. We investigated the effect of six single nucleotide polymorphisms of the RecQ1, RAD54L, XRCC2, and XRCC3 genes on overall survival of 378 patients with pancreatic adenocarcinoma who were treated at University of Texas M.D. Anderson Cancer Center during February 1999 to October 2004 and were followed up to October 2005. Genotypes were determined using the MassCode method. Survival was determined from pathologic diagnosis to death. Patients who were alive at the last follow-up evaluation were censored at that time. Kaplan-Meier plot, log-rank test, and Cox regression were used to compare overall survival by genotypes. A significant effect on survival of all patients was observed for RecQ1 and RAD54L genes. The median survival time was 19.2, 14.7, and 13.2 months for the RecQ1 159 AA, AC, and CC genotypes, and 16.4, 13.3, and 10.3 months for RAD54L 157 CC, CT, and TT genotypes, respectively. A significantly reduced survival was associated with the variant alleles of XRCC2 R188H and XRCC3 A17893G in subgroup analysis. When the four genes were analyzed in combination, an increasing number of adverse alleles were associated with a significantly decreased survival. Subgroup analyses have shown that the genotype effect on survival was present among patients without metastatic disease or among patients who receive radiotherapy. These observations suggest that polymorphisms of genes involved in the repair of DNA double-strand breaks significantly affect the clinical outcome of patients with pancreatic cancer. (Cancer Res 2006; 66(6): 3323-30)

DNA repair has been termed a double-edged sword because decreased DNA repair may increase the risk of developing cancer but improve survival in patients already diagnosed with cancer when treated with DNA-damaging agents. Previous studies have shown that single nucleotide polymorphisms (SNP) of nucleotide excision repair genes affected clinical outcome in patients treated with platinum-based therapy (15). Studies on the predictive and prognostic role of other DNA repair genes and clinical outcome are limited.

Pancreatic cancer is usually diagnosed at a late stage of the disease and surgical intervention is not an option for the majority of patients. Pancreatic tumors are highly aggressive and resistant to most treatment. Gemcitabine and radiotherapy [X-ray therapy (XRT)] are the current main therapeutic modalities for advanced pancreatic cancer (6, 7). However, other than stage, it is not clear what factors influence the clinical response to such treatment.

Gemcitabine is a radiosensitizer. Unlike other radiosensitizers, which either increase radiation-induced DNA damage or decrease the rate of DNA repair, gemcitabine neither increases double-strand breaks nor decreases the rate of their repair (8). Gemcitabine inhibits DNA synthesis via a process called masked chain termination. After insertion of the drug into the DNA strand, one or more nucleotide base pairs incorporate normally before the DNA chain elongation is terminated. This process locks gemcitabine into the DNA strand and prevents proofreading enzymes from detecting, excising, and repairing the DNA lesion (9). Little is known about DNA repair pathways that may alter cytotoxicity or radiosensitivity with gemcitabine. Studies in Chinese hamster ovary cell lines deficient in base excision repair, nucleotide excision repair, homologous recombination repair, and nonhomologous end joining showed similar sensitivity to gemcitabine as their parental repair-proficient cells, indicating that these pathways are most likely incapable of modulating the cytotoxicity of gemcitabine (10). However, another study has shown that gemcitabine induces radiosensitization in base excision repair–deficient cells but not in homologous recombination repair–deficient cells (11). Gemcitabine also induces substantial enhancement of the cytotoxic effect of mitomycin C in homologous recombination repair–proficient cells but not in homologous recombination repair–deficient cells (11). These observations suggest that homologous recombination repair may play an important role in gemcitabine-mediated cell killing.

For tumor cells, the most important factor influencing radiosensitivity is the expression of oncogenes and tumor suppressor genes (12). Other factors that may also alter radiosensitivity include cell cycle regulation, detoxification and stress response, and DNA repair (13). Double-strand breaks in DNA are the most common type of radiation lesions that lead to mammalian cell death. Homologous recombination repair is a major pathway of double-strand breaks repair in all eukaryotes (14) and gemcitabine-mediated radiosensitization seems to depend on the homologous recombination repair mechanism (11). To test the hypothesis that genetic variations in homologous recombination repair affect clinical response to gemcitabine/XRT therapy and, in turn, the prognosis of pancreatic cancer, we have selected six common SNPs of four homologous recombination repair genes (i.e., RecQ1, RAD54L, X-ray repair complementing (XRCC)-2 and XRCC3) and examined their association with overall survival of patients with pancreatic cancer.

RecQ1 is a member of the RecQ DNA helicase family, which is involved in recombination and in various types of DNA repair, including mismatch repair, nucleotide excision repair, and direct repair (15). Three of the five human RecQ genes (i.e., BLM, WRN, and RecQ4) have been associated with genetic disorders of Bloom, Werner, and Rothmund-Thomson syndromes, respectively, all of which are characterized by predisposition to malignancies and chromosome instability (16). RecQ helicases play multiple roles in DNA recombination and repair, S-phase checkpoint, and telomere maintenance, and thus are considered the caretakers of the genome and tumor suppressors (17, 18). The biological significance of the remaining two RecQ genes, RecQ1 and RecQ5, remains unknown. It has been suggested that RecQ1 and RecQ5 genes maybe indispensable for cell viability and may contribute to cancer susceptibility in general (17, 18). RecQ1 gene is located on chromosome 12p12, the same region harboring the K-ras gene. RecQ1 is known to be able to unwind a diverse set of DNA substrates (19, 20), to catalyze efficient strand annealing between complementary ssDNA molecules (20), and to interact with several important DNA repair factors required for DNA mismatch repair (21). Thus, it is possible that this gene plays a role in genetic predisposition to cancer and in response to cytotoxic therapy. We examined two of the most prevalent SNPs of this gene [i.e., RecQ1 3′-untranslated region A157C (rs#13035) and IVS3 A-86G (rs#4987276)] in this study. Neither of the two polymorphisms has previously been studied in association with disease risk or functional significance.

