Li et al (2013) performed an enrichment analysis of genes related to Rb through Gen Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database [21, 22]. They determined that 119 genes were related to Rb compared to normal retina. The enrichment analysis of the 119 genes generated 2 GO terms with significant false discovery rate (FDR) < 0.01 relevant for Rb: cell cycle (GO:0007049) and M phase of mitotic cell cycle (GO:0000087). For KEGG analysis, only the cell cycle pathway (hsa04110) was significantly enriched. However, the most influential gene in retinoblastoma is RB1 [21, 22].
Rb is caused by mutations of the RB1 gene altering functional proteins, triggering cell division in the retina, and leading to the development of tumors [23]. According to Leone et al (2003), a previous study in Ecuadorians with Rb has described new mutations and SNPs [24]. For instance, a mutation found in exon 15 with a replacement of G to A (g.76920 G>A), and a mutation found in exon 22 with a replacement of T to C (g.IVS22–14 T>C). Additionally, three SNPs were found, two were deletions in introns 15 (g.76983) and 16 (g.78064) and the third one was a transition C to T in intron 26.
On the other hand, several mechanisms are involved in the development of Rb such as the disruption of the DNA repair system [25]. The genomic alteration of this system has been associated with other types of cancer such as colorectal cancer (CRC) [26], glioma [27], lung cancer [28, 29], head and neck squamous cell carcinoma [30], melanoma [31] and breast cancer [32].
The disruption of the DNA repair system may be caused by the inter-individual variability in the capacity of repairing the genetic material, due to the presence of SNPs in several DNA repair genes found in coding or regulating regions [33]. The XPC, XPD, XPG, XRCC1 and XRCC3 repair genes may present polymorphisms leading to replacement of amino acids that may affect the function of theresulting proteins. These changes occur in a relatively high frequency, affecting this way a wide section of the world population [34]. The deficient result to DNA damage caused by hexogen and endogen agents may lead to genetic alterations in the DNA repair pathway, triggering serious biological effects [35].
NER pathway is involved in the elimination of short segments of nucleotides that have damaged bases by exposure to UV radiation. Important members of this pathway are ERCC2, XPC, and XPG. ERCC2 synthesizes the XPD protein [36]. This protein is an essential subunit of a group of proteins called transcription factor IIH (TFIIH) complex. This complex is involved in gene transcription process and it helps to repair damaged DNA. According to Lanara et al (2013), a huge meta-analysis study has demonstrated that ERCC2 Lys751Gln is positively correlated with breast and lung cancers [37], and this study contributes in understanding the association between this SNP and Rb in Ecuador.
A higher frequency of the A allele (0.58) was obtained for the Lys939Gln polymorphism of the XPC gene, whereas the C allele was represented by 0.42. In contrast with a meta-analysis that studied 679 cases of several types of cancer and 902 controls, the most prevalent allele was A with 0.62 [38], coinciding the allele frequency of the studied population. In a meta-analysis made in a Chinese population, the Lys939Gln polymorphism was significantly associated with the risk of CRC in the A/C heterozygous pattern (OR = 1.40, CI of 95% = 1.16–1.69; p < 0.05) [39]. Another research demonstrated that the patients with the C/C genotype have 2.09 times more risk of developing bladder cancer than normal A/A genotype [40]. In this study was found that the C/C genotype has 3.47 times more risk of developing retina cancer than a normal A/A genotype (p < 0.05). According to He et al (2013), the risk of developing any type of cancer may be assumed due to the fact that the polymorphisms of the XPC gene may influence the capacity of DNA repair and the function of the protein of an individual, affecting genetic instability and modifying predisposition to cancer, since this gene is involved in the recognition of DNA damage; thus, XPC is the main component to initiate NER pathway [41].
