Prevalence of G6721T polymorphism of XRCC7 in an Iranian population

Abstract

Genetic polymorphism G6721T (rs.7003908) in gene encoding DNA-dependent protein kinase (DNA-PKcs, encoded by the XRCC7 gene) has been defined. In order to get more insight into the genetic structure of Iranian population the present study was carried out on Iranian Persian population living in Shiraz (Fars province, southwest Iran). The total study subjects consisted of 935 (195 males, 740 females) unrelated healthy individuals. Genotypes of XRCC7 G6721T were detected by PCR-RFLP based method. There was no significant difference between males and females for the XRCC7 polymorphism (χ²=1.275, df=2, P=0.529). Prevalence of the G allele was 0.473 (95 % CI: 0.441-0.505) in our sample. The study population was at Hardy-Weinberg equilibrium for the XRCC7 polymorphism (χ²=0.980, df=1, P=0.323). The allelic frequency of the G allele showed high frequency in Iranian population compared to other populations.

Introduction

DNA-dependent protein kinase (DNA-PKcs, encoded by the XRCC7 gene, MIM:600899, NM_001469) is recruited to DNA double-strand break (DSB) sites by the Ku70/Ku80 heterodimer to form the active DNA-PK complex (Gottlieb and Jackson 1993[5]). DNA-PK activity is activated by binding to free DNA ends and catalyzes rejoining of DSB (Hartley et al., 1995[6]). Thus, DNA-PK activity is essential for non-homologous end joining and V(D)J recombination. Deficiencies in DNA-PK activity are clinically significant. Mice with inactivated components of DNA-PK show severe combined immunodeficiency as well as ionizing radiation hypersensitivity (Singleton et al., 1997[20]; Ferguson et al., 2000[3]).

The genetic G6721T polymorphism of XRCC7 (rs.7003908), in intron 8, may regulate splicing and cause mRNA instability (Sipley et al., 1995[21]). The association between G6721T polymorphism of XRCC7 and cancers has been studied (Wang et al., 2004[23], 2008[24]; Hirata et al., 2006[7], 2007[8]; Liu et al., 2007[9]; Gangwar et al., 2009[4]).

Iran has one of the most heterogeneous populations of the world (Amirshahi et al., 1989[1]; Walter et al., 1991[22]; Rafiee et al., 2010[12]). The distribution of serum proteins, blood groups, and red cell enzymes in Iranian populations has been studied by different investigators (Amirshahi et al., 1989[1]; Walter et al., 1991[22]). Very recently we had reported the frequencies of some genetic polymorphisms from several Iranian populations using DNA analysis (Saadat et al., 2004[15][17][19], 2007[18]; Saadat and Dadbine-Pour 2005[16]; Saadat 2006[14], 2010[13]; Bazrgar et al., 2008[2]; Mohamadynejad and Saadat 2008[11]; Masoudi et al., 2009[10]).

Since genetic polymorphism of XRCC7 and cancer susceptibility varies in different ethnic groups and no report is available on the prevalence of G6721T polymorphism of XRCC7 in Iranian population, and also to get more insight into the genetic structure of Iranian population, the present study was carried out on healthy individuals.

Materials and Methods

Subjects

The present study was performed in Shiraz (Fars province, southern Iran). The total study subjects consisted of 935 (195 males, 740 females) unrelated adult healthy blood donors. All individuals were healthy as assessed by medical history. The mean age (SD; Min-Max) of the participants was 39.2 (9.2; 23-50) years.

Informed consent was obtained from each subject before the study. The study was approved by the institutional review board at our department.

DNA extraction and genotyping analysis

Genomic DNA was extracted from whole blood samples. Genotypic analysis for the polymorphism of XRCC7 was determined by PCR-RFLP assay, as described previously (Wang et al., 2004[23]).

To test for contamination, negative controls (tubes containing the PCR mixture, without the DNA template) were incubated in every run. Any sample with ambiguous result due to low yield was retested and a random selection of 15 % of all samples was repeated. No discrepancies were discovered upon replicate testing.

Statistical analysis

A Chi-square test was performed for XRCC7 polymorphism to determine if the sample groups demonstrated Hardy-Weinberg equilibrium. The difference in genotypic frequencies between sex groups was determined using the Chi-square test of goodness of fit. A probability of P<0.05 was considered statistically significant. All P-values were two-tailed.

Results and Discussion

Genotypic frequencies of XRCC7 among study population are shown in Table 1(Tab. 1). There were no significant gender differences for the XRCC7 polymorphism (χ²=1.275, df=2, P=0.529). Prevalence of the G allele for the total study group was 0.473 (95 % CI: 0.441-0.505) (Table 2(Tab. 2)). The study population was at Hardy-Weinberg equilibrium (χ²=0.980, df=1, P=0.323).

Table 1. Distribution of the G7621T XRCC7 genotypes among healthy blood donors in Shiraz population (southern Iran).

Table 2. Allelic frequency for the XRCC7 G7621T polymorphism among healthy blood donors in Shiraz population (southern Iran).

Table 3(Tab. 3) shows the prevalence of the G allele in several populations using published articles or data presented on NCBI Entrez SNP (www.ncbi.nlm.nih.gov/projects/snp). The frequency of the polymorphic allele varies among populations, suggesting an ethnic distribution (Wang et al., 2004[23], 2008[24]; Hirata et al., 2006[7], 2007[8]; Liu et al., 2007[9]; Gangwar et al., 2009[4]).

Table 3. Distribution of the G allele of XRCC7 G7621T polymorphism among African, Asian and Caucasian populations.

There were significant differences in terms of the G allele frequency between the three major ethnic groups (Wang et al., 2004[23], 2008[24]; Hirata et al., 2006[7], 2007[8]; Liu et al., 2007[9]; Gangwar et al., 2009[4]). The frequency of the G allele was about 38 % among Caucasians (Wang et al., 2004[23]; NCBI Entrez SNP). The prevalence of the G allele was lower among Africans and Asian populations (Hirata et al., 2006[7], 2007[8]; Liu et al., 2007[9]; Wang et al., 2008[24]; NCBI Entrez SNP). The allelic frequency of the G in our sample (about 47 %) seems to be more similar to the Caucasians than to Asians. The G allele showed high frequency in Iranian (=47.1 %) and Indian (=44.8 %) populations (Gangwar et al., 2009[4]; present study). We know that both Indian and Iranian ethnic groups biologically belong to Caucasoid. Our present data showed high similarity between these two populations for the prevalence of the G allele.

Previous reports for other genetic polymorphisms, such as GSTM1, GSTT1, GSTO2, XRCC1, CC16 and GRIN1, showed intermediate frequency of the Iranian gene pool showed in comparison with European Caucasians and Asians (Saadat et al., 2004[15][17][19], 2007[18]; Saadat and Dadbine-Pour 2005[16]; Saadat 2006[14], 2010[13]; Bazrgar et al., 2008[2]; Mohamadynejad and Saadat 2008[11]; Masoudi et al., 2009[10]). However the present study on the XRCC7 polymorphism did not coincide with this conclusion. Some evolutionary forces may be responsible for this difference.

Acknowledgements

The authors are indebted to the participants for their close cooperation. The authors are indebted to Dr. Maryam Ansari-Lari for critical reading of the manuscript and for her contribution in discussion. This study was supported by Shiraz University.

Disclosure Statement

No competing financial interests exist.