RAD54L belongs to the DEAD-like helicase superfamily (22) and it plays a role in homologous recombination repair of DNA double-strand breaks (23). The binding of this protein to double-strand DNA induces a DNA topological change, which is thought to facilitate homologous DNA pairing and stimulate DNA recombination (24). RAD54L gene is located at chromosome 1p32. A synonymous C157T (also known as 2290C/T, A730A, rs#1048771) polymorphism of the RAD54L gene has been associated with increased risk for meningioma (25). Whether this gene contributes to cellular radiosensitivity is unknown.

XRCC2 and XRCC3 are members of the RecA/Rad51-related protein family that participate in homologous recombination repair (26, 27). XRCC2 is a core component in the homologous recombination repair pathway and it forms a heterodimer with Rad51-like protein (28). High levels of aneuploidy, chromosome rearrangement, and haploinsufficiency have been observed in XRCC2 gene knockout cells (29). XRCC3 has a remarkable diverse set of functions and acts both early and late in the homologous recombination repair pathway (30). A rare microsatellite polymorphism in this gene was found to be associated with clinical radiosensitivity in cancer patients (31). XRCC2 and XRCC3 genes are located on chromosomes 7q36.1 and 14q32.3, respectively. We examined three polymorphisms of the two genes [i.e., XRCC2 R188H (exon 3 G442A, rs#3218536), XRCC3 A17893G (IVS7-14, rs#1799796), and XRCC3 T241M (exon 8 C-53T, rs#861539)]. The XRCC2 R188H variant allele has been associated with reduced cell survival after mitomycin C exposure (32). The XRCC3 A17893G polymorphism resides in the intron region and the functional significance of this SNP has not been investigated. The XRCC3 T241M variant allele has been found to have a mild effect on cell survival after radiation exposure (33).

Patient recruitment. A total of 378 patients with pathologically confirmed pancreatic ductal adenocarcinoma of all stages were recruited prospectively at the University of Texas M.D. Anderson Cancer Center (Houston, TX) between January 1999 and October 2004. These individuals participated in a larger ongoing molecular epidemiologic study in which demographic (age, sex, and race) and risk factor information (smoking status, medical history, family history of cancer, and exposures) were collected by personal interview and a blood sample was collected for genotyping at the time of enrollment. The study was approved by the Institutional Review Board of M.D. Anderson.

For this analysis, all 378 patients were treated at M.D. Anderson between January 1999 and October 2004 and were followed up to October 20, 2005. We chose October 2004 as the last month of eligibility to have at least 12 months of follow-up for all patients. We chose patients treated at our institute because information about patients treated elsewhere was often sparse, and sometimes patients treated outside were not given standard treatments or observed in standard fashions.

Clinical information was collected by reviewing the medical records of consenting patients. This included date of pathologic diagnosis, treatment received before evaluation at M.D. Anderson, clinical tumor stage (localized, locally advanced, and metastatic), performance status at first visit to M.D. Anderson, serum carbohydrate antigen 19-9 (CA19-9) values (units/mL) at diagnosis, surgical procedure and date, pre- and postoperative chemotherapy regimen and radiation, and date of death or last follow-up.

DNA extraction and genotyping. Whole blood was collected in heparinized tubes from patients at the time of enrollment into an on-going molecular epidemiology study examining pancreatic cancer risk. DNA was extracted from peripheral lymphocytes using the Qiagen DNA Isolation kit (Qiagen, Valencia, CA). Polymorphisms were detected using the MassCode technique by BioServe (Laurel, MD). About 10% of the samples were analyzed in duplicate and discrepancies were seen in <0.1% of the samples. Those with discordant results from two analyses were excluded from the final data analysis. The no call rate was 6% for RecQ1 A159C and <4% for the remaining five polymorphisms.

Survival measurements. Our primary end point was overall survival from the time of pathologic diagnosis to date of death or last follow-up for all patients. Patients who were not deceased were censored at the last date they were known to be alive based on the date of last contact. Median follow-up time was computed among censored observations only. The minimum follow-up time is 12 months and the maximum follow-up time is 60 months. Dates of death were obtained and cross-checked using at least one of the following three methods: Social Security Death Index, inpatient medical records, and the M.D. Anderson tumor registry. Date of death was obtained most often through the Social Security Death Index, but in unusual instances in which the patient's date of death was not reported there (either due to death within 3 months of the data collection or some other reason), date of death was obtained through at least one of the other sources listed. This date was verified by inpatient records and/or confirmation with the patient's primary care physician and/or family.

Statistical methods. The distribution of genotypes was compared by racial groups as well as by tumor stage using Pearson χ2 tests. Tests for Hardy-Weinberg equilibrium were conducted by goodness-of-fit χ2 test to compare the observed genotype frequencies with the expected genotype frequencies with 1 degree of freedom. Linkage disequilibrium of the two polymorphic variants of the RecQ1 and XRCC3 genes was measured by using the SNPAlyze software (Dynacom, Inc., Mobara, Japan). The association between overall survival and each SNP was estimated using the method of Kaplan and Meier and assessed using the log-rank test. The combined genotype effect on survival was examined by the number of at-risk alleles. Hazard ratio and 95% confidence interval (95% CI) were estimated using both univariate and multivariate Cox proportional regression models. The multivariate models included all factors that showed a significant association with overall survival in univariate analysis. All statistical tests were conducted using the SPSS software version 12.0 (SPSS, Chicago, IL).

