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PLOS ONE logoLink to PLOS ONE
. 2013 Nov 21;8(11):e81129. doi: 10.1371/journal.pone.0081129

One-Carbon Metabolism Pathway Gene Variants and Risk of Clear Cell Renal Cell Carcinoma in a Chinese Population

Lei Zhang 1,#, Xiaoxin Meng 1,#, Xiaobing Ju 1,#, Hongzhou Cai 1, Pu Li 1, Qiang Cao 1, Pengfei Shao 1, Chao Qin 1,*, Changjun Yin 1,*
Editor: Yong-Gang Yao2
PMCID: PMC3837692  PMID: 24278388

Abstract

Background

One-carbon metabolism is the basement of nucleotide synthesis and the methylation of DNA linked to cancer risk. Variations in one-carbon metabolism genes are reported to affect the risk of many cancers, including renal cancer, but little knowledge about this mechanism is known in Chinese population.

Methods

Each subject donated 5 mL venous blood after signing the agreement. The study was approved by the Institutional Review Board of the Nanjing Medical University, Nanjing, China. 18 SNPs in six one-carbon metabolism-related genes (CBS, MTHFR, MTR, MTRR, SHMT1, and TYMS) were genotyped in 859 clear cell renal cell carcinoma (ccRCC) patients and 1005 cancer-free controls by the Snapshot.

Results

Strong associations with ccRCC risk were observed for rs706209 (P = 0.006) in CBS and rs9332 (P = 0.027) in MTRR. Compared with those carrying none variant allele, individuals carrying one or more variant alleles in these two genes had a statistically significantly decreased risk of ccRCC [P = 0.001, adjusted odds ratio (OR) = 0.73, 95% confidence interval (CI) = 0.06–0.90]. In addition, patients carrying one or more variant alleles were more likely to develop localized stage disease (P = 0.002, adjusted OR = 1.37, 95%CI = 1.11–1.69) and well-differentiated ccRCC (P<0.001, adjusted OR = 1.42, 95%CI = 0.87–1.68). In the subgroup analysis, individuals carrying none variant allele in older group (P = 0.007, adjusted OR = 0.67, 95%CI = 0.49–0.91), male group (P = 0.007, adjusted OR = 0.71, 95%CI = 0.55–0.92), never smoking group (P = 0.002, adjusted OR = 0.68, 95%CI = 0.53–0.88) and never drinking group (P<0.001, adjusted OR = 0.68, 95%CI = 0.53–0.88) had an increased ccRCC risk.

Conclusions

Our results suggest that the polymorphisms of the one-carbon metabolism-related genes are associated with ccRCC risk in Chinese population. Future population-based prospective studies are required to confirm the results.

Introduction

Renal cell carcinoma (RCC), one lethal urologic cancer accounting for 2% of all cancer deaths, is the third most common cancer of the genitourinary tract, just next to prostate and bladder cancer [1]. The most common subtype of RCC is the clear cell type (ccRCC), accounting for 75% of all cases. The incidence of RCC has increased rapidly worldwide over the past few decades [2]. Although the exact causes of RCC remain unknown, a few well-established lifestyle risk factors have been identified, including: cigarette smoking, obesity, hypertension and diabetes [3]. Recent studies have demonstrated that genetic polymorphisms of candidate genes were associated with susceptibility and/or prognosis of cancers, including RCC [4], [5], [6], [7].

One-carbon metabolism refers to a system of interdependent metabolic pathways facilitating the transfer of one-carbon units, which are the basement of nucleotide synthesis and the methylation of DNA. Methylation is responsible for gene expression control, chromatin structure stability and the maintenance of genomic stability. It has been proved that tumor-suppressor genes are silenced by hypermethylation of the promoter region in various cancers, leading to carcinogenesis and cancer progression [8]. In RCC, genes encoding von Hippel-Lindan (VHL), E-cadherin and RASSF1A have been reported to be inactivated by promoter hypermethylation [9], [10], [11]. DNA hypomethylation begets chromosomal instability as a result of changes in chromatin structure [12], [13].

The connection between the polymorphisms in one-carbon metabolism pathway genes, such as methylenetetrahydrofolate reductase (MTHFR), has been widely studied in various cancers [14], [15], [16], [17], [18]. The MTHFR promoter polymorphism rs3737965 has been intensively studied, but the results were conflicting, especially in lung cancer [16], [19], [20], [21], [22]. Besides, two large case-control studies for RCC have been conducted in Europe to analyze the candidate genes in one-carbon metabolism pathway. The studies found the association between the one-carbon metabolism pathway genes polymorphisms and RCC risk [14], [15]. However, there are some discrepancies in these two studies, as evidenced by the confusing connection between the TYMS polymorphisms and RCC risk. Given the importance of this pathway in carcinogenesis, ethnic differences and the discrepancies in previous studies, the present case-control study was conducted to define the association between the one-carbon metabolism pathway genes polymorphisms and the ccRCC risk in Chinese population, through testing the polymorphism in six key genes (CBS, MTHFR, MTR, MTRR, SHMT1, and TYMS) in this pathway.

