Mol Biol Rep (2014) 41:713–719 DOI 10.1007/s11033-013-2910-y
Meta-analysis on the association of nucleotide excision repair gene XPD A751C variant and cancer susceptibility among Indian population Raju Kumar Mandal • Suraj Singh Yadav Aditya K. Panda
•
Received: 19 June 2013 / Accepted: 13 December 2013 / Published online: 22 December 2013 Ó Springer Science+Business Media Dordrecht 2013
Abstract Polymorphism A751C (A[C) in XPD gene has shown susceptibility to many cancers in Indian population; however the results of these studies are inconclusive. Thus, we performed this meta-analysis to estimate the association between XPD A751C polymorphism and overall cancer susceptibility. We quantitavely synthesized all published studies of the association between XPD A751C polymorphism and cancer risk. Pooled odds ratios (ORs) and 95 % CI were estimated for allele contrast, homozygous, heterozygous, dominant and recessive genetic model. A total of thirteen studies including 3,599 controls and 3,087 cancer cases were identified and analyzed. Overall significant results were observed for C allele carrier (C vs. A: p = 0.001; OR 1.372, 95 % CI 1.172–1.605) variant homozygous (CC vs. AA: p = 0.001; OR 1.691, 95 % CI 1.280–2.233) and heterozygous (AC vs. AA: p = 0.001; OR 1.453, 95 % CI 1.215–1.737) genotypes. Similarly dominant (CC?AC vs. AA: p = 0.001; OR 1.512, 95 % CI 1.244–1.839) and recessive (CC vs. AA?AC: p = 0.001; OR 1.429, 95 % CI 1.151–1.774) genetic models also demonstrated risk of developing cancer. This meta-analysis suggested that XPD A751C polymorphism likely contribute to cancer susceptibility in Indian R. K. Mandal (&) Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raibareli Road, Luknow, India e-mail: [email protected] S. S. Yadav Department of Pharmacology, King George Medical University, Lucknow, India A. K. Panda Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
population. Further studies about gene–gene and gene– environment interactions are required. Keywords DNA repair gene Nucleotide excision repair Meta-analysis Cancer Polymorphism
Introduction Human genome constantly damaged by exogenous and endogenous stresses [1]. DNA disruptions can lead to gene rearrangements, translocations, amplifications, and deletions, which can in turn contribute to cancer development [2]. DNA repair pathways play a critical role in maintaining the genomic integrity, as well as in the prevention of carcinogenesis, and therefore defect in these genes can lead to higher susceptibility to multiple cancers [3]. Molecular epidemiology studies have also documented that genetic variants of DNA repair genes and reduced DNA repair capacity (DRC) are thought to contribute higher risk of developing cancers [4, 5]. Xeroderma pigmentosum group D (XPD or ERCC2) is a key gene of nucleotide excision repair (NER) pathway and the gene product play a major role in repair to bulky DNA lesions and genetic damage induced by tobacco, UV induced photolesions and other chemical carcinogens [6, 7]. The XPD protein has an ATP-dependent DNA helicase activity and essential part of the basal transcription factor BTF2/TFIIH complex [8]. Mutations in the XPD gene can prevent the DNA strand opening and dual incision steps, resulting in a defect in NER, in transcription, and in an abnormal response to apoptosis [9]. It has been documented that polymorphism in XPD gene is associated with reduced DRC because of a possible reduction in helicase activity [10]. Several single nucleotide polymorphisms
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Table 1 Main characteristics of all thirteen studies included in the meta-analysis First authors and year
Types of cancer
Study design
Genotyping method
Control
Cases
Kumar et al. 2012 [13]
SCCHN
HB
PCR–RFLP
278
278
Sobti et al. 2012 [14]
Bladder
HB
PCR–RFLP
252
270
Sobti et al. 2012 [15]
Prostate
HB
PCR–RFLP
150
150 250
Samson et al. 2011 [16]
Breast
HB
Taq Man
500
Wang et al. 2010 [17]
Colorectal
HB
PCR–RFLP
291
302
Mandal et al. 2010 [18]
Prostate
HB
PCR–RFLP
200
171
Srivastava et al. 2010 [19]
Gallbladder
HB
PCR–RFLP
230
230
Syamala et al. 2009 [20]
Breast
HB
PCR–RFLP
367
359
Gangwar et al. 2009 [21]
Bladder
HB
PCR–RFLP
250
206
Mitra et al. 2009 [22]
Breast
HB
PCR–RFLP
215
155
Mitra et al. 2009 [22] Sreeja et al. 2008 [23]
SCCHN Lung
HB HB
PCR–RFLP PCR–RFLP
385 211
275 211
Sobti et al. 2007 [24]
Esophageal
HB
PCR–RFLP
160
120
Ramachandran et al. 2006 [25]
Oral
HB
PCR–RFLP
110
110
SCCHN squamous cell carcinomas of the head and neck, HB hospital based
