**9. P53**

530 DNA Repair

individuals carrying the XRCC3 Met/Met genotype showed a. small cancer risk under a recessive genetic model. Specifically, the XRCC3 Met/Met genotype showed significantly increased risk of breast cancer, but not significant risk of cancer for head and neck, bladder, and non-melanoma skin cancer. This meta analysis results support that the XRCC3 might represent a low penetrance susceptible gene especially for cancer of breast, bladder, head

The X-Ray Cross Complementing group I XRCC1 gene belongs to The Base Excision Repair IBER) pathway. The XRCC1 gene product plays an important role in the BER pathway by acting as a scolfold for the other DNA repair proteins, such as DNA polymerase B (Kubota et al., 1996), and DNA ligase III (Caldecott, 2003). Few common single nucleotide polymoprhisms of the XRCC1 gene have been identified at codon 194 (G>T substitution at position 26304, exon 6, Arg to Trp), codon 280 (G>A substitution at position 27466, exon 9, Arg to His) and 399 (G>A substitution at position 28152, exon 10, Arg to Gln). The individuals carrying XRCC1 399 variants have been shown to have higher levels of DNA adduct (Lunn et al., 2000) and to be at greater risk for tobacco related DNA damage (Lei et al., 2002). Few studies reported XRCC1 399AA genotype to be significantly associated with lung cancer risk in Caucasian population (Divine et al., 2001; Zhou et al., 2003), Korean population (Park et al., 2002), and Indian population

Xeroderma Pigmentosum group D (XPD) also known as ERCC2 (Excision Repair Cross Completing group 2) gene encodes a helicase, a major DNA repair protein, which is involved in transcription-coupled NER and in the removal of a variety of structurally unrelatedas DNA lesions (Lehmann, 2001) including those induced by tobacco carcinogens (Leadon & Cooper, 1993), (Tang et al., 2002). The normal functioning XPD protein plays an essential role in NER and participates in the unwinding of DNA at the site of deleterious DNA lesions (Hoeijmakers et al., 1996). Several studies have reported association between A751C variant of XPD and increased risk of lung cancer (Hou et al., 2002; Spitz et al 2003; Ramachandran et al., 2006). Hou et al., 2003 reported a marginally increased risk for those carrying heterozygous A>C transversions, compared to those with wildtype homozygous, indicating that heterozygosity also carry the risk. In a Northeastern Chinese population, XPD 751 AC heterozygous genotype carriers were at 2.7 fold higher risk of lung cancer than carrier of AA genotype (Yin et al., 2006). A significant association of XPD variants in modulating NSCLC risk was reported by Zienolddiny et al (2006) in Norwegian lung cancer population. So also, in an Indian population, Sreeja et al., (2008) also reported significant association of XPD heterozygous variants in modulating Non small cell lung cancer risk. SNPs in genes involved in nucleotide excision repair (ERCC1, XPD, XPC, XPA, XPF and XPG) and mismatch repair genes (MLH1 and MSH2) in 577 colorectal cancer cases and 307 case-affected sibling controls were examined by Joshi et al., (2009). Their results showed that consumption of red meat, heavily brown on the outside or inside, increased colorectal cancer risk only among subjects with XPD codon 751 Lys/Lys or XPD codon 312 Asp/Asp

and neck, and non-melanoma skin cancer.

**7. XRCC1** 

(Sreeja et al., 2008).

**8. XPD (ERCC2)** 

genotypes.

The P53 gene plays a critical role in cell cycle control, the initiation of apoptosis, and maintenance of genomic stability and in DNA repair (Levine, 1997). TP53 is highly polymorphic in coding and non coding regions and some of these polymorphisms have been shown to increase cancer susceptibility and modify cancer phenotypes in TP53 mutation carriers (Whibley et al., 2009). Over 80 TP53 polymorphisms have been identified and validated in human populations. (IARC TP53 Database, R13). Nearly 90% are located in introns, outside splice sites, or in non coding exons. Among the P53 polymorphism, the codon 72 polymorphism (Arg72 Pro) in exon 4 of TP53 is the most extensively studied, both in experimental and population studies. Codon 72 is located within a proline rich region and Arg72 has been reported to be more effective in inducing apoptosis than Pro72. The Arg/Pro polymorphism at codon 72 of the P53 gene alters the ability of the P53 protein to induce apoptosis, influences the behaviour of mutant P53, decreases the DNA repair capacity and has been linked to with an increased risk of cancer, especially lung cancer. Several studies have examined the associations between P53 codon 72 (Arg72Pro) polymorphism and risk of different cancers, but with in consistent results. Few studies reported higher risk for lung cancer in individuals with the Arg/Pro or Pro/Pro genotype and especially Pro/Pro genotype with smoking induced lung cancer (Weston et al., 1992; Jin et al., 1995 ; Fan et al., 2000; Zhou et al., 2001). In a Chilean population, Fan et al., (2000) investigated the influence of polymorphic genotype TP53 on lung cancer susceptibility and the Pro/Pro genotype of TP53 was found to contribute significantly to lung cancer susceptibility risk [ OR 3.88 (95% CI 1.16 – 13.39) ]. The study by Alexandrov et al (2002) were consistent with the hypothesis that Benzo(a)pyrene (Polycyclic aromatic hydrocarbon, PAH) induce G : C to T : A transverse mutations in the hotspot codons of TP53 and are hence involved in the malignant transformation of the lung tissue of smokers. In an Indian case – control study involving 211 lung cancer cases and 211 controls, Sreeja et al (2007) reported an OR of 2.5 (95% CI 1.470 4.302 , p= 0.001) for the TP53 Pro/Pro variant genotype for lung cancer susceptibility and the risk tended to be higher for women [ OR =2.4 , p=0.003 ] . Recently, Ahmd Aizat (2011) reported a significant association of Pro/Pro homozygous variant of p53 with sporadic colorectal cancer susceptibility (OR = 1.886, CI: 1,046 – 3.399 , p= 0,035) and suggested that p53 Pro72Pro genotype carriers might be having a higher risk for Colorectal cancer susceptibility in Malaysian population (personal communication, unpublished data) However, meta-analysis on the risk association of TP53 Arg72Pro polymorphism with lung cancer (Matakidou et al., 2003) and breast cancer (Schmidt et al., 2007) do not support a significant role for this polymorphism in susceptibility.