Materials and Methods

Study Subjects

859 ccRCC patients and 1005 cancer-free controls were enrolled in our case-control study. All subjects were genetically unrelated ethnic Han Chinese recruited from May 2004 to January 2012 at the First Affiliated Hospital of Nanjing Medical University, Nanjing, China, the Affiliated Hospital of Medical College Qingdao University, Qingdao, China and the Third Affiliated Hospital of Soochow University, Changzhou, China [23]. The cases were newly diagnosed with incident ccRCC and had been histopathologically confirmed without history of other malignancies and previous chemotherapy or radiotherapy. A standard questionnaire was administered through face-to-face interviews by trained interviewers to collect demographic data and related information. Each subject donated 5 mL venous blood after signing the agreement. The disease was classified by the World Health Organization criteria and stage according to the American Joint Committee on Cancer (AJCC) TNM (tumor-node-metastasis) classification. The Fuhrman scale was used to assess tumor nuclear grade and the disease stage was divided into two subgroups (localized group: stage I and stage II and advanced group: stage III and stage IV). The controls were individuals without history of cancer who were seeking health care in the outpatient departments matched to the cases' sex and age (±5 years) on frequency. We subdivided the patients and controls into two groups (younger group: age ≤57 and older group: age >57) according to the mean age of the cohort (57 years old). Smokers were defined as those who smoked daily for more than 1 year. Drinkers were those who drank at least 3 times per week and more than 6 months. The study was approved by the Institutional Review Board of the Nanjing Medical University, Nanjing, China.

DNA extraction and genotyping

Genomic DNA was seperated and purified from leucocytes of peripheral blood by proteinase K digestion and phenol/chloroform extraction. Genotyping of the polymorphism was performed by the Snapshot. The SNaPshot SNP assay was performed to detect the dimorphism at the two SNP loci. PCR was performed in a 20 µl reaction mixture containing 1 µl (10 ng) of template DNA, 1 µM of each primer, 0.3 mM of each deoxynucleotide triphosphate, 3.0 mM of MgCl2, and 1 U HotStarTaq polymerase (Qiagen Inc., USA) with 1× HotStarTaq buffer. The PCR program consisted of an initial melting step of 15 minutes at 95°C; 11 cycles of 20 seconds at 94°C, 40 seconds at 65°C-0.5°C/cycle, and 90 seconds at 72°C; 24 cycles of 20 seconds at 94°C, 30 seconds at 59°C, and 90 seconds at 72°C; and a final elongation step of 2 minutes at 72°C. To purify the PCR products, 1 U SAP and 1 U Exonuclease I were mixed with 10 µl PCR product for 1 hour at 37°C and 15 minutes at 75°C.The extension reaction was performed in a 10 µl reaction mixture containing 5 µl of the SNaPshot Multiplex Kit (Applied Biosystems, USA), 2 µl of purified PCR products, 0.8 µM of the extension reaction primer, and 2 µl water. The PCR program was 1 minute at 96°C; 28 cycles of 10 seconds at 96°C, 5 seconds at 50°C, and 30 seconds at 60°C; and 4°C as the holding temperature. Finally, 10 µl of the extension product was purified with 1 U SAP for 1 hour at 37°C and inactivated for 15 minutes at 75°C.The resulting data were analyzed with an ABI3130XL sequencer and GeneMapper™ 4.0 Software (Applied Biosystems, Co. Ltd., USA). All the sequences of primers for each SNP are listed in Table S1. Positive controls by sequencing and negative controls were used to ensure the accuracy of genotyping. To ensure quality control (QC), genotyping was performed by researchers blinded to the case/control status of the subjects, and a random sample of 5% of the cases and controls was genotyped twice by different persons, with a reproducibility of 100%.

Statistical analysis

Statistical analysis were performed by software SAS 9.1.3 (SAS Institute, Cary, NC). Allele frequencies were tested against departure from Hardy-Weinberg equilibrium through goodness-of-fit χ2 test before analysis. Differences in the distributions of demographic characteristics, selected variables, and frequencies of genotypes between cases and controls were evaluated by Student's t-test (for continuous variables) or χ2-test (for categorical variables). OR and 95% CIs from unconditional logistic regression analysis with the adjustment for possible confounders were used to estimate the association between the polymorphism and the risk of ccRCC. All of the statistical tests were two-sided and P<0.05 was considered statistically significant.

