VDR FokI br Olfat G Shaker Mahmoud A Senousy br
Olfat G. Shaker, Mahmoud A. Senousy
Frequency, N (%) Adjusted OR
SNP-SNP Interaction Genotype Genotype Control
Combinations with zero frequencies in either group were omitted.
Abbreviations: BC ¼ breast cancer; CI ¼ confidence interval; CHI3L1 ¼ chitinase-3elike protein 1; OPG ¼ osteoprotegerin; OR ¼ odds ratio; RANKL ¼ receptor activator of nuclear factor kB ligand; SNP ¼ single nucleotide polymorphism; VDR ¼ vitamin D receptor. aAdjusted for age and family history in logistic regression model. bBonferroni-corrected P. Statistically significant (P < .05).
Haplotype Analysis and BC Risk
Interaction of Haplotypes With BC Pathologic Data
We stratified BC patients into different disease subtypes (positive vs. negative ER/PR status, bone metastatic vs. nonmetastatic, and large vs. small tumor size); their causes and risk factors are therefore different. A separate analysis of the association of haplotypes with these pathologic data was performed using multiple regression models controlling for age and family history (Table 6). Analysis revealed that the TCCCTG haplotype was inversely correlated with positive ER/PR (adjusted OR ¼ 0.05; 95% CI, 0.01-0.71; P ¼ .029) in the recessive model. TCTCTA was positively associ-ated with bone metastasis (adjusted OR ¼ 7.37; 95% CI, 2.9-18.6; P ¼ .01) in the FHPI model. Conversely, TCTCTG (adjusted OR ¼ 0.03; 95% CI, 0.004-0.24; P < .0001) and TGTCTG (adjusted OR ¼ 0.05; 95% CI, 0.007-0.48; P < .0001) were inversely correlated with metastasis in the recessive model. No haplotype was significantly correlated with tumor size (P > .05).
Results of Functional Annotation Analysis
Selected common biological processes and pathways for the studied genes are presented in Table 1. Investigating protein interaction with the selected gens revealed 13 proteins commonly interacting with our 4-gene list, of which signal transducer and activator of transcription (STAT) 5B, STAT, STAT1, SRY, BACH2, and IK3 revealed statistically significant interactions (P < .05) (Table 7).
Recent reports have focused on SNPs and their epistatic in-teractions to explore the unexplained genetic susceptibility of BC risk.10,11 To our knowledge, this is the first study investigating the association of SNP-SNP interactions with BC predisposition in Egyptian women. In this explanatory study, we identified multiple SNP-SNP interactions between RANKL, OPG, CHI3L1, and VDR genes that were strongly associated with BC susceptibility and contributed to an overall higher risk than individual SNPs, sug-gesting the role of SNP-SNP interactions between these genes in BC development. Analysis of the combined genotypes of studied genes revealed a significant increase in BC risk, with increasing numbers of high-risk alleles. We demonstrated that the TCTCTG haplotype, which contains 4 high-risk alleles of RANKL-rs9533156, OPG-rs2073618, OPG-rs2073617, and VDR FokI-rs2228570 was significantly associated with an 8-fold higher risk of BC compared to controls. It is noteworthy that all studied SNPs had weak single-locus effects on BC susceptibility in our study and were candidates for SNP-SNP interaction analysis. In addition, all studied SNPs were functional and were observed or predicted to affect gene expression level or structure, and thus secretion or function, of their corresponding proteins.30-36
We further carried out functional annotation analysis to explore possible biological insights into the observed SNP-SNP interactions. We observed that the SNP-SNP interactions in the studied genes
SNP6 A G G A