#### **10. MMR genes**

In the maintenance of genomic stability, the DNA mismatch repair (MMR) systems comprising of various MMR genes play a key role. MMR genes mediate DNA repair through removal of mismatched nucleotide pairs and insertion/ deletion heterologies generated during DNA replication. Germ line mutations as well as hypermethylation in MMR genes have been reported in familial/hereditary forms of colorectal cancer. So, it was hypothesized that common variants in relevant genes encoding DNA MMR enzymes might impact the risk of sporadic form of CRC and studies have been carried out to explore this possibility. Even though the functional relevance of majority of polymorphisms in the genes

Low Penetrance Genetic Variations in DNA Repair Genes and Cancer Susceptibility 533

There is wide population variability in repair capability phenotype on account of the variation in the polymorphic allele frequencies of DNA repair genes between different ethnic groups. Even through majority of SNPs are common to at least three historic human populations (Caucasians, Africans, Asians), some SNPs are specific to different ethnicities. These differences among human populations has highlighted the need to consider ethnic genetic differences while conducting genetic association studies evaluating disease risk, treatment response and outcome studies. This could also be accounting for a several fold variation in cancer risk and significant heterogeneity across all included studies. So susceptibility factor in one population may not be a factor in another population. Thus, different study designs, differences in the prevalence of genetic polymorphisms and linkage disequilibrium in different ethnic populations are possible explanations for the varying results obtained in different studies across the world. Effect modification by environmental or other genetic risk factors that differ between study populations are also alternative causes. This warrants the need to undertake large studies on homogeneous populations to

It is hoped that in future, advances in genotyping utilizing high throughput genotyping methods could facilitate the analysis of multiple polymorphisms within DNA repair genes and also the analysis of multiple genes within DNA repair pathways. Data generated from multiple polymorphisms within a gene can be combined to create haplotypes , the set of multiple alleles on a single chromosome. Because of higher heterozygosity and tighter linkage disequilibrium within disease causing mutations, haplotype analysis can increase the power to detect disease associations. Haplotype analysis also allows for the possibility of an ungenotyped functional variant to be in linkage disequilibrium with the genotyped polymorphisms. Investigations on gene-gene interactions or pathway analysis also would provide more comprehensive insight into the role of low penetrance genetic variants of DNA repair genes in cancer susceptibility. The identification of common, moderate or low penetrance genes for cancer will potentially be of great benefit , because it allows screening to be targeted to those at greatest risk which in turn will help in implementing cancer

The author would like to express his sincere thanks and gratitude to Mr. Ahmad Aizat and Mr. Au Zian Liang, postgraduate students in Human Genome Center, University Sains Malaysia, Malaysia for their valuable help in word processing and reference collection

Ahmad Aizat AA, Siti Nurfatimah MS, Aminudin MB, Biswa BM, Venkatesh RN, Zaidi Z,

Ahmad Aizat AA , Siti Nurfatimah MS, Aminudin MM, Zaidi Z , Ahmad Shanwani MS ,

 Ahmad Shanwani MS, Ankathil R. Polymorphism Thr241Met of the XRCC3 Gene and Lack of Association with Colorectal Cancer Susceptibility Risk among Malaysian Population –A Preliminary Report (Accepted to publish in International

Muhammad Radzi AH , Ankathil R . Increased risk of sporadic Colorectal Cancer

avoid such influences. .

prevention strategies.

related to this work.

**13. References** 

**12. Acknowledgements** 

Medical Journal in next issue)

involved in MMR is not known, recent studies suggest an influence of SNPs or biochemical interaction between components of the MMR pathways or on epigenetic mediated functional regulation (Chen et al., 2007).