Results

Characteristics of ccRCC patients and controls

Clinical and pathologic characteristics of the 859 cases and 1005 controls are presented in Table 1 (negative results listed in Table S2). No significant differences were found between the cases and controls in regards to age, gender and drinking status (all P>0.05). However, there were more high BMI, smoking habit, hypertension and diabetes subjects in ccRCC patients than those in controls (P = 0.003, P = 0.040, P<0.001 and P = 0.040, respectively). Among 859 ccRCC cases, 577 (67.2%) patients were diagnosed with stage I disease, 170 (19.8%) patients with stage II, 57 (6.7%) patients with stage III, and 55 (6.4%) patients with stage IV. The percent of nuclear grade from I to IV was 20.5%, 54.7%, 19.9%, and 4.9%, respectively.

Table 1. Distribution of selected variables between the clear cell renal cell carcinoma cases and control subjects.

Variables Cases (n = 859) Controls (n = 1005) P-valuea
N % N %
Age (years) (mean ± SD) 57.0±11.7 57.2±12.4 0.758
BMI (kg/m2) (mean ± SD) 24.2±2.9 23.8±3.2 0.003
Gender
Male 557 64.8 688 68.5 0.098
Female 302 35.2 317 31.5
Smoking status
Never 530 61.7 666 66.3 0.040
Ever 329 38.3 339 33.7
Drinking status
Never 619 72.1 757 75.3 0.110
Ever 240 27.9 248 24.7
Hypertension
No 522 60.8 675 67.2 <0.001
Yes 337 39.2 251 25.0
Diabetes
No 748 87.6 870 86.6 <0.001
Yes 111 12.4 56 5.6
Clinical stage
I 577 67.2
II 170 19.8
III 57 6.7
IV 55 6.4
Grade
I 176 20.5
II 470 54.7
III 171 19.9
IV 42 4.9
a

Student's t-test for age and BMI distributions between cases and controls; two-sided χ2-test for others selected variables between cases and controls.

Association of SNPs with the risk of ccRCC

As shown in Table 2, except the rs1788484 in CBS gene and rs10520873 in MTRR gene, the genotype distributions of all other SNPs were in agreement with Hardy-Weinberg equilibrium in controls. Therefore, the rs1788484 and rs10520873 were excluded for further analysis. Table 2 shows ccRCC risks were associated with each single polymorphism. We presented each of the associations in additive, dominative and recessive models. In CBS gene, the genotype of rs706209 polymorphism distribution between cases and controls was significantly different (P = 0.006). In the dominant model, when compared with the homozygous wild-type reference group, TC+CC genotype was significantly associated with a decreased risk of ccRCC (P = 0.002, adjusted OR = 0.76, 95%CI = 0.62–0.91). In MTRR gene, the genotype of rs9332 polymorphism distribution between cases and controls was significantly different (P = 0.027). In the dominant model, CT+TT genotype was significantly associated with a decreased risk of ccRCC (P = 0.010, adjusted OR = 0.74, 95%CI = 0.60–0.92), when compared with the CC group. The rs2966952 seemed to be a bordering positive result. In the recessive models, TT genotype was slightly associated with an increased risk of ccRCC (P = 0.050, adjusted OR = 1.34, 95%CI = 1.00–1.80), compared with the CC+CT genotype. In TYMS gene, the genotype of rs2853741 polymorphism distribution between cases and controls had no significantly difference (P = 0.096). In the dominant model, TC+CC genotype was significantly associated with an increased risk of ccRCC (P = 0.032, adjusted OR = 1.25, 95%CI = 1.02–1.53), when compared with the TT group. Similarly, for the rs699517, the polymorphism distribution between cases and controls had no significantly difference (P = 0.108). In the recessive models, CC genotype was seemed to be associated with an increased risk of ccRCC (P = 0.172, adjusted OR = 1.25, 95%CI = 1.03–1.51).

Table 2. Polymorphism in one-carbon metabolism genes and clear cell renal cell carcinoma risk.