(SNPs) have been described in the XPD gene, among them codon 751 (A[C substitution at position 35931, exon 23, Lys[Gln, rs1052559) polymorphism, located in the C-terminal region, undergoes a major change in the conformation of the respective amino acid [11]. Individuals with XPD 751 CC genotype have been revealed to have suboptimal DRC to remove UV photoproducts when compared to the 751Lys/Lys and Lys/Gln genotypes [12]. Having known the functional significance of this genetic variant in DRC, several molecular epidemiological studies investigated the impact of XPD exon 23 A[C polymorphism on the susceptibility to various cancers in Indian population (Table 1) [13–25]. However, the findings from these studies remain inconsistent. To clarify the role of XPD exon 23 A[C polymorphism and susceptibility to cancer risk in Indian population, we performed this metaanalysis based on published case–control studies to make a more comprehensive and compelling evaluation of the overall cancer risk associated with this polymorphism, as well as to evaluate this polymorphism as potential marker for screening of cancer in Indian population.
Materials and methods Identification of eligible studies Literature search was conducted within in the PubMed (Medline) and EMBASE database up to February 2013, using the keywords ‘‘XPD’’ or ‘‘ERCC2’’ polymorphism and cancer or carcinoma in Indian population. Additionally, we also used the ‘‘Related Articles’’ option in PubMed to identify additional studies on the same topic.
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Criteria for inclusion and exclusion To minimize heterogeneity and facilitate the proper elucidation of results, all eligible studies had to fulfill all the following criteria: (a) original research article evaluated XPD exon 23 A[C and cancer risk, (b) use of case–control or cohort studies of Indian population, (c) recruited pathologically confirmed cancer patients and cancer free controls, (d) have available genotype frequency in case and control. Also, when the case– control study was included by more than one article using the same case series, we selected the study that included the largest number of individuals. The major reasons for exclusion of studies were, (a) overlapping of data, (b) case-only studies, (c) review articles, (d) editorials, (e) animal studies. Data extraction and quality assessment For each publication, the methodological quality assessment and data extraction was independently abstracted in duplicate by two independent investigators using a standard protocol. Data accuracy was ensured using data-collection form according to the inclusion criteria listed above. In case of disagreement on any item of the data collected from the retrieved studies, the problem would be fully discussed to reach a consensus. Data extracted from these studies included the name of first author, year of publication, type of cancer, number of cases and controls, types of study and genotyping methods and frequencies. Evaluations of statistical associations Hardy–Weinberg equilibrium (HWE) was examined in the control subjects using a goodness of fit chi-square test for
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Table 2 Genotypic distribution of XPD A751C (rs1052559) gene polymorphism included in meta-analysis Authors and year
Controls
Cancer cases
Genotype
Minor allele
Genotype
HWE Minor allele
AA
AC
CC
MAF
AA
AC
CC
MAF
p value
Kumar et al. 2012 [13]
129
110
39
0.44
92
125
61
0.33
0.05
Sobti et al. 2012 [14]
104
81
67
0.53
74
104
92
0.42
\0.0001
Sobti et al. 2012 [15] Samson et al. 2011 [16]
67 235
69 214
14 51
0.36 0.36
62 107
67 102
21 41
0.32 0.316
0.53 0.82
Wang et al. 2010 [17]
137
117
37
0.32
138
130
34
0.32
0.13
89
94
17
0.32
73
84
14
0.32
0.25
Srivastava et al. 2010 [19]
113
90
27
0.37
93
103
34
0.31
0.17
Syamala et al. 2009 [20]
247
98
22
0.36
148
161
50
0.19
0.005
Gangwar et al. 2009 [21]
110
121
19
0.33
86
104
16
0.31
0.06
Mitra et al. 2009 [22]
84
98
33
0.57
30
73
52
0.38
0.61
Mitra et al. 2009 [22]
163
179
43
0.41
88
148
39
0.34
0.55
Sreeja et al. 2008 [23]
139
61
11
0.27
109
89
13
0.19
0.21
Sobti et al. 2007 [24]
63
77
20
0.31
52
61
7
0.36
0.63
Ramachandran et al. 2006 [25]
71
31
8
0.34
49
46
15
0.21
0.09
Mandal et al. 2010 [18]
MAF Minor allele frequency, HWE Hardy–Weinberg equilibrium
each study, Odds ratio (OR) with 95 % confidence intervals (CI) was used to assess the strength of association between the XPD exon 23 A[C gene polymorphism and cancer risk. Heterogeneity was assessed with standard Q-statistic test. If heterogeneity existed, the random effects model was adopted to calculate the overall OR value [26]. Otherwise, the fixed effect model was used [27]. Begg’s funnel plots and Egger’s regression test were undertaken to assess the potential publication bias [28]. p value less than 0.05 was judged significant. All the data analysis was performed using a comprehensive meta-analysis (CMA) V2 software (Biostat, USA).