Several studies have shown that SNPs of the XPG gene are associated with several cancers. The Asp1104Hist polymorphism helped to increase the risk of CRC [25, 42]. He et al (2014) reported a significant decrease in the risk of melanoma for the C/C genotype (OR = 0.32; CI of 95% = 0.13–0.75; p < 0.05) [25]. In other studies a statistically significant risk of prostate cancer in individuals with C/C genotype (OR = 2.53, CI of 95% = 0.99–6.56; p < 0.05) was found. Concerning Rb, we had no significant results for G/C + C/C; thus, these are not associated with the disease (OR = 0.47, CI: 0.23–0.97, p > 0.05).
BER pathway repairs the oxidative DNA damage caused by alkylating agents. The XRCC1 gene is an important component of this pathway. The Arg399Gln polymorphism of the XRCC1 gene showed more frequency of G allele (0.63) in contrast with A allele (0.37). Vaezi, Feldman, & Niedernhofer (2011) suggest that the mutant G allele correlates with lower capacity of DNA repair, leading to increased genomic instability and sensibility to agents that damage DNA [43]. In a meta-analysis of CRC, the frequency of G allele was significantly different among three populations, being highest in the black population (0.83), intermediate in Taiwanese origin (0.74), and lowest in whites (0,63). These differences suggest a possible ethnic variability in allele distribution of XRCC1 [44]. Another study analyzed 1,635 patients with cervical cancer and 2,361 controls, showing that the Arg399Gln polymorphism decreases the susceptibility of such cancer (G vs. A: OR = 0.39, CI of 95% = 0.29–0.51; p < 0.05) [45]. In a meta-analysis in the Caucasian populations, it was found that the A/G and G/G genotypes were associated with the risk of developing lung cancer [46]. Likewise, a meta-analysis showed that the association between the Arg399Gln polymorphism and the risk of prostate cancer is affected by ethnicity; significantly marked associations were found among Asians, rather than African people [47]. In the current study it was also found an association between the Arg399Gln polymorphism with the risk of developing retina cancer for A/G genotype (OR = 9.74; CI: 4.45–21.08; p < 0.05), as well as for the combined genotype A/G + G/G (OR = 7.55; CI: 3.57–16.00; p < 0.05).
MMR pathway plays an important role in maintaining genomic stability and repairs damage mainly caused in base-base imbalance and the insertion/deletion errors generated during DNA replication and recombination [48]. MSH2 belongs to this repair pathway. In a study on patients with lymphoma, it was found that 22.73% of these individuals had a replacement of T with C in intron junction site of the MSH2, whereas only 7.50% of the same variation was observed in normal individuals (p < 0.01); consequently, the allele frequency of the group was 0.95 for the T allele, 0.05 for the C mutant allele, and there were no homozygotes for the C allele in the group with lymphoma, suggesting this replacement probably influences susceptibility to cancer because it is twice more often in people who have developed lymphoma, rather than a non-carcinogenic population [17]. In this research no significant differences were obtained for the C/T heterozygote (OR = 1.43; CI: 0.46–3.92; p > 0.05), which suggests that such polymorphism has no association with the risk of Rb.
Several replication errors cause double-chain breaks that are generated by hexogen agents, such as ionizing radiation. The pathway that repairs such damages is homologous recombination to which the RAD54 and XRCC3 genes belong. As for the RAD54 gene, according to Paz-y-Miño et al (2010), a statistically significant association was found between frequencies calculated for the subgroup with chronic myelogenous leukemia (0.14), in contrast with the control group [49]. Concerning meningioma, an association between the T allele and the development of meningioma tumor (p < 0.05) was found [20]. In this research an association of the RAD54 with Rb was not found (OR = 0.63; CI: 0.25–1.52; p > 0.05). Regarding the XRCC3 gene, in an analysis of melanoma a significant association of the T/T genotype and cancer (TT versus CC: OR = 1.06; CI of 95% = 0.87–1.29) was found. Another study showed a protective effect in the individuals with the C/C genotype (OR: 0.32; p < 0.05), whereas the T/T mutant genotype indicated that the risk of developing lung cancer is 4 times higher. In this study a statistically significant association with Rb was not found since the OR was of 1.31 for C/T + T/T with a p > 0.05.