Position MAF Cases, n (%) Controls, n (%) P-valuea Adjusted OR (95% CI)b P trenda HWE
CBS
rs1788484 promoter 0.222
CC 535(62.3) 543(54.0) <0.001 Ref. 0.022 <0.001
CT 275(32.0) 425(42.3) 0.62(0.51–0.76)
TT 49(5.7) 37(3.7) 1.27(0.79–2.20)
TT vs. CC+CT 0.038 1.53(0.97–2.41)
CT+TT vs. CC <0.001 0.67(0.55–0.82)
rs706209 3′UTR 0.329
TT 401(46.7) 396(39.4) 0.006 Ref. 0.007 0.379
TC 358(41.7) 480(47.8) 0.76(0.62–0.92)
CC 100(11.6) 129(12.8) 0.74(0.55–1.01)
CC vs. TT+TC 0.434 0.87(0.65–1.16)
TC+CC vs. TT 0.002 0.76(0.62–0.91)
MTRR
rs2966952 promoter 0.333
CC 371(43.2) 463(46.1) 0.120 Ref. 0.064 0.978
CT 374(43.5) 438(43.6) 1.07(0.88–1.31)
TT 114(13.3) 104(10.4) 1.40(1.03–1.91)
TT vs. CC+CT 0.050 1.34(1.00–1.80)
CT+TT vs. CC 0.213 1.13(0.93–1.36)
rs9332 3′UTR 0.188
CC 651(75.8) 708(70.5) 0.027 Ref. 0.007 0.434
CT 196(22.8) 275(27.4) 0.75(0.60–0.93)
TT 12(1.4) 22(2.2) 0.65(0.31–1.33)
TT vs. CC+CT 0.203 0.70(0.34–1.43)
CT+TT vs. CC 0.010 0.74(0.60–0.92)
rs10520873 3′UTR 0.311
AA 593(69.0) 648(64.5) 0.063 Ref. 0.098 0.032
AG 240(27.9) 331(32.9) 0.79(0.64–0.97)
GG 26(3.0) 26(2.6) 1.15(0.65–2.04)
GG vs. AA+AG 0.566 1.24(0.70–2.19)
AG+GG vs. AA 0.038 0.82(0.67–1.00)
TYMS
rs2853741 promoter 0.411
TT 264(30.7) 356(35.4) 0.096 Ref. 0.046 0.982
TC 439(51.1) 484(48.2) 1.25(1.01–1.54)
CC 156(18.2) 165(16.4) 1.24(0.93–1.64)
CC vs. TT+TC 0.321 1.08(0.84–1.39)
TC+CC vs. TT 0.032 1.25(1.02–1.53)
rs699517 3′UTR 0.3
TT 420(48.9) 537(53.4) 0.108 Ref.
TC 358(41.7) 391(38.9) 1.25(1.02–1.52) 0.035 0.619
CC 81(9.4) 77(7.7) 1.26(0.89–1.78)
CC vs. TT+TC 0.172 1.25(1.03–1.51)
TC+CC vs. TT 0.051 1.15(0.82–1.61)
a

Two-sided χ2-test for either genotype distributions or trend between the cases and controls.

b

genotype-specific ORs were adjusted for age, gender, BMI, smoking status, drinking status, diabetes and hypertension in logistic regression model.

Combined Analysis of Polymorphisms

Rs706209 or rs9332 alone being associated with ccRCC risk, we combined these two polymorphisms based on the number of the variant alleles. As shown in Table 3, statistically significant difference was obviously found between the subgroups and the risk of ccRCC. Meanwhile, individuals carrying 1, 2, 3, or 4 variant alleles in these two genes were associated with a statistically significantly decreased risk of ccRCC compared with individuals carrying none variant alleles (P = 0.001, adjusted OR = 0.73, 95%CI = 0.06–0.90).

Table 3. Combined genotype frequencies among the case patients and control subjects and their collection to clear cell renal cell carcinoma.

Variables Case (n = 859) Controls (n = 1005) P-valuea Adjusted OR (95% CI)b
n % n %
rs706209 and rs9332
Number of risk allele
 0 304 35.4 286 28.5
 1 358 41.7 432 43.0 0.022 0.79(0.64–0.99)
 2 171 19.9 237 23.6 0.003 0.68(0.52–0.88)
 3 26 3.0 49 4.9 0.006 0.48(0.29–0.81)
 4 0 0 1 0
Recombined groups
 0 304 35.4 286 28.5
 1–4 555 64.6 719 71.5 0.001 0.73(0.06–0.90)
a

Two-sided χ2 test for the distributions of genotypes.

b

Adjusted for age, gender, BMI, smoking status, drinking status, hypertension and diabetes in logistic regression model.

Stratified Analysis of the Two Polymorphisms and Clinicopathologic Characteristics and Risk of ccRCC

We further evaluated the association between the combined genotypes of rs706209 and rs9332 polymorphisms and clinicopathologic characteristics of ccRCC. These two polymorphisms were combined based on the number of the variant alleles. As shown in Table 4, a significantly increased risk appeared in ccRCC patients with localized stage (P = 0.002, adjusted OR = 1.37, 95%CI = 1.11–1.69) and in patients with well-differentiated ccRCC (P<0.001, adjusted OR = 1.42, 95%CI = 1.14–1.76).