Results Characteristics of published studies A total of thirteen articles were retrieved through literature search from the PubMed (Medline) and EMBASE database. All retrieved articles were examined by reading the titles, abstracts and the full texts for the potentially relevant publications. Articles were further checked for their suitability for this meta-analysis. In addition to the database search, the reference lists of the retrieved articles were also screened for other potential relevant articles. Studies comprising XPD polymorphism to predict survival in cancer patients or considering XPD variant as an indicator for response to therapy were excluded. Studies related to investigation of the levels of XPD mRNA or protein
expression or review articles were also excluded. Strict criteria were followed in article search, only case–control or cohort design studies having frequency of all the three genotypes were included. Following the careful screening and strict inclusion and exclusion criteria, thirteen eligible original published studies were achieved and included in the study (Table 1). Distribution of genotypes, Minor allele frequency (MAF) and HWE p values has been tabulated in the Table 2. Publication bias Begg’s funnel plot and Egger’s test were performed to evaluate the publication bias among the included studies for this meta-analysis. The shape of funnel plots did not reveal any evidence of obvious asymmetry in all comparisons, and the Egger’s test was used to provide statistical evidence of funnel plot. The results did not show any evidence of publication bias in all genetic models (Table 3). Test of heterogeneity Q-test and I2 statistics were used to test for heterogeneity among the studies. Heterogeneity was observed in all the models, such as allele (C vs. A), homozygous (CC vs. AA), heterozygous (AC vs. AA), recessive (CC vs. AA?AC) and dominant (CC?AC vs. AA) models, which was included for this analysis. Thus, we applied random effect model to calculate the pooled OR and 95 % CI (Table 3).
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Table 3 Statistics to test publication bias and heterogeneity in meta-analysis Comparisons
Egger’s regression analysis Intercept
95 % CI
Heterogeneity analysis p value
Q value
pheterogeneity
2
I (%)
Model used for meta-analysis
C vs. A
-1.30
-8.72 to 6.11
0.70
58.36
\0.0001
77.72
Random
CC vs. AA
-2.11
-6.25 to 2.02
0.28
37.65
\0.0001
65.47
Random
AC vs. AA
-0.25
-6.28 to 5.78
0.92
35.71
0.001
63.60
Random
CC?AC vs. AA
-0.73
-7.64 to 6.16
0.81
48.29
\0.0001
73.08
Random
CC vs. AA?AC
-1.79
-4.91 to 1.33
0.23
26.39
0.01
50.74
Random
Fig. 1 Forest plot of a meta-analysis of the association between XPD exon 23 A[C polymorphism (C vs. A; AC vs. AA; CC vs. AA) and overall cancer risk
Overall effects of XPD exon 23 A[C polymorphism and cancer susceptibility All the thirteen studies were pooled together which resulted into 3,599 controls and 3,087 cancer cases was used to assess the overall association between the XPD exon 23 A[C polymorphism and risk of cancer. The pooled data indicated an evidence for a significant association between
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the XPD exon 23 A[C polymorphism and susceptibility to cancer in all the models. Variant allele C demonstrated significant risk of developing cancer in terms of the frequency with wild allele (A) comparison (C vs. A: p = 0.001; OR 1.372, 95 % CI 1.172–1.605). Similarly, homozygous mutant CC (CC vs. AA; p = 0.001; OR 1.691, 95 % CI 1.280–2.233) and heterozygous AC (AC vs. AA: p = 0.001; OR 1.453, 95 % CI 1.215–1.737)
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Fig. 2 Forest plot of a meta-analysis of the association between XPD exon 23 A[C (CC?AC vs. AA; CC vs. AA?AC) and overall cancer risk
genotypes revealed significantly increased risk for the occurrence of cancer as compared with the homozygous AA genotype (Fig. 1). Additionally, analysis of recessive (CC vs. AA?AC: p = 0.001; OR 1.429, 95 % CI 1.151–1.774) and dominant (CC?AC vs. AA: p = 0.001; OR 1.512, 95 % CI 1.244–1.839) genetic models indicated 1.4- and 1.5-fold increased risk of developing cancer (Fig. 2).