Patient characteristics and overall survival. The median age of the 378 patients in this study was 63 years (range, 38-89 years); 13.2% were <50, 27.5% were 51 to 60, 33.9% were 61 to 70, and 25.47% were >70 years of age. Caucasians, Hispanics, and African Americans constituted 87.8%, 5.8%, and 5.0% of the study population, respectively. The male-to-female ratio was 1.2:1. There were 271 (72%) deaths among the 378 cases. The median survival time (MST) was 15.4 months. The median follow-up time was 24.2 months for the living patients. Age, race, sex, cigarette smoking, and history of diabetes did not show any significant effect on overall survival (Table 1).

Table 1.

Patient characteristics and overall survival

VariableNo. patientsNo. deathsMST (mo)Hazard ratio (95% CI)*P
Age (y)      
    ≤50 50 34 20.3 1.0  
    51-60 104 74 14.6 1.07 (0.72-1.61) 0.73 
    61-70 128 91 14.5 1.04 (0.70-1.54) 0.85 
    >70 96 72 16.5 1.15 (0.77-1.73) 0.50 
Sex      
    Male 207 150 14.4 1.0  
    Female 171 121 17.0 0.83 (0.66-1.06) 0.14 
Race      
    White 332 237 15.8 1.0  
    Hispanics 22 17 12.8 1.22 (0.75-2.00) 0.43 
    African American 19 12 18.1 0.85 (0.47-1.52) 0.58 
    Other 16.5 1.62 (0.67-3.94) 0.29 
Smoking      
    Never 141 102 16.4 1.0  
    Ever 237 169 14.7 1.05 (0.81-1.33) 0.72 
Diabetes      
    No 290 203 16.3 1.0  
    Yes 88 68 13.3 1.24 (0.94-1.64) 0.12 
Stage      
    Localized 107 61 24.5 1.0  
    Locally advanced 185 133 15.4 1.73 (1.28-2.35) <0.001 
    Metastatic 86 77 9.8 3.32 (2.35-4.69) <0.001 
Performance status      
    0 59 42 15.8 1.0  
    1 270 185 16.4 0.99 (0.71-1.40) 0.99 
    2/3 47 44 11.5 1.85 (1.21-2.83) 0.005 
Serum CA19-9 (units/mL)      
    ≤47 85 58 19.2 1.0  
    48-1,000 189 123 17.3 1.08 (0.79-1.47) 0.65 
    1,001-3,000 48 38 11.2 1.66 (1.10-2.50) 0.02 
    >3,000 55 51 9.7 2.46 (1.68-3.60) <0.001 
Surgical      
    No 235 201 10.7 1.0  
    Yes 143 70 29.8 0.26 (0.20-0.35) <0.001 
Cytotoxic treatment      
    Chemotherapy 123 110 11.0 1.0  
    Gemcitabine/XRT 139 87 21.7 0.41 (0.31-0.54) <0.001 
    5-FU/XRT 105 64 19.2 0.47 (0.35-0.65) <0.001 
VariableNo. patientsNo. deathsMST (mo)Hazard ratio (95% CI)*P
Age (y)      
    ≤50 50 34 20.3 1.0  
    51-60 104 74 14.6 1.07 (0.72-1.61) 0.73 
    61-70 128 91 14.5 1.04 (0.70-1.54) 0.85 
    >70 96 72 16.5 1.15 (0.77-1.73) 0.50 
Sex      
    Male 207 150 14.4 1.0  
    Female 171 121 17.0 0.83 (0.66-1.06) 0.14 
Race      
    White 332 237 15.8 1.0  
    Hispanics 22 17 12.8 1.22 (0.75-2.00) 0.43 
    African American 19 12 18.1 0.85 (0.47-1.52) 0.58 
    Other 16.5 1.62 (0.67-3.94) 0.29 
Smoking      
    Never 141 102 16.4 1.0  
    Ever 237 169 14.7 1.05 (0.81-1.33) 0.72 
Diabetes      
    No 290 203 16.3 1.0  
    Yes 88 68 13.3 1.24 (0.94-1.64) 0.12 
Stage      
    Localized 107 61 24.5 1.0  
    Locally advanced 185 133 15.4 1.73 (1.28-2.35) <0.001 
    Metastatic 86 77 9.8 3.32 (2.35-4.69) <0.001 
Performance status      
    0 59 42 15.8 1.0  
    1 270 185 16.4 0.99 (0.71-1.40) 0.99 
    2/3 47 44 11.5 1.85 (1.21-2.83) 0.005 
Serum CA19-9 (units/mL)      
    ≤47 85 58 19.2 1.0  
    48-1,000 189 123 17.3 1.08 (0.79-1.47) 0.65 
    1,001-3,000 48 38 11.2 1.66 (1.10-2.50) 0.02 
    >3,000 55 51 9.7 2.46 (1.68-3.60) <0.001 
Surgical      
    No 235 201 10.7 1.0  
    Yes 143 70 29.8 0.26 (0.20-0.35) <0.001 
Cytotoxic treatment      
    Chemotherapy 123 110 11.0 1.0  
    Gemcitabine/XRT 139 87 21.7 0.41 (0.31-0.54) <0.001 
    5-FU/XRT 105 64 19.2 0.47 (0.35-0.65) <0.001 
*

Hazard ratio (95% CI) from univariate Cox proportional regression.