Table 4. Association between the combined genotypes of rs706209 and rs9332 polymorphisms and clinicopathologic characteristics of clear cell renal cell carcinoma.

Variables Risk allele P-valuea Adjusted OR (95% CI)b
0 1–4
n % n %
Control (n = 1005) 286(28.5) 719(71.5) Ref.
Case (n = 859)
Clinical stage
Localized (I+II) 265(35.5) 482 (64.5) 0.002 1.37 (1.11–1.69)
Advanced (III+IV) 39 (34.8) 73 (65.2) 0.160 1.30 (0.86–1.98)
Grade
Well- differentiated (I+II) 234 (36.2) 412 (63.8) <0.001 1.42 (1.14–1.76)
Moderately and Poorly differentiated(III+IV) 70 (32.9) 143 (67.1) 0.199 1.21 (0.87–1.68)
a

Two-sided χ2 test for the distributions of genotypes.

b

Adjusted for age, gender, BMI, smoking status, drinking status, hypertension and diabetes in logistic regression model.

As shown in Table 5, the analysis was stratified by age, gender, smoking status, and drinking status. Individuals carrying none variant allele in older group (P = 0.007, adjusted OR = 0.67, 95%CI = 0.49–0.91), male group (P = 0.007, adjusted OR = 0.71, 95%CI = 0.55–0.92), never smoking group (P = 0.002, adjusted OR = 0.68, 95%CI = 0.53–0.88) and never drinking group (P<0.001, adjusted OR = 0.68, 95%CI = 0.53–0.88) had an increased ccRCC risk.

Table 5. Association between the combined genotypes of rs706209 and rs9332 polymorphisms and clear cell renal cell carcinoma in stratified analysis.

Variables Risk allele P-valuea Adjusted OR (95% CI)b
0 1–4
Case(n,%) control(n,%) case(n,%) control(n,%)
Age
< = 57 161(36.2) 164(30.4) 284(63.8) 376(69.6) 0.054 0.78(0.60–1.02)
>57 143(34.5) 122(26.2) 271(65.5) 343(73.8) 0.007 0.67(0.49–0.91)
Gender
Male 192(34.5) 188(27.3) 365(65.5) 500(72.7) 0.007 0.71(0.55–0.92)
Female 121(37.1) 98(30.9) 190(62.9) 219(69.1) 0.105 0.77(0.55–1.08)
Smoke
Never 193(36.4) 187(28.1) 337(63.6) 479(71.9) 0.002 0.68(0.53–0.88)
Ever 111(33.7) 99(29.2) 218(66.3) 240(70.8) 0.207 0.83(0.59–1.17)
Drink
Never 229(37.0) 202(26.7) 390(63.0) 555(73.3) <0.001 0.68(0.53–0.88)
Ever 75(31.3) 84(33.9) 165(68.8) 164(66.1) 0.537 0.83(0.59–1.17)
a

Two-sided χ2 test for the distributions of genotypes.

b

Adjusted for age, gender, BMI, smoking status, drinking status, hypertension and diabetes in logistic regression model.

Discussion

Our study supports a role that CBS, MTRR, and TYMS play in modifying ccRCC risk. Meanwhile, we also notice the discrepancies between our findings and the results reported by the two European studies. Moore et al. reported that MTHFR and TYMS had effect on RCC risk, while CBS, MTR, or MTRR had no [14]. Gibson et al. reported that the strongest association between RCC risk and MTHFR, not CBS, MTR, MTRR, SHMT1 or TYMS, was observed [15]. The discrepancies might be due to the different aspect of study, different ethnic population and other unknown factors. Our current study is focus on the ccRCC, which is one part of RCC.The pathologic characteristics of ccRCC in our study may be relatively simple, when compared with these two European articals. In the dbSNP database, the minor allele frequency (MAF) of rs706209 was T allele  = 0.403 in European, but the MAF in Chinese was C allele  = 0.402, close to our data C allele  = 0.482. As involved in one-carbon metabolism pathway, the CBS gene encodes cystathionine beta synthase (CBS), which is the central enzyme in the transsulfuration pathway irreversibly metabolizing homocysteine (Hcy) to cystathionine [24]. Evidences showed that functional CBS gene SNP could impair CBS gene function, leading to an increase in the concentration on tHcy that further influenced aberrant DNA methylation patterns and CBS gene SNP had associations with lung cancer, colorectal cancer and head and neck squamous cell carcinoma [16], [25], [26]. Whether rs706209 has the similar influence on the CBS gene function needs further functional studies. MTRR catalyzes reductive methylation of cob (II)alamin by using SAM as a methyl donor to reactivate MTR. Thus, MTRR may act as a key regulator of the homocysteine conversion to methionine [27]. Our study demonstrated that CT+TT genotype of rs9332 was significantly associated to a decreased risk of ccRCC. Other report demonstrated that rs9332 in MTRR had connections with spina bifida and conotruncal heart defects [28]. Although little information about the function of this polymorphism was known, it is known that 3′UTR of the MTRR gene may influence miRNA or siRNA binding target site, causing the degradation of the mRNA, or inhibiting translation initiation. This polymorphism has a protective role in the risk of ccRCC. More researches should be done to reveal the relationship between them.