Discussion Common genetic polymorphisms or mutation in the DNA repair genes may alter protein function and play a major role in carcinogenesis. In the recent years, interest in the genetic susceptibility to cancers has led to a growing attention to the study of polymorphisms of genes involved in carcinoma. Several studies has been supported an important role for genetics in determining the risk for cancer, and association studies are apposite for searching susceptibility genes involved in cancer [29]. Till date,
series of epidemiological studies have been performed to explore the role of XPD exon 23 A[C polymorphism on cancer susceptibility in worldwide and in Indian population, but the results remain controversial. Some studies are limited by their sample size and subsequently suffer from too low power to detect effects that may exist. Meta-analysis is a powerful tool for summarizing the results from different studies and gives more reliable results than a single case–control study, where individual sample sizes are small and inadequate statistical power [30]. Combining data from many studies has the advantage of reducing random error [31]. Hence, in order to improve the statistical power and determine the effect size of XPD exon 23 A[C polymorphism, we performed this meta- analysis with thirteen eligible studies to provide the more comprehensive and reliable association between XPD exon 23 A[C polymorphism and overall cancer risk for Indian population. Results of the present meta-analysis showed that XPD exon 23 A[C polymorphism is significantly associated with increased cancer risk in Indian population. Subjects
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with C allele and variants homozygous CC had 1.3- and 1.6-fold increased risk of developing cancer as compared with the wild A allele and homozygous AA genotype, respectively. Similarly, heterozygous, dominant and recessive models have shown increased risk of cancer. Based upon the above results and importance of XPD’s role in the pathogenesis of cancer, it is biologically plausible that XPD exon 23 A[C polymorphism may modulate the risk of cancer and could be a genetic factor for inter-individual differences in susceptibility to cancer disease. It has been suggested that functional and common sequence variations of DNA repair genes may be potential cancer susceptibility factors in the general population exposed to environmental carcinogens such as polycyclic aromatic hydrocarbons (PAHs) [12, 32]. Earlier, Lunn et al. studied the functional significance of XPD polymorphisms with respect to chromosome aberrations and Hou et al. also reported that common variant alleles of codon 751 of XPD gene was associated with reduced repair of aromatic DNA adducts [33, 34]. Genome wide association study suggested that XPD exon 23 A[C polymorphism has reduced DRC and contribute to increase risk of cancer [35]. It is of a great concern; that genetic susceptibility to cancer is polygenic type [36]; hence single genetic variant is usually inadequate to predict the risk of this deadly disease. Some limitations should be addressed which may affect the result, i.e., first, in this meta-analysis we found inter-study heterogeneity. Many factors might contribute to this heterogeneity, because regional lifestyle varied among populations from different parts of India [37], another recruitment of control group the controls were not uniformly defined, some studies used a healthy population as the reference group where as other selected hospital patients without cancer as the reference group. Second, the present meta-analysis was based primarily on unadjusted effect estimates and CIs. Third, the gene–gene and gene– environment interactions were not addressed. In spite of these limitations, our meta-analysis has some advantages. First, we did not detect publication bias, indicated that the results are statistically robust. Second, we performed strict data extraction and analysis to make satisfactory and reliable conclusion. In conclusion, this meta-analysis indicates that, XPD exon 23 A[C polymorphism would be a risk factor for cancer susceptibility in Indian population. The importance of this polymorphism as a predictor of the risk of cancer is very high and the screening utility of this genetic variant in symptomatic individuals may be warranted. Future well designed large scale studies in the same NER pathway with gene-environment interaction might be necessary to investigate the association between DNA repair gene SNPs and risk of cancer.
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Mol Biol Rep (2014) 41:713–719 Conflict of interest
None.