At diagnosis, there were 107 localized resectable tumors, 185 locally advanced (including 65 potentially or borderline resectable tumors), and 86 metastatic tumors. The MST was 24.5, 15.4, and 9.8 months for patients with localized, locally advanced, and metastatic disease, respectively (P < 0.001, log-rank test). As expected, both performance status and serum CA19-9 levels at diagnosis were significant predictors of survival in this patient population. Patients with Eastern Cooperative Oncology Group performance status grade 0 and 1 had better survival than those with grade 2 and 3. Patients with a CA19-9 value of >1,000 units/mL had at least 6 months shorter survival than those with a value of <1,000 units/mL. There were 143 patients who received tumor resection surgery and these patients survived much longer than those who did not receive tumor resection. In this patient series, 6.2%, 3.8%, and 6.2% patients received chemotherapy, radiotherapy, and tumor resection surgery before their first visit to M.D. Anderson. During the entire disease process, 29 (7.7%) patients received gemcitabine alone; 53 (14%) received gemcitabine-based chemoradiation; 86 (22.8%) received gemcitabine-based chemoradiation plus other type of chemotherapy; 33 (8.7%) received 5-fluorouracil (5-FU)-based chemoradiation; 72 (19%) received 5-FU-based chemoradiation plus other type of chemotherapy; 95 (25.1%) received combined chemotherapy without radiation; and 11 (2.9%) received no cytotoxic therapy. Overall, 84.4% of the patients received gemcitabine, 70.4% received radiation to the tumor, 53.4% received cisplatin (or oxaliplatin), and 43.1% received 5-FU (or capecitabine). In addition, ∼20.6% of patients received investigational therapy, such as bevacuzumab, celecoxib, α-IFN, and others. Because of the heterogeneity of the patient population and the small number of patients, treatment regimens during the entire disease process were collapsed into three groups [i.e., chemotherapy alone, 5-FU-based chemoradiation (5-FU/XRT), and gemcitabine-based chemoradiation (gemcitabine/XRT)]. The 11 patients who did not receive any cytotoxic therapy were excluded from the treatment subgroup analyses. Patients who received gemcitabine/XRT or 5-FU/XRT did significantly better than those received chemotherapy alone.

Genotype and survival. The six SNPs were successfully amplified in 93.6% to 98.2% of the patients. No homozygous AA genotype was detected for the RecQ1 A-86G SNP. Genotype frequencies for all six SNPs were found to be in Hardy-Weinberg equilibrium (χ2 = 0.21-2.9, P > 0.1). There was a significant difference in the racial distribution of the RAD54L and XRCC3 T241M genotypes. For RAD54L, African Americans had a higher frequency (94.7%) of the CC wild-type than Caucasians (77.2%) and Hispanics (81.0%; P = 0.03, χ2 test). The frequency of the XRCC3 CC wild-type was 68.4% in African Americans compared with 36.3% in Caucasians and 42.9% in Hispanics (P = 0.046). There were no significant differences in the genotype distributions by age, sex, disease stage, and surgical status (data not shown). The two SNPs of the RecQ1 gene are in linkage disequilibrium with a D′ value of 0.90 (P = 0.02). The two SNPs of he XRCC3 gene are in complete linkage disequilibrium and the D′ value is 0.99 (P < 0.001; Table 2).

Table 2.

Genotype frequency and overall survival

GenotypeNo. patientsNo. deathsMST (mo)Univariate
Multivariate
Hazard ratio (95% CI)PHazard ratio (95% CI)*P
RecQ1 A159C        
    AA 129 84 19.2 1.0  1.0  
    AC 157 119 14.7 1.44 (1.08-1.92) 0.010 1.22 (0.90-1.64) 0.195 
    CC 68 50 13.2 1.60 (1.12-2.27) 0.009 1.45 (1.01-2.10) 0.045 
    P (LR)   0.011     
RecQ1 A-89G        
    GG 348 249 15.8 1.0  1.0  
    GA 16 14 13.7 1.24 (0.72-2.11) 0.440 1.58 (0.91-2.73) 0.106 
    P (LR)   0.440     
RAD54L C157T        
    CC 288 203 16.4 1.0  1.0  
    CT 74 57 13.3 1.31 (0.98-1.76) 0.070 1.31 (0.97-1.76) 0.080 
    TT 10.3 2.05 (0.84-4.99) 0.120 3.30 (1.34-8.15) 0.010 
    P (LR)   0.066     
XRCC2 R188H        
    GG 319 226 16.4 1.0  1.0  
    GA 40 31 11.4 1.22 (0.84-1.78) 0.290 1.41 (0.95-2.08) 0.088 
    AA 5.1 10.75 (2.58-44.7) 0.001 9.72 (2.30-41.1) 0.002 
    GA/AA 42 33 11.4 1.29 (0.89-1.85) 0.178 1.29 (0.89-1.87) 0.183 
    P (LR)   0.0002 (0.176)     
XRCC3 17893        
    AA 169 119 15.3 1.0  1.0  
    AG 165 118 16.3 1.04 (0.81-1.35) 0.750 1.15 (0.88-1.50) 0.304 
    GG 37 29 14.7 1.19 (0.79-1.78) 0.410 1.35 (0.89-2.06) 0.159 
    P (LR)   0.703     
XRCC3 T241M        
    CC 143 105 16.5 1.0  1.0  
    CT 182 130 14.7 1.13 (0.87-1.46) 0.370 1.05 (0.80-1.38) 0.704 
    TT 42 28 18.9 0.83 (0.55-1.26) 0.370 0.75 (0.88-2.08) 0.191 
    P (LR)   0.298     
GenotypeNo. patientsNo. deathsMST (mo)Univariate
Multivariate
Hazard ratio (95% CI)PHazard ratio (95% CI)*P
RecQ1 A159C        
    AA 129 84 19.2 1.0  1.0  
    AC 157 119 14.7 1.44 (1.08-1.92) 0.010 1.22 (0.90-1.64) 0.195 
    CC 68 50 13.2 1.60 (1.12-2.27) 0.009 1.45 (1.01-2.10) 0.045 
    P (LR)   0.011     
RecQ1 A-89G        
    GG 348 249 15.8 1.0  1.0  
    GA 16 14 13.7 1.24 (0.72-2.11) 0.440 1.58 (0.91-2.73) 0.106 
    P (LR)   0.440     
RAD54L C157T        
    CC 288 203 16.4 1.0  1.0  
    CT 74 57 13.3 1.31 (0.98-1.76) 0.070 1.31 (0.97-1.76) 0.080 
    TT 10.3 2.05 (0.84-4.99) 0.120 3.30 (1.34-8.15) 0.010 
    P (LR)   0.066     
XRCC2 R188H        
    GG 319 226 16.4 1.0  1.0  
    GA 40 31 11.4 1.22 (0.84-1.78) 0.290 1.41 (0.95-2.08) 0.088 
    AA 5.1 10.75 (2.58-44.7) 0.001 9.72 (2.30-41.1) 0.002 
    GA/AA 42 33 11.4 1.29 (0.89-1.85) 0.178 1.29 (0.89-1.87) 0.183 
    P (LR)   0.0002 (0.176)     
XRCC3 17893        
    AA 169 119 15.3 1.0  1.0  
    AG 165 118 16.3 1.04 (0.81-1.35) 0.750 1.15 (0.88-1.50) 0.304 
    GG 37 29 14.7 1.19 (0.79-1.78) 0.410 1.35 (0.89-2.06) 0.159 
    P (LR)   0.703     
XRCC3 T241M        
    CC 143 105 16.5 1.0  1.0  
    CT 182 130 14.7 1.13 (0.87-1.46) 0.370 1.05 (0.80-1.38) 0.704 
    TT 42 28 18.9 0.83 (0.55-1.26) 0.370 0.75 (0.88-2.08) 0.191 
    P (LR)   0.298     