Moreover, we found that TYMS SNPs (rs2966952 and rs699517) had some of connections with ccRCC risk. Skibola et al. reported that C allele in rs699517 was approximately 100% correlated with TYMS 1496 insertion and T allele in rs699517 was also approximately 100% correlated with TYMS 1496 deletion. The TYMS 1496 deletion polymorphism was associated with decreased mRNA stability and low expression in tumor tissue than the wild type polymorphism [29], [30], [31]. Evidence demonstrated that the level of thymidylate synthetase (TS) activity was correlated with both the progression of the stage and the increase of the grade of RCC, and the activity of TS was approximately 5-fold higher in RCC compared with normal kidney [32].

There were several limitations in our present study. Firstly, our standard questionnaire contained no environmental factors, such as occupational exposure, and personal habits, such as diet and physical activity. So our study may have a limited statistical power, such as that we could not do further analysis in gene-environment interaction. Secondly, more and more studies indicated that gene-gene interaction may also have contribution to the risk of cancer [33], [34]. In the current study, we did little analysis about the interaction among genes in the one-carbon metabolism pathway. So the results may exist some interaction bias. Furthermore, our study was designed as a hospital-based study, so the possibility of selection bias of subjects could not be ruled out. Thirdly, the genotype distributions of rs1788484 in CBS gene and rs10520873 in MTRR gene were departed from Hardy-Weinberg equilibrium in controls. The probability of genotyping error was very low. Meanwhile, Galbiatti et al. also reported that polymorphism of CBS gene was not in Hardy-Weinberg equilibrium [26]. The departure from the Hardy-Weinberg equilibrium may result from selection bias, disease model adopted, and evolutionary factors which may influence changes in the genotype frequencies [35], [36]. On the other hand, this disequilibrium should be expected, in the case that it reflected biological and genetic characteristics in complex disease models [37].

In summary, the data indicates that the common variation in CBS, MTRR and TYMS may significantly modify ccRCC risk.

Supporting Information

Table S1

All the sequences of primers for each SNP.(DOC).

(DOC)

Table S2

Polymorphism in one-carbon metabolism genes and clear cell renal cell carcinoma. (DOC).

(DOC)

Funding Statement

This work was supported by the Program for Development of Innovative Research Team in the First Affiliated Hospital of Nanjing Medical University, Provincial Initiative Program for Excellency Disciplines of Jiangsu Province, the National Natural Science Foundation of China [grant number 81171963, 81102089, and 81201998]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