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Meta-analysis on the association of nucleotide excision repair gene XPD A751C variant and cancer susceptibility among Indian population Raju Kumar Mandal • Suraj Singh Yadav Aditya K. Panda
•
Received: 19 June 2013 / Accepted: 13 December 2013 / Published online: 22 December 2013 Ó Springer Science+Business Media Dordrecht 2013
Abstract Polymorphism A751C (A[C) in XPD gene has shown susceptibility to many cancers in Indian population; however the results of these studies are inconclusive. Thus, we performed this meta-analysis to estimate the association between XPD A751C polymorphism and overall cancer susceptibility. We quantitavely synthesized all published studies of the association between XPD A751C polymorphism and cancer risk. Pooled odds ratios (ORs) and 95 % CI were estimated for allele contrast, homozygous, heterozygous, dominant and recessive genetic model. A total of thirteen studies including 3,599 controls and 3,087 cancer cases were identified and analyzed. Overall significant results were observed for C allele carrier (C vs. A: p = 0.001; OR 1.372, 95 % CI 1.172–1.605) variant homozygous (CC vs. AA: p = 0.001; OR 1.691, 95 % CI 1.280–2.233) and heterozygous (AC vs. AA: p = 0.001; OR 1.453, 95 % CI 1.215–1.737) genotypes. Similarly dominant (CC?AC vs. AA: p = 0.001; OR 1.512, 95 % CI 1.244–1.839) and recessive (CC vs. AA?AC: p = 0.001; OR 1.429, 95 % CI 1.151–1.774) genetic models also demonstrated risk of developing cancer. This meta-analysis suggested that XPD A751C polymorphism likely contribute to cancer susceptibility in Indian R. K. Mandal (&) Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raibareli Road, Luknow, India e-mail: [email protected] S. S. Yadav Department of Pharmacology, King George Medical University, Lucknow, India A. K. Panda Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
population. Further studies about gene–gene and gene– environment interactions are required. Keywords DNA repair gene Nucleotide excision repair Meta-analysis Cancer Polymorphism
Introduction Human genome constantly damaged by exogenous and endogenous stresses [1]. DNA disruptions can lead to gene rearrangements, translocations, amplifications, and deletions, which can in turn contribute to cancer development [2]. DNA repair pathways play a critical role in maintaining the genomic integrity, as well as in the prevention of carcinogenesis, and therefore defect in these genes can lead to higher susceptibility to multiple cancers [3]. Molecular epidemiology studies have also documented that genetic variants of DNA repair genes and reduced DNA repair capacity (DRC) are thought to contribute higher risk of developing cancers [4, 5]. Xeroderma pigmentosum group D (XPD or ERCC2) is a key gene of nucleotide excision repair (NER) pathway and the gene product play a major role in repair to bulky DNA lesions and genetic damage induced by tobacco, UV induced photolesions and other chemical carcinogens [6, 7]. The XPD protein has an ATP-dependent DNA helicase activity and essential part of the basal transcription factor BTF2/TFIIH complex [8]. Mutations in the XPD gene can prevent the DNA strand opening and dual incision steps, resulting in a defect in NER, in transcription, and in an abnormal response to apoptosis [9]. It has been documented that polymorphism in XPD gene is associated with reduced DRC because of a possible reduction in helicase activity [10]. Several single nucleotide polymorphisms
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Mol Biol Rep (2014) 41:713–719
Table 1 Main characteristics of all thirteen studies included in the meta-analysis First authors and year
Types of cancer
Study design
Genotyping method
Control
Cases
Kumar et al. 2012 [13]
SCCHN
HB
PCR–RFLP
278
278
Sobti et al. 2012 [14]
Bladder
HB
PCR–RFLP
252
270
Sobti et al. 2012 [15]
Prostate
HB
PCR–RFLP
150
150 250
Samson et al. 2011 [16]
Breast
HB
Taq Man
500
Wang et al. 2010 [17]
Colorectal
HB
PCR–RFLP
291
302
Mandal et al. 2010 [18]
Prostate
HB
PCR–RFLP
200
171
Srivastava et al. 2010 [19]
Gallbladder
HB
PCR–RFLP
230
230
Syamala et al. 2009 [20]
Breast
HB
PCR–RFLP
367
359
Gangwar et al. 2009 [21]
Bladder
HB
PCR–RFLP
250
206
Mitra et al. 2009 [22]
Breast
HB
PCR–RFLP
215
155
Mitra et al. 2009 [22] Sreeja et al. 2008 [23]
SCCHN Lung
HB HB
PCR–RFLP PCR–RFLP
385 211
275 211
Sobti et al. 2007 [24]
Esophageal
HB
PCR–RFLP
160
120
Ramachandran et al. 2006 [25]
Oral
HB
PCR–RFLP
110
110
SCCHN squamous cell carcinomas of the head and neck, HB hospital based
