Despite evidence of the high-penetrance phenotype of nucleotide excision repair (NER) deficiency in xeroderma pigmentosum patients, relatively little is known about the importance of common inherited variants in DNA repair pathways and their interactions with host factors in causing melanoma. There are some published data on select genetic polymorphisms in DNA repair genes and melanoma risk. However, previous studies have not given extensive consideration to multiple genes and polymorphisms in the pathways. To our knowledge this is the most comprehensive evaluation of common variation in these 60 candidate DNA-damage repair and response pathway genes in relation to melanoma risk. We comprehensively evaluated the association between the genetic variants in DNA repair genes and melanoma risk and conducted a replication study for the top two SNPs. Our data suggest the possible involvement of the PARP1 rs3219125 in the melanoma development, especially among patients with lesions on sun-exposed body sites such as the head/neck.
Specific DNA repair pathways are responsible for the repair of different types of DNA damage [13
]. (1) Base excision repair (BER) is responsible for a wide variety of non-bulky exogenous and endogenous oxidative DNA damage and single-strand breaks [24
]. (2) NER is a versatile repair system that removes a wide variety of bulky, helix-distorting lesions and UV-induced DNA photoproducts. (3) Homologous recombination (HR) and non-homologous end-joining (NHEJ) are two distinct mechanisms in the repair of double-strand breaks (DSBs) in mammalian cells. DSBs can be induced by other exogenous agents and endogenous reactive oxygen species. UV-induced photoproducts cause blockage of DNA replication, which can lead to the formation of DSBs, chromosomal aberrations, and recombination during the course of replication arrest. (4) Mismatch repair (MMR) is responsible for the repair of base mispairs and insertion/deletion mispairs. Mutations in genes involved in MMR (MSH2
, and PMS2
) result in microsatellite instability (MSI) and replication errors. (5) The O6
-methylguanine DNA methyltransferase (MGMT
) is the gene involved in the direct reversal DNA repair that removes alkyl or methyl adducts from the O6
position of guanine. (6) Other candidates include Fanconi Anemia complementation groups; DNA polymerases, nucleases, and helicases; and genes involved in DNA damage recognition and response.
By analyzing the main effect of 1,463 genetic variants across 60 DNA repair-related pathway genes in the discovery stage of this study, we found that the genes with the smallest P value for additive models were ATR and PARP1. We failed to replicate the association of the ATR polymorphism and melanoma risk in the replication sets. The risk association with the PARP1 rs3219125 variant was significant in both the discovery and the HPFS replication set, and it remained significant after adjusting for melanoma-related risk factors in the joint analysis.
To account for chance associations from multiple tests of individual SNPs with melanoma risk, we calculated the false positive report probability (FPRP) [25
]. We set a FPRP threshold of 0.5 as suggested for an initial study of a relatively rare cancer, and selected two levels of prior probability as 0.01 and 0.001, which were expected as the range for a candidate gene [25
]. With the prior probability of 0.01 and 0.001, the FPRP to detect an odds ratio of 1.89 as estimated in the joint analysis for rs3219125 in our study was 0.065 and 0.414, respectively, which suggested that our finding was noteworthy.
Given that DNA repair protects against UV-induced melanoma, the sun-exposed body sites are more prone to insufficiency in DNA repair capacity. In subgroup analysis, the risk effect of the PARP1 rs3219125 variant was significantly more pronounced in patients with melanoma in head/neck than those in other sites (heterogeneity P = 0.036). This further suggested the possible involvement of this locus in the etiology of melanoma via its influence on DNA repair capacity. In addition, there were significantly fewer head/neck melanoma cases in the NHS replication set (P value < 0.001), which may explain the failure of the replication in this set.
It has been reported that poly(ADP-ribose) polymerase-1 (PARP-1) is a zinc-finger DNA-binding protein encoded by the ADP-ribosyltransferase (ADPRT
) gene that modifies various nuclear proteins by poly(ADP-ribosyl)ation and functions as a key enzyme in DNA-damage signaling, BER, and recombination [26
]. It specifically binds DNA single-strand breaks, recruits other factors to the site of damage, and serves as an energy source for ligation [28
]. Previous studies reported lower PARP activity in breast and laryngeal cancer cases than in the normal controls [30
]. The Val762Ala polymorphism, located in the most conserved region coding for the COOH-terminal catalytic domain, was associated with lower enzymatic activity [32
] and altered risk of multiple cancers [32
]. We found neither an association of Val762Ala with melanoma risk nor strong LD between this polymorphism and the rs3219125. It was noted that the rs3219125 located in the intron region next to the Val762Ala polymorphism (351 bp downstream) might have an effect in mRNA splicing. We examined the potential alteration of this variation on splicing and transcription factor binding ability by using in silico tools (BDGP: NNSPLICE 0.9 version; NetGene2 server; ASSP, Alternative Splice Site Predictor; AliBaba2.1 and TFSEARCH). However, there was no evidence showing this locus as a splicing site or transcription factor binding site with either of the two alleles. It is possible that the linked SNPs in the PARP1 gene or even in a nearby gene are casual variants for this signal. Further work on fine-mapping and on the functional characterization of this and linked SNPs in this region is required.