References

  • 1. Siegel R, Ward E, Brawley O, Jemal A (2011) Cancer statistics, 2011: the impact of eliminating socioeconomic and racial disparities on premature cancer deaths. CA Cancer J Clin 61: 212–236. [DOI] [PubMed] [Google Scholar]
  • 2. Chow WH, Dong LM, Devesa SS (2010) Epidemiology and risk factors for kidney cancer. Nat Rev Urol 7: 245–257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3. Mathew A, Devesa SS, Fraumeni JF Jr, Chow WH (2002) Global increases in kidney cancer incidence, 1973–1992. Eur J Cancer Prev 11: 171–178. [DOI] [PubMed] [Google Scholar]
  • 4. Hirata H, Hinoda Y, Nakajima K, Kikuno N, Suehiro Y, et al. (2009) The bcl2 -938CC genotype has poor prognosis and lower survival in renal cancer. J Urol 182: 721–727. [DOI] [PubMed] [Google Scholar]
  • 5. Lin J, Horikawa Y, Tamboli P, Clague J, Wood CG, et al. (2010) Genetic variations in microRNA-related genes are associated with survival and recurrence in patients with renal cell carcinoma. Carcinogenesis 31: 1805–1812. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6. Kleinrath T, Gassner C, Lackner P, Thurnher M, Ramoner R (2007) Interleukin-4 promoter polymorphisms: a genetic prognostic factor for survival in metastatic renal cell carcinoma. J Clin Oncol 25: 845–851. [DOI] [PubMed] [Google Scholar]
  • 7. Kawai Y, Sakano S, Korenaga Y, Eguchi S, Naito K (2007) Associations of single nucleotide polymorphisms in the vascular endothelial growth factor gene with the characteristics and prognosis of renal cell carcinomas. Eur Urol 52: 1147–1155. [DOI] [PubMed] [Google Scholar]
  • 8. Teodoridis JM, Strathdee G, Plumb JA, Brown R (2004) CpG-island methylation and epigenetic control of resistance to chemotherapy. Biochem Soc Trans 32: 916–917. [DOI] [PubMed] [Google Scholar]
  • 9. Shinojima T, Oya M, Takayanagi A, Mizuno R, Shimizu N, et al. (2007) Renal cancer cells lacking hypoxia inducible factor (HIF)-1alpha expression maintain vascular endothelial growth factor expression through HIF-2alpha. Carcinogenesis 28: 529–536. [DOI] [PubMed] [Google Scholar]
  • 10. Kawakami T, Okamoto K, Ogawa O, Okada Y (2003) Multipoint methylation and expression analysis of tumor suppressor genes in human renal cancer cells. Urology 61: 226–230. [DOI] [PubMed] [Google Scholar]
  • 11. Morrissey C, Martinez A, Zatyka M, Agathanggelou A, Honorio S, et al. (2001) Epigenetic inactivation of the RASSF1A 3p21.3 tumor suppressor gene in both clear cell and papillary renal cell carcinoma. Cancer Res 61: 7277–7281. [PubMed] [Google Scholar]
  • 12. Eden A, Gaudet F, Waghmare A, Jaenisch R (2003) Chromosomal instability and tumors promoted by DNA hypomethylation. Science 300: 455. [DOI] [PubMed] [Google Scholar]
  • 13. Feinberg AP (2007) Phenotypic plasticity and the epigenetics of human disease. Nature 447: 433–440. [DOI] [PubMed] [Google Scholar]
  • 14. Moore LE, Hung R, Karami S, Boffetta P, Berndt S, et al. (2008) Folate metabolism genes, vegetable intake and renal cancer risk in central Europe. Int J Cancer 122: 1710–1715. [DOI] [PubMed] [Google Scholar]
  • 15. Gibson TM, Brennan P, Han S, Karami S, Zaridze D, et al. (2011) Comprehensive evaluation of one-carbon metabolism pathway gene variants and renal cell cancer risk. PLoS One 6: e26165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16. Flores KG, Stidley CA, Mackey AJ, Picchi MA, Stabler SP, et al. (2012) Sex-specific association of sequence variants in CBS and MTRR with risk for promoter hypermethylation in the lung epithelium of smokers. Carcinogenesis 33: 1542–1547. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17. Shen M, Rothman N, Berndt SI, He X, Yeager M, et al. (2005) Polymorphisms in folate metabolic genes and lung cancer risk in Xuan Wei, China. Lung Cancer 49: 299–309. [DOI] [PubMed] [Google Scholar]
  • 18. Curtin K, Slattery ML, Ulrich CM, Bigler J, Levin TR, et al. (2007) Genetic polymorphisms in one-carbon metabolism: associations with CpG island methylator phenotype (CIMP) in colon cancer and the modifying effects of diet. Carcinogenesis 28: 1672–1679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19. Cui LH, Yu Z, Zhang TT, Shin MH, Kim HN, et al. (2011) Influence of polymorphisms in MTHFR 677 C–>T, TYMS 3R–>2R and MTR 2756 A–>G on NSCLC risk and response to platinum-based chemotherapy in advanced NSCLC. Pharmacogenomics 12: 797–808. [DOI] [PubMed] [Google Scholar]