(SNPs) have been described in the XPD gene, among them codon 751 (A[C substitution at position 35931, exon 23, Lys[Gln, rs1052559) polymorphism, located in the C-terminal region, undergoes a major change in the conformation of the respective amino acid [11]. Individuals with XPD 751 CC genotype have been revealed to have suboptimal DRC to remove UV photoproducts when compared to the 751Lys/Lys and Lys/Gln genotypes [12]. Having known the functional significance of this genetic variant in DRC, several molecular epidemiological studies investigated the impact of XPD exon 23 A[C polymorphism on the susceptibility to various cancers in Indian population (Table 1) [13–25]. However, the findings from these studies remain inconsistent. To clarify the role of XPD exon 23 A[C polymorphism and susceptibility to cancer risk in Indian population, we performed this metaanalysis based on published case–control studies to make a more comprehensive and compelling evaluation of the overall cancer risk associated with this polymorphism, as well as to evaluate this polymorphism as potential marker for screening of cancer in Indian population.
Materials and methods Identification of eligible studies Literature search was conducted within in the PubMed (Medline) and EMBASE database up to February 2013, using the keywords ‘‘XPD’’ or ‘‘ERCC2’’ polymorphism and cancer or carcinoma in Indian population. Additionally, we also used the ‘‘Related Articles’’ option in PubMed to identify additional studies on the same topic.
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Criteria for inclusion and exclusion To minimize heterogeneity and facilitate the proper elucidation of results, all eligible studies had to fulfill all the following criteria: (a) original research article evaluated XPD exon 23 A[C and cancer risk, (b) use of case–control or cohort studies of Indian population, (c) recruited pathologically confirmed cancer patients and cancer free controls, (d) have available genotype frequency in case and control. Also, when the case– control study was included by more than one article using the same case series, we selected the study that included the largest number of individuals. The major reasons for exclusion of studies were, (a) overlapping of data, (b) case-only studies, (c) review articles, (d) editorials, (e) animal studies. Data extraction and quality assessment For each publication, the methodological quality assessment and data extraction was independently abstracted in duplicate by two independent investigators using a standard protocol. Data accuracy was ensured using data-collection form according to the inclusion criteria listed above. In case of disagreement on any item of the data collected from the retrieved studies, the problem would be fully discussed to reach a consensus. Data extracted from these studies included the name of first author, year of publication, type of cancer, number of cases and controls, types of study and genotyping methods and frequencies. Evaluations of statistical associations Hardy–Weinberg equilibrium (HWE) was examined in the control subjects using a goodness of fit chi-square test for
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Table 2 Genotypic distribution of XPD A751C (rs1052559) gene polymorphism included in meta-analysis Authors and year
Controls
Cancer cases
Genotype
Minor allele
Genotype
HWE Minor allele
AA
AC
CC
MAF
AA
AC
CC
MAF
p value
Kumar et al. 2012 [13]
129
110
39
0.44
92
125
61
0.33
0.05
Sobti et al. 2012 [14]
104
81
67
0.53
74
104
92
0.42
\0.0001
Sobti et al. 2012 [15] Samson et al. 2011 [16]
67 235
69 214
14 51
0.36 0.36
62 107
67 102
21 41
0.32 0.316
0.53 0.82
Wang et al. 2010 [17]
137
117
37
0.32
138
130
34
0.32
0.13
89
94
17
0.32
73
84
14
0.32
0.25
Srivastava et al. 2010 [19]
113
90
27
0.37
93
103
34
0.31
0.17
Syamala et al. 2009 [20]
247
98
22
0.36
148
161
50
0.19
0.005
Gangwar et al. 2009 [21]
110
121
19
0.33
86
104
16
0.31
0.06
Mitra et al. 2009 [22]
84
98
33
0.57
30
73
52
0.38
0.61
Mitra et al. 2009 [22]
163
179
43
0.41
88
148
39
0.34
0.55
Sreeja et al. 2008 [23]
139
61
11
0.27
109
89
13
0.19
0.21
Sobti et al. 2007 [24]
63
77
20
0.31
52
61
7
0.36
0.63
Ramachandran et al. 2006 [25]
71
31
8
0.34
49
46
15
0.21
0.09
Mandal et al. 2010 [18]
MAF Minor allele frequency, HWE Hardy–Weinberg equilibrium
each study, Odds ratio (OR) with 95 % confidence intervals (CI) was used to assess the strength of association between the XPD exon 23 A[C gene polymorphism and cancer risk. Heterogeneity was assessed with standard Q-statistic test. If heterogeneity existed, the random effects model was adopted to calculate the overall OR value [26]. Otherwise, the fixed effect model was used [27]. Begg’s funnel plots and Egger’s regression test were undertaken to assess the potential publication bias [28]. p value less than 0.05 was judged significant. All the data analysis was performed using a comprehensive meta-analysis (CMA) V2 software (Biostat, USA).