NOTE: The numbers of patients for each genotype do not add up to 378 because of failure of genotyping assays in some patients.

*

Multivariate Cox regression with adjustment for race, stage, surgery, performance status, CA19-9 level, and cytotoxic treatment.

P value in parentheses was from log-rank test of GG versus GA/AA genotype.

A significant effect of the RecQ1 A159C and RAD54L C157T genotype on overall survival was observed. The MST was 19.2, 14.7, and 13.2 months for the RecQ1 A157C AA, AC, and CC genotypes, and 16.4, 13.3, and 10.3 months for the RAD54L CC, CT, and TT genotypes, respectively. The RecQ1 159 CC and RAD54L 157 TT genotypes remained as significant predictors for survival in Cox proportional regression models with adjustment of all other significant clinical predictors. The XRCC2 R188H AA genotype was associated with a significantly shorter survival than the GG/GA genotype but the risk estimate was not precise (hazard ratio, 10.75; 95% CI, 2.58-44.7) because of the extremely low frequency of the AA genotype (n = 2 only). Neither of the two XRCC3 gene polymorphisms showed any significant effect on survival.

Subgroup analysis by stage and surgery. Because disease stage and curative surgery are known to be the most significant predictors of survival, we have separated the patients into three groups in the subgroup analysis; i.e., patients with localized and locally advanced tumor and achieved tumor resection (Surgical group, n = 143), patients with localized and locally advanced tumors and did not achieve tumor resection (nonsurgical group, n = 149), and patients with metastatic tumors (metastatic group, n = 86). The MST for the surgical, nonsurgical, and metastatic groups was 29.8, 11.7, and 9.8 months, respectively (P < 0.001). The effect of RecQ1 and RAD54L gene on survival was clearly seen in patients with localized disease (i.e., the combined surgical and nonsurgical groups; Fig. 1) but was completely absent in patients with metastatic disease (data not shown). The XRCC2 R188H variant allele showed a significant association with poorer survival in nonsurgical patients only. When the RecQ1, RAD54L, and XRCC2 SNPs were analyzed in combination, a significantly reduced survival was associated with an increasing number of adverse alleles in both surgical and nonsurgical patients (Table 3).

Figure 1.

Survival plot for pooled surgical and nonsurgical patients (patients without metastatic disease) by RecQ1 A159C (A), RAD54L C157T (B), XRCC2 R188H (C), and combined genotype of these three SNPs (D). The numbers 0, 1, and ≥2 in (D) indicate the number of alleles that are associated with reduced survivals (i.e., RecQ1 AC/CC, RAD54L CT/TT, and XRCC2 GA/AA alleles). 0, having none of these alleles; 1, having at least one of the three alleles; ≥2, having two or three of these alleles. The survival plot shows the more adverse alleles one have, the shorter the survival. P values from log-rank test, hazard ratios, and 95% confidence intervals are shown in Table 3.

Figure 1.

Survival plot for pooled surgical and nonsurgical patients (patients without metastatic disease) by RecQ1 A159C (A), RAD54L C157T (B), XRCC2 R188H (C), and combined genotype of these three SNPs (D). The numbers 0, 1, and ≥2 in (D) indicate the number of alleles that are associated with reduced survivals (i.e., RecQ1 AC/CC, RAD54L CT/TT, and XRCC2 GA/AA alleles). 0, having none of these alleles; 1, having at least one of the three alleles; ≥2, having two or three of these alleles. The survival plot shows the more adverse alleles one have, the shorter the survival. P values from log-rank test, hazard ratios, and 95% confidence intervals are shown in Table 3.

Close modal
Table 3.