Several common polymorphisms in DNA repair genes representing different repair pathways have been reported. Many studies have been carried out to elucidate the association between DNA repair gene polymorphisms and cancer susceptibility. But studies have shown inconsistent associations. The impact of many these polymorphisms on repair phenotype and cancer susceptibility remain uncertain (Berwick & Vineis, 2000; Au et al., 2004). In a study on 5 DNA repair genes (XRCC1 Arg194Trp and Arg399gln, PARP Val762Ala and Lys940Arg, XPD Asp312Asn and Lys751Gln, OGG1 Ser326Cys MGMT Leu84Phe) in Singaporean Chinese population, Stern et al., (2007) provided support to the hypothesis that selected variants in DNA repair genes may contribute to colorectal cancer risk and may modify the effects of relevant life style risk factors that have been inconsistently associated with the disease. This study which reported the overall effects of PARP on colorectal cancer risk and XRCC1 SNPs as modifiers of the effects of smoking and alcohol on colorectal cancer risk, also highlighted the role of the base excision repair pathway in colorectal carcinogenesis. Vinies et al (2009) conducted meta-analyses of 241 associations between variants in DNA repair genes and cancer and had found sparse association signals with strong epidemiological credibility. Using 1087 datasets and publicly available data from genome wide association platforms, meta-analysis using dominant and recessive models were performed on 241 associations between individual variants and specific cancer types that had been tested in two or more independent studies. Thirty one nominally statistically significant (P<0.05 without adjustment for multiple comparisons) associations were recorded for 16 genes in dominant and/or recessive model analyses (BRCA2, CCND1, ERCC1, ERCC2, ERCC4, ERCC5, MGMT, NBN, PARP1, POL1, TP53, XPA, XRCC1, XRCC2, XRCC3 and XRCC4). XRCC1, XRCC2, TP53, and ERCC2 variants were each nominally associated with several types of cancer. Three associations were graded as having "strong" credibility, another four had "modest" credibility and 24 had "weak" credibility based on Vinies criteria. Requiring more stringent P values to account for multiplicity of comparisons, only the associations of ERCC2 codon 751 (recessive model) and of XRCC1-77 T>C (dominant-model) with lung cancer had P≤ 0.0001 and retained P≤ 0.001 even when the first published studies on the respective associations were excluded. The analyses suggested that the vast majority of postulated associations between DNA repair alleles and cancer risk have not been replicated sufficiently to give them strong credibility. This meta-analysis implies that larger scale studies would be necessary to establish specific associations of genetic variants in DNA repair and cancer and that the added risk conferred by single variants in DNA repair genes may be small. In another recent meta analysis, (Kiyohara et al.) found XPA G23A, OGG1 Ser326Cys and XPD Lys751Gln polymorphisms were associated with lung cancer risk .

#### **11. Limitations and future prospectives**

In SNP association studies, the most important critical point is associated with often too small size of cohort of cases and controls, resulting in a low statistical power and false, by chance, positive or negative outcomes. Another important aspect concerns inclusion of different ethnic groups. Different results may be expected due to intrinsic difference in genetic background among Caucasians, Asians, Afro Americans and other ethnic groups. There is wide population variability in repair capability phenotype on account of the variation in the polymorphic allele frequencies of DNA repair genes between different ethnic groups. Even through majority of SNPs are common to at least three historic human populations (Caucasians, Africans, Asians), some SNPs are specific to different ethnicities. These differences among human populations has highlighted the need to consider ethnic genetic differences while conducting genetic association studies evaluating disease risk, treatment response and outcome studies. This could also be accounting for a several fold variation in cancer risk and significant heterogeneity across all included studies. So susceptibility factor in one population may not be a factor in another population. Thus, different study designs, differences in the prevalence of genetic polymorphisms and linkage disequilibrium in different ethnic populations are possible explanations for the varying results obtained in different studies across the world. Effect modification by environmental or other genetic risk factors that differ between study populations are also alternative causes. This warrants the need to undertake large studies on homogeneous populations to avoid such influences. .

It is hoped that in future, advances in genotyping utilizing high throughput genotyping methods could facilitate the analysis of multiple polymorphisms within DNA repair genes and also the analysis of multiple genes within DNA repair pathways. Data generated from multiple polymorphisms within a gene can be combined to create haplotypes , the set of multiple alleles on a single chromosome. Because of higher heterozygosity and tighter linkage disequilibrium within disease causing mutations, haplotype analysis can increase the power to detect disease associations. Haplotype analysis also allows for the possibility of an ungenotyped functional variant to be in linkage disequilibrium with the genotyped polymorphisms. Investigations on gene-gene interactions or pathway analysis also would provide more comprehensive insight into the role of low penetrance genetic variants of DNA repair genes in cancer susceptibility. The identification of common, moderate or low penetrance genes for cancer will potentially be of great benefit , because it allows screening to be targeted to those at greatest risk which in turn will help in implementing cancer prevention strategies.

#### **12. Acknowledgements**

The author would like to express his sincere thanks and gratitude to Mr. Ahmad Aizat and Mr. Au Zian Liang, postgraduate students in Human Genome Center, University Sains Malaysia, Malaysia for their valuable help in word processing and reference collection related to this work.