Results Characteristics of published studies A total of thirteen articles were retrieved through literature search from the PubMed (Medline) and EMBASE database. All retrieved articles were examined by reading the titles, abstracts and the full texts for the potentially relevant publications. Articles were further checked for their suitability for this meta-analysis. In addition to the database search, the reference lists of the retrieved articles were also screened for other potential relevant articles. Studies comprising XPD polymorphism to predict survival in cancer patients or considering XPD variant as an indicator for response to therapy were excluded. Studies related to investigation of the levels of XPD mRNA or protein
expression or review articles were also excluded. Strict criteria were followed in article search, only case–control or cohort design studies having frequency of all the three genotypes were included. Following the careful screening and strict inclusion and exclusion criteria, thirteen eligible original published studies were achieved and included in the study (Table 1). Distribution of genotypes, Minor allele frequency (MAF) and HWE p values has been tabulated in the Table 2. Publication bias Begg’s funnel plot and Egger’s test were performed to evaluate the publication bias among the included studies for this meta-analysis. The shape of funnel plots did not reveal any evidence of obvious asymmetry in all comparisons, and the Egger’s test was used to provide statistical evidence of funnel plot. The results did not show any evidence of publication bias in all genetic models (Table 3). Test of heterogeneity Q-test and I2 statistics were used to test for heterogeneity among the studies. Heterogeneity was observed in all the models, such as allele (C vs. A), homozygous (CC vs. AA), heterozygous (AC vs. AA), recessive (CC vs. AA?AC) and dominant (CC?AC vs. AA) models, which was included for this analysis. Thus, we applied random effect model to calculate the pooled OR and 95 % CI (Table 3).
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Table 3 Statistics to test publication bias and heterogeneity in meta-analysis Comparisons
Egger’s regression analysis Intercept
95 % CI
Heterogeneity analysis p value
Q value
pheterogeneity
2
I (%)
Model used for meta-analysis
C vs. A
-1.30
-8.72 to 6.11
0.70
58.36
\0.0001
77.72
Random
CC vs. AA
-2.11
-6.25 to 2.02
0.28
37.65
\0.0001
65.47
Random
AC vs. AA
-0.25
-6.28 to 5.78
0.92
35.71
0.001
63.60
Random
CC?AC vs. AA
-0.73
-7.64 to 6.16
0.81
48.29
\0.0001
73.08
Random
CC vs. AA?AC
-1.79
-4.91 to 1.33
0.23
26.39
0.01
50.74
Random
Fig. 1 Forest plot of a meta-analysis of the association between XPD exon 23 A[C polymorphism (C vs. A; AC vs. AA; CC vs. AA) and overall cancer risk
Overall effects of XPD exon 23 A[C polymorphism and cancer susceptibility All the thirteen studies were pooled together which resulted into 3,599 controls and 3,087 cancer cases was used to assess the overall association between the XPD exon 23 A[C polymorphism and risk of cancer. The pooled data indicated an evidence for a significant association between
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the XPD exon 23 A[C polymorphism and susceptibility to cancer in all the models. Variant allele C demonstrated significant risk of developing cancer in terms of the frequency with wild allele (A) comparison (C vs. A: p = 0.001; OR 1.372, 95 % CI 1.172–1.605). Similarly, homozygous mutant CC (CC vs. AA; p = 0.001; OR 1.691, 95 % CI 1.280–2.233) and heterozygous AC (AC vs. AA: p = 0.001; OR 1.453, 95 % CI 1.215–1.737)
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Fig. 2 Forest plot of a meta-analysis of the association between XPD exon 23 A[C (CC?AC vs. AA; CC vs. AA?AC) and overall cancer risk
genotypes revealed significantly increased risk for the occurrence of cancer as compared with the homozygous AA genotype (Fig. 1). Additionally, analysis of recessive (CC vs. AA?AC: p = 0.001; OR 1.429, 95 % CI 1.151–1.774) and dominant (CC?AC vs. AA: p = 0.001; OR 1.512, 95 % CI 1.244–1.839) genetic models indicated 1.4- and 1.5-fold increased risk of developing cancer (Fig. 2).