Effect of genotypes on survival in patients with localized and locally advanced tumors

GenotypeSurgical
Nonsurgical
Surgical & Nonsurgical
No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)
RecQ1 159             
    AA 53 22 60.0 1.0 51 40 13.3 1.0 104 62 24.4 1.0 
    AC 56 31 24.3 1.59 (0.88-2.86) 58 50 11.9 1.13 (0.73-1.74) 114 81 16.4 1.29 (0.91-1.82) 
    CC 24 12 24.5 1.56 (0.72-3.36) 31 26 9.7 1.38 (0.82-2.32) 55 38 14.6 1.48 (0.97-2.25) 
    P (LR)*   0.070    0.278    0.016  
RAD54L 157             
    CC 112 50 38.6 1.0 111 92 12.4 1.0 223 142 19.0 1.0 
    CT 24 16 21.7 1.69 (0.95-3.00) 31 27 9.9 1.54 (0.99-2.39) 55 43 13.7 1.57 (1.11-2.22) 
    TT 10.3 4.98 (1.13-21.9) 7.7 3.19 (0.96-10.5) 10.3 3.67 (1.47-9.18) 
    P (LR)   0.055    0.026    0.009  
XRCC2 R188H             
    GG 118 56 35.9 1.0 129 105 12.6 1.0 247 161 19.0 1.0 
    GA/AA 17 10 24.5 1.10 (0.54-2.27) 15 15 9.0 2.64 (1.47-4.74) 32 25 10.1 1.99 (1.29-3.09) 
    P (LR)   0.268    0.005    0.052  
Combined             
    0 27 § 1.0 33 25 14.3 1.0 60 32 28.0 1.0 
    1 95 50 27.5 2.82 (1.22-6.51) 83 68 13.1 1.25 (0.79-1.99) 178 118 18.5 1.61 (1.08-2.40) 
    ≥2 19 12 21.4 3.92 (1.46-10.5) 32 30 8.5 2.06 (1.19-3.57) 51 42 11.8 2.52 (1.57-4.04) 
    P (LR)   0.004    0.005    <0.001  
GenotypeSurgical
Nonsurgical
Surgical & Nonsurgical
No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)
RecQ1 159             
    AA 53 22 60.0 1.0 51 40 13.3 1.0 104 62 24.4 1.0 
    AC 56 31 24.3 1.59 (0.88-2.86) 58 50 11.9 1.13 (0.73-1.74) 114 81 16.4 1.29 (0.91-1.82) 
    CC 24 12 24.5 1.56 (0.72-3.36) 31 26 9.7 1.38 (0.82-2.32) 55 38 14.6 1.48 (0.97-2.25) 
    P (LR)*   0.070    0.278    0.016  
RAD54L 157             
    CC 112 50 38.6 1.0 111 92 12.4 1.0 223 142 19.0 1.0 
    CT 24 16 21.7 1.69 (0.95-3.00) 31 27 9.9 1.54 (0.99-2.39) 55 43 13.7 1.57 (1.11-2.22) 
    TT 10.3 4.98 (1.13-21.9) 7.7 3.19 (0.96-10.5) 10.3 3.67 (1.47-9.18) 
    P (LR)   0.055    0.026    0.009  
XRCC2 R188H             
    GG 118 56 35.9 1.0 129 105 12.6 1.0 247 161 19.0 1.0 
    GA/AA 17 10 24.5 1.10 (0.54-2.27) 15 15 9.0 2.64 (1.47-4.74) 32 25 10.1 1.99 (1.29-3.09) 
    P (LR)   0.268    0.005    0.052  
Combined             
    0 27 § 1.0 33 25 14.3 1.0 60 32 28.0 1.0 
    1 95 50 27.5 2.82 (1.22-6.51) 83 68 13.1 1.25 (0.79-1.99) 178 118 18.5 1.61 (1.08-2.40) 
    ≥2 19 12 21.4 3.92 (1.46-10.5) 32 30 8.5 2.06 (1.19-3.57) 51 42 11.8 2.52 (1.57-4.04) 
    P (LR)   0.004    0.005    <0.001  

NOTE: Hazard ratio was adjusted for race, performance status, CA19-9 values, stage, and cytotoxic treatment for all groups. Surgery was adjusted for the pooled surgical and nonsurgical patients.

*

P values by log-rank test.

The GA and AA genotypes were combined because only one AA genotype was detected in these patients.

Number of variant alleles of the three SNPs listed in this table.

§

Median survival time could not be calculated.

Subgroup analysis by treatment. Among patients with localized disease (the surgical and nonsurgical groups), there are 45 patients who did not receive radiotherapy during the entire course of the disease. There are 138 and 101 patients who received gemcitabine-based and 5-FU-based chemoradiation, respectively. The MST was 13.7, 23.4, and 18.7 months for patients who received chemotherapy alone, gemcitabine/XRT, and 5-FU/XRT, respectively (P = 0.003). No significant genotype effect was observed in patients who received chemotherapy alone. The gemcitabine group consisted more of surgical patients (55.8% versus 47.5%; P = 0.21, χ2 test) and less of locally advanced disease (54.37% versus 70.3%; P = 0.01, χ2 test) than the 5-FU group. The significant effects of RecQ1 and RAD54L genes on survival were observed among patients who received gemcitabine-based chemoradiation whereas the effects of XRCC2 and XRCC3 genes were observed in patients who received 5-FU-based chemoradiation only. When the four genes were analyzed in combination, a significantly decreased survival was observed as the number of adverse alleles increased in both gemcitabine/XRT and 5-FU/XRT groups (Table 4).

Table 4.

