The xeroderma pigmentosum (XP) syndrome genes are mutant in XP patients but are rarely targets for somatic mutation in melanoma. This includes the TLS polymerase Polη, which is encoded by PolH also known as the XPV gene (Masutani et al. 1999), and has a role in UVR lesion repair at the replication fork and in G2 phase repair (Auclair et al., 2010; Gohler et al., 2011). In addition to these, several NER components have been reported to have common SNPs significantly associated with melanoma. PolH has several SNPs with an increased risk of >2 (Di Lucca et al., 2009). Polymorphisms in XPD (Li et al., 2006; Millikan et al., 2006), XPF, and ERCC1 (Povey et al., 2007) are also associated with a modest (<2 fold) increased risk of melanoma. There is some evidence that there is reduced efficiency of NER associated with melanocortin-1 receptor (MC1R) variants responsible for the red hair phenotype (Kadekaro et al., 2010), but in most cases, NER capability of melanomas appears relatively unaffected (Gaddameedhi et al., 2010). In addition to these, MEN1 is expressed in low levels in a high proportion of melanomas and loss of MEN1 reduces the expression of homologous recombination genes as well as the homologous recombination repair (Fang et al., 2013).
Defective G1 phase checkpoint signaling was found to be a common feature of melanoma cells. Approximately 70% of a large panel of melanoma cell lines screened for checkpoint functionality following exposure to ionizing radiation demonstrated a defective G1 checkpoint arrest (Carson et al., 2012; Kaufmann et al., 2008). A gene expression signature, including CDKN1A, DDB2, CDC7 and GEMININ, was associated with the defective G1 phase checkpoint, demonstrating that this was due to defective p53 function despite the relatively low level (20%) of p53 mutation in melanoma (Box and Terzian, 2008; Hodis et al., 2012). Moreover, the identified gene signature was prognostic of metastatic spread suggesting the involvement of p53 as protective against metastasis.
Another G1 phase mechanism that responds to extensive DNA damage is p16-mediated senescence (Robles and Adami, 1998; Shapiro et al., 1998). The melanoma susceptibility gene CDKN2A which encodes the cell cycle inhibitor p16 INK4A (p16) is commonly defective in melanoma (Bartkova et al., 1996; Castellano et al., 1997; Hayward, 2003). P16 inhibits CDK4/6-cyclin D activity and thereby blocks Rb inactivation promoting a G1 phase arrest. P16 is a major driver of senescence in melanocytes and is largely responsible for the oncogene-induced senescence in nevi driven by either BRAF or NRAS mutation (Gray-Schopfer et al., 2006; Haferkamp et al., 2009; Michaloglou et al., 2005). Melanoma associated mutations of p16 disrupt its ability to promote senescence arrest (Haferkamp et al., 2008). In addition to this role, increased p16 expression has been correlated with the G2 phase checkpoint arrest in response to suberythemal UVR (Abd Elmageed et al., 2009; Pavey et al., 1999, 2001; Wang et al., 1996). Loss or mutation of p16 or CDK4 is associated with loss of the checkpoint arrest (Milligan et al., 1998; Wigan et al., 2012), although the mechanistic relationship between p16 and the G2 phase arrest is not clear. ATR can phosphorylate and regulate the stability of p16 and its binding to CDK4/6 (Al-Khalaf et al., 2011; Gabrielli et al., 1999), and inhibition of CDK4 can promote a G2 phase delay (Burgess et al., 2006; Gabrielli et al., 1999), possibly through the regulation of the G2/M phase transcriptional regulator FOXM1 (Anders et al., 2011).
Other defects that may contribute to disruption of the p16-dependent responses are cyclin D overexpression and amplification in melanoma (Lazar et al., 2009; Utikal et al., 2005; Vizkeleti et al., 2012). CDK4R24 mutations that render CDK4 insensitive to p16 are uncommon (Soufir et al., 1998; Wolfel et al., 1995), and CDK4 is rarely overexpressed in melanomas (Muthusamy et al., 2006; Smalley et al., 2008a). Reduced Rb protein levels are also infrequently found in melanoma (Bartkova et al., 1996; Castellano et al., 1997; Roesch et al., 2005). In addition to p16-dependent senescence, there appear to be p16-independent mechanisms that are regulated through PTEN-PI3K-AKT signaling. This is demonstrated by the appearance of nevi on Tyr-BRAFV600E mice that are bred onto a p16 null background (Dhomen et al., 2009), and depletion of PTEN or inhibition of PI3K signaling was sufficient to overcome BRAFV600E induced senescence without affecting p16 levels (Vredeveld et al., 2012).
The G2 phase checkpoint response to ionizing radiation-induced DNA double-strand breaks has been reported to be defective in 1/3 of melanoma cell lines and was significantly associated with BRAF mutation (Kaufmann et al., 2008; Omolo et al., 2013). Likewise, the G2 phase decatenation checkpoint triggered in response to failure of the TopoII-dependent resolution of the DNA strand catenations that normally occurs during replication (Deming et al., 2001) and is defective in at least 1/3 of melanoma cell lines (Brooks et al., 2013a). The G2 phase checkpoint response to the post-replication repair of the ssDNA gaps produced by lesion bypass of unrepaired UVR lesions is defective in a higher proportion of melanoma cell lines (Wigan et al., 2012). Both the former responses are dependent on ATM for the checkpoint arrest (Bower et al., 2010), while the later is ATR dependent. GWAS studies have identified SNPs in the DNA damage response genes ATM, PARP1 and APEX1 with significant association with melanoma (Law et al., 2012). The SNP in ATM was found to be protective, suggesting that it is unlikely to contribute to the ATM-dependent checkpoint defects (Barrett et al., 2011).