  • 20. Shi Q, Zhang Z, Li G, Pillow PC, Hernandez LM, et al. (2005) Sex differences in risk of lung cancer associated with methylene-tetrahydrofolate reductase polymorphisms. Cancer Epidemiol Biomarkers Prev 14: 1477–1484. [DOI] [PubMed] [Google Scholar]
  • 21. Boccia S, Boffetta P, Brennan P, Ricciardi G, Gianfagna F, et al. (2009) Meta-analyses of the methylenetetrahydrofolate reductase C677T and A1298C polymorphisms and risk of head and neck and lung cancer. Cancer Lett 273: 55–61. [DOI] [PubMed] [Google Scholar]
  • 22. Mao R, Fan Y, Jin Y, Bai J, Fu S (2008) Methylenetetrahydrofolate reductase gene polymorphisms and lung cancer: a meta-analysis. J Hum Genet 53: 340–348. [DOI] [PubMed] [Google Scholar]
  • 23. Qin C, Cao Q, Ju X, Wang M, Meng X, et al. (2012) The polymorphisms in the VHL and HIF1A genes are associated with the prognosis but not the development of renal cell carcinoma. Ann Oncol 23: 981–989. [DOI] [PubMed] [Google Scholar]
  • 24. Yi P, Melnyk S, Pogribna M, Pogribny IP, Hine RJ, et al. (2000) Increase in plasma homocysteine associated with parallel increases in plasma S-adenosylhomocysteine and lymphocyte DNA hypomethylation. J Biol Chem 275: 29318–29323. [DOI] [PubMed] [Google Scholar]
  • 25. Le Marchand L, Donlon T, Hankin JH, Kolonel LN, Wilkens LR, et al. (2002) B-vitamin intake, metabolic genes, and colorectal cancer risk (United States). Cancer Causes Control 13: 239–248. [DOI] [PubMed] [Google Scholar]
  • 26. Galbiatti AL, Ruiz MT, Raposo LS, Maniglia JV, Pavarino-Bertelli EC, et al. (2010) The association between CBS 844ins68 polymorphism and head and neck squamous cell carcinoma risk - a case-control analysis. Arch Med Sci 6: 772–779. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27. Leclerc D, Wilson A, Dumas R, Gafuik C, Song D, et al. (1998) Cloning and mapping of a cDNA for methionine synthase reductase, a flavoprotein defective in patients with homocystinuria. Proc Natl Acad Sci U S A 95: 3059–3064. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28. Shaw GM, Lu W, Zhu H, Yang W, Briggs FB, et al. (2009) 118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects. BMC Med Genet 10: 49. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29. Skibola CF, Forrest MS, Coppede F, Agana L, Hubbard A, et al. (2004) Polymorphisms and haplotypes in folate-metabolizing genes and risk of non-Hodgkin lymphoma. Blood 104: 2155–2162. [DOI] [PubMed] [Google Scholar]
  • 30. Mandola MV, Stoehlmacher J, Zhang W, Groshen S, Yu MC, et al. (2004) A 6 bp polymorphism in the thymidylate synthase gene causes message instability and is associated with decreased intratumoral TS mRNA levels. Pharmacogenetics 14: 319–327. [DOI] [PubMed] [Google Scholar]
  • 31. Ulrich CM, Curtin K, Potter JD, Bigler J, Caan B, et al. (2005) Polymorphisms in the reduced folate carrier, thymidylate synthase, or methionine synthase and risk of colon cancer. Cancer Epidemiol Biomarkers Prev 14: 2509–2516. [DOI] [PubMed] [Google Scholar]
  • 32. Mizutani Y, Wada H, Yoshida O, Fukushima M, Nonomura M, et al. (2003) Significance of thymidylate synthase activity in renal cell carcinoma. Clin Cancer Res 9: 1453–1460. [PubMed] [Google Scholar]
  • 33. Zhong R, Liu L, Zou L, Sheng W, Zhu B, et al. (2013) Genetic variations in the TGFbeta signaling pathway, smoking and risk of colorectal cancer in a Chinese population. Carcinogenesis 34: 936–942. [DOI] [PubMed] [Google Scholar]
  • 34. Liu L, Wu C, Wang Y, Zhong R, Wang F, et al. (2011) Association of candidate genetic variations with gastric cardia adenocarcinoma in Chinese population: a multiple interaction analysis. Carcinogenesis 32: 336–342. [DOI] [PubMed] [Google Scholar]
  • 35. Xu J, Turner A, Little J, Bleecker ER, Meyers DA (2002) Positive results in association studies are associated with departure from Hardy-Weinberg equilibrium: hint for genotyping error? Hum Genet 111: 573–574. [DOI] [PubMed] [Google Scholar]
  • 36. Llorca J, Prieto-Salceda D, Combarros O, Dierssen-Sotos T, Berciano J (2005) [Competing risks of death and Hardy-Weinberg equilibrium in case-control studies of gene-disease association]. Gac Sanit 19: 321–324. [DOI] [PubMed] [Google Scholar]
  • 37. Wittke-Thompson JK, Pluzhnikov A, Cox NJ (2005) Rational inferences about departures from Hardy-Weinberg equilibrium. Am J Hum Genet 76: 967–986. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Table S1

All the sequences of primers for each SNP.(DOC).

(DOC)

Table S2

Polymorphism in one-carbon metabolism genes and clear cell renal cell carcinoma. (DOC).

(DOC)


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