Genotype and survival by treatment in patients with localized and locally advanced tumors

VariableChemotherapy alone
Gemcitabine/XRT
5-FU/XRT
No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)
RecQ1 159             
    AA 18 14 13.3 1.0 48 24 28.7 1.0 37 23 22.5 1.0 
    AC 18 16 15.8 0.47 (0.22-1.12) 49 36 19.9 1.57 (0.93-2.68) 43 26 15.8 1.64 (0.89-3.03) 
    CC 13.7 0.73 (0.24-4.22) 32 21 15.3 1.73 (0.93-3.20) 15 10 24.5 1.82 (0.84-3.92) 
    P (LR)*   0.542    0.028    0.244  
RAD54L 157             
    CC 35 29 14.3 1.0 109 67 22.7 1.0 72 40 20.3  
    CT 10 12.6 1.10 (0.50-2.44) 21 15 14.6 2.18 (1.22-3.88) 24 19 13.7 1.56 (0.88-2.74) 
    TT   10.3 4.29 (1.23-14.9) 7.7 3.58 (0.80-16.0) 
    P (LR)   0.808    0.007    0.134  
XRCC2 R188H             
    GG 41 36 13.3 1.0 117 73 22.0 1.0 81 47 20.3 1.0 
    GA/AA 9.8 1.71 (0.37-8.02) 16 12 14.6 2.18 (1.15-4.12) 13 11 9.0 2.45 (1.20-5.02) 
    P (LR)   0.927    0.263    0.012  
XRCC3 17893             
    AA 15 14 14.3 1.0 65 39 22.5 1.0 48 29 20.3 1.0 
    AG 23 19 13.7 1.43 (0.62-3.30) 57 36 21.4 1.12 (0.69-1.82) 44 26 19.2 1.25 (0.72-2.19) 
    GG 11.8 0.93 (0.32-2.69) 11 18.2 1.43 (0.63-3.25) 10.6 4.12 (1.67-10.2) 
    P (LR)   0.932    0.819    0.032  
Combined             
    0 12 10 14.3 1.0 26 12 32.9 1.0 18 40.1 1.0 
    1 18 16 13.7 0.79 (0.31-2.00) 68 42 20.6 1.64 (0.85-3.19) 44 28 18.6 2.94 (1.27-6.83) 
    2 12.6 0.92 (0.29-2.98) 23 20 14.7 3.03 (1.46-6.29) 24 16 10.3 4.36 (1.72-11.0) 
    3 11.8 0.55 (0.13-2.29) 4.6 12.9 (2.66-62.5) 7.4 25.4 (5.29-122) 
    P (LR)   0.974    0.004    0.0003  
VariableChemotherapy alone
Gemcitabine/XRT
5-FU/XRT
No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)No. patientsNo. deathsMST (mo)Hazard ratio (95% CI)
RecQ1 159             
    AA 18 14 13.3 1.0 48 24 28.7 1.0 37 23 22.5 1.0 
    AC 18 16 15.8 0.47 (0.22-1.12) 49 36 19.9 1.57 (0.93-2.68) 43 26 15.8 1.64 (0.89-3.03) 
    CC 13.7 0.73 (0.24-4.22) 32 21 15.3 1.73 (0.93-3.20) 15 10 24.5 1.82 (0.84-3.92) 
    P (LR)*   0.542    0.028    0.244  
RAD54L 157             
    CC 35 29 14.3 1.0 109 67 22.7 1.0 72 40 20.3  
    CT 10 12.6 1.10 (0.50-2.44) 21 15 14.6 2.18 (1.22-3.88) 24 19 13.7 1.56 (0.88-2.74) 
    TT   10.3 4.29 (1.23-14.9) 7.7 3.58 (0.80-16.0) 
    P (LR)   0.808    0.007    0.134  
XRCC2 R188H             
    GG 41 36 13.3 1.0 117 73 22.0 1.0 81 47 20.3 1.0 
    GA/AA 9.8 1.71 (0.37-8.02) 16 12 14.6 2.18 (1.15-4.12) 13 11 9.0 2.45 (1.20-5.02) 
    P (LR)   0.927    0.263    0.012  
XRCC3 17893             
    AA 15 14 14.3 1.0 65 39 22.5 1.0 48 29 20.3 1.0 
    AG 23 19 13.7 1.43 (0.62-3.30) 57 36 21.4 1.12 (0.69-1.82) 44 26 19.2 1.25 (0.72-2.19) 
    GG 11.8 0.93 (0.32-2.69) 11 18.2 1.43 (0.63-3.25) 10.6 4.12 (1.67-10.2) 
    P (LR)   0.932    0.819    0.032  
Combined             
    0 12 10 14.3 1.0 26 12 32.9 1.0 18 40.1 1.0 
    1 18 16 13.7 0.79 (0.31-2.00) 68 42 20.6 1.64 (0.85-3.19) 44 28 18.6 2.94 (1.27-6.83) 
    2 12.6 0.92 (0.29-2.98) 23 20 14.7 3.03 (1.46-6.29) 24 16 10.3 4.36 (1.72-11.0) 
    3 11.8 0.55 (0.13-2.29) 4.6 12.9 (2.66-62.5) 7.4 25.4 (5.29-122) 
    P (LR)   0.974    0.004    0.0003  

NOTE: Hazard ratio was adjusted for race, performance status, CA19-9 values, stage, and surgery.

*

P values by log-rank test.

The GA and AA genotypes were combined because only one AA genotype was present in these patients.

Number of variant alleles for the four SNPs listed in this table.

In this study, we evaluated the effect of six SNPs of four homologous recombination repair genes (i.e., RecQ1, RAD54L, XRCC2, and XRCC3) on overall survival of patients with pancreatic adenocarcinoma. We showed that the variant alleles of these genes, independently or jointly, are associated with significantly decreased overall survival. The genotype effect was present in patients with localized disease or in patients who received radiotherapy but absent in patients with metastatic disease or in patients who did not receive radiotherapy. These observations for the first time showed the significant effect of homologous recombination repair genes on cancer patient survival.