Discussion Common genetic polymorphisms or mutation in the DNA repair genes may alter protein function and play a major role in carcinogenesis. In the recent years, interest in the genetic susceptibility to cancers has led to a growing attention to the study of polymorphisms of genes involved in carcinoma. Several studies has been supported an important role for genetics in determining the risk for cancer, and association studies are apposite for searching susceptibility genes involved in cancer [29]. Till date,
series of epidemiological studies have been performed to explore the role of XPD exon 23 A[C polymorphism on cancer susceptibility in worldwide and in Indian population, but the results remain controversial. Some studies are limited by their sample size and subsequently suffer from too low power to detect effects that may exist. Meta-analysis is a powerful tool for summarizing the results from different studies and gives more reliable results than a single case–control study, where individual sample sizes are small and inadequate statistical power [30]. Combining data from many studies has the advantage of reducing random error [31]. Hence, in order to improve the statistical power and determine the effect size of XPD exon 23 A[C polymorphism, we performed this meta- analysis with thirteen eligible studies to provide the more comprehensive and reliable association between XPD exon 23 A[C polymorphism and overall cancer risk for Indian population. Results of the present meta-analysis showed that XPD exon 23 A[C polymorphism is significantly associated with increased cancer risk in Indian population. Subjects
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with C allele and variants homozygous CC had 1.3- and 1.6-fold increased risk of developing cancer as compared with the wild A allele and homozygous AA genotype, respectively. Similarly, heterozygous, dominant and recessive models have shown increased risk of cancer. Based upon the above results and importance of XPD’s role in the pathogenesis of cancer, it is biologically plausible that XPD exon 23 A[C polymorphism may modulate the risk of cancer and could be a genetic factor for inter-individual differences in susceptibility to cancer disease. It has been suggested that functional and common sequence variations of DNA repair genes may be potential cancer susceptibility factors in the general population exposed to environmental carcinogens such as polycyclic aromatic hydrocarbons (PAHs) [12, 32]. Earlier, Lunn et al. studied the functional significance of XPD polymorphisms with respect to chromosome aberrations and Hou et al. also reported that common variant alleles of codon 751 of XPD gene was associated with reduced repair of aromatic DNA adducts [33, 34]. Genome wide association study suggested that XPD exon 23 A[C polymorphism has reduced DRC and contribute to increase risk of cancer [35]. It is of a great concern; that genetic susceptibility to cancer is polygenic type [36]; hence single genetic variant is usually inadequate to predict the risk of this deadly disease. Some limitations should be addressed which may affect the result, i.e., first, in this meta-analysis we found inter-study heterogeneity. Many factors might contribute to this heterogeneity, because regional lifestyle varied among populations from different parts of India [37], another recruitment of control group the controls were not uniformly defined, some studies used a healthy population as the reference group where as other selected hospital patients without cancer as the reference group. Second, the present meta-analysis was based primarily on unadjusted effect estimates and CIs. Third, the gene–gene and gene– environment interactions were not addressed. In spite of these limitations, our meta-analysis has some advantages. First, we did not detect publication bias, indicated that the results are statistically robust. Second, we performed strict data extraction and analysis to make satisfactory and reliable conclusion. In conclusion, this meta-analysis indicates that, XPD exon 23 A[C polymorphism would be a risk factor for cancer susceptibility in Indian population. The importance of this polymorphism as a predictor of the risk of cancer is very high and the screening utility of this genetic variant in symptomatic individuals may be warranted. Future well designed large scale studies in the same NER pathway with gene-environment interaction might be necessary to investigate the association between DNA repair gene SNPs and risk of cancer.
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Mol Biol Rep (2014) 41:713–719 Conflict of interest
None.
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