Among the four genes examined in the current study, the RecQ1 and RAD54L genes showed a significant effect on survival when all 378 patients were included in the analysis. The homozygous variant allele of either gene conferred an average 6-month shorter survival compared with the wild-type. The frequency of the homozygous variant allele was 19.2% and 1.9% for the RecQ1 A159C and RAD54L C157T, respectively. Both variant alleles remained as significant predictor for survival after adjusting for all known significant clinical predictors. These data support an important role of the RecQ1 and RAD54L genes in pancreatic tumor progression or response to clinical therapy. RecQ1 belongs to the DNA helicase RecQ gene family including the Werner, Bloom, and Rothmund-Thomson causative genes WRN, BLM, and RecQ4. Previous studies have shown that under BLM-impaired conditions, RecQ1 acted as a backup mechanism for the helicase function in cell viability (34). Recent studies have also shown that RecQ1 may play a role in DNA strand break repair and mismatch repair (21, 22). The RecQ1 A159C SNP is located on the 3′-untranslated region of the gene and it exerted its effect in a dominant inheritance mode (i.e., one variant allele is required to alter the chance of survival). It is possible that this SNP may affect the translation efficiency and mRNA stability of the gene. If the variant allele confers a higher activity of the RecQ1 protein, it may repair the therapy-related DNA damages more efficiently and, in turn, a poorer clinical response. RAD54L is also a DNA helicase and it is known to play a role in repairing DNA double-strand breaks (35, 36). RAD54L has been proposed as a candidate tumor suppressor gene in tumors bearing a nonrandom deletion of chromosome 1p32 (25, 37, 38). The RAD54L C157T SNP has previously been associated with increased risk of meningiomas (17). The current study found that the RAD54L C157T variant allele was associated with a significantly poorer survival in patients treated with chemoradiation. This effect was perhaps directly related to the repair efficiency of radiation-induced DNA double-strand breaks. However, the C157T SNP is a silent polymorphism (Ala730Ala) that does not induce any amino acid change. We can only speculate that the observed effect on survival was related to linkage disequilibrium of this SNP with other SNPs of the same gene or with other genes on the same chromosome. The same possibility that the RecQ1 A159C SNP is in linkage disequilibrium with other SNPs of the gene or with other genes cannot be excluded. Whereas haplotype analysis and in vitro experiments will be needed to clarify the exact role of these two SNPs in response to genotoxic stress, the association between these two polymorphic variants and cancer patient survival should be verified in other patient populations. If confirmed, it may have a significant effect on the clinical management of cancer patients.

XRCC2 and XRCC3 are Rad51 paralogues that are expressed in mitotically growing cells and are thought to play mediating roles in homologous recombination repair, although their precise functions remain unclear. Loss of either XRCC2 or XRCC3 was sufficient to sensitize cells to agents that induce DNA double-strand breaks (39). The current study observed a poorer survival of patients carrying the heterozygous and homozygous variant alleles of XRCC2 R188H or the homozygous mutant allele of XRCC3 17893, which suggests that these mutant alleles may affect the repair efficiency of radiation-induced DNA double-strand breaks and, in turn, clinical outcome. Because most of the significant associations with survival was observed in subgroup analysis and the study power is limited by the small sample size, these observations need to be interpreted with caution.

Among patients with metastatic disease, none of the genotypes or any other factors significantly affected survival. Individuals with metastatic disease may already have too many genetic alterations driving tumor progression or treatment resistance so that any subtle effect of genotypes to alter DNA repair capacity is overwhelmed.

Although our data could not definitely discriminate whether the genetic effect on survival was mediated through response to treatment or by affecting tumor aggressiveness, some preliminary observations suggest that the effect of these genotypes was probably related to radiation responsiveness. For example, the distribution of the SNPs was not significantly different by disease stage and the genetic effects on overall survival were observed in patients treated with radiotherapy but not in patients who did not receive radiotherapy. Whether or not the survival differences by genotypes truly reflect a radiation-related outcome may be best tested through studies that employ prospective study designs. If proven, modulation of these enzymes may serve as a therapeutic target to increase tumor cell radiosensitivity. The current study did not find evidence to support a specific role of any of these tested genes in gemcitabine response although both RecQ1 and RAD54L genes seemed to have a stronger effect on survival in patients who received gemcitabine-based therapy than in those who received 5-FU-based therapy. Because the former group had more early-stage patients and surgical patients than the latter group, the current observations cannot be accurately interpreted. Whether or not RecQ1 and RAD54L play a specific role in the repair of gemcitabine-induced DNA damage needs to be tested in a clinical trial with a well-defined patient population.

The current study observed a significantly reduced survival associated with an increasing number of adverse genotypes. Because DNA repair is a complex process, it takes many proteins to act in concert to maintain cell viability and genome integrity. Each single SNP of the low penetrance genes may have a weak effect at the functional level but the combined effect of several genes may have significant clinical value in predicting response to therapy and prognosis. The strength of this study is a large sample size and adequate statistical power. The limitation of the study is the heterogeneity of the patients, which makes data interpretation more difficult. Some subgroup analyses were conducted to overcome this problem but the small sample size in each group may increase the chance of false-positive result. It is important to confirm these observations in other patient populations. If confirmed, such information may provide opportunities for discovery of novel therapeutic targets and genetic profiles that can direct the choice of therapy and predict the treatment tolerance, response, and overall outcome (40).

Grant support: NIH RO1 grant CA098380 (D. Li), Specialized Program of Research Excellence P20 grant CA101936 (J.L. Abbruzzese), NIH Cancer Center Core grant CA16672, and a research grant from the Lockton Research Funds (D. Li).

The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

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