BsmI rs SNPs have individually demonstrated

 BsmI-rs1544410 SNPs have individually demonstrated weak or nonsignificant statistical effects on BC susceptibility in different studies.23-29 However, the influence of their combination and SNP-SNP interactions on BC risk is not known.
Therefore, this study investigated the potential SNP-SNP in-teractions of these selected SNPs in RANKL, OPG, CHI3L1, and VDR Erlotinib and the possible association of their allele combinations (haplotypes) with the genetic predisposition of BC in Egyptian women.
Patients and Methods
Subject Population
This caseecontrol retrospective study was conducted in the Medical Biochemistry Department, Faculty of Medicine, Cairo University, using data from Egyptian women with histologically confirmed BC who were recruited from the general surgery department at Kasr Al-Einy Hospital between 2012 and 2016. Written informed consent was obtained from all subjects. The study protocol was approved by the ethics committee of the Faculty of Pharmacy, Cairo University, and conformed to 1975 Declaration of Helsinki.
A total of 276 eligible data points from 146 Egyptian women with histologically confirmed BC and 130 cancer-free controls were available for the study. BC patients’ age ranged from 29 to 70 years, with a median age of 52 years. A total of 8.7% of patients with BC were aged < 40 years. About 50% of the women had a family history of BC. In order to create a more representative sample of patients without enrichment for genetic risk factors such as family history, we ensured that the other 50% of data were from patients who had no family history of BC. Control data were from partici-pants who were proven to be cancer-free during a routine checkup, with no previous cancer history, and controls were age-matched to members of the BC group. In total 115 BC cases and 120 controls whose data included all the 6 investigated SNPs were selected for use in this study.
Selection of SNPs and Genotyping Method
We analyzed the effect of combination and SNP-SNP in-teractions between 6 SNPs with reported relation to BC risk and of 4 genes acting on common cancer pathways. Three of the selected SNPs had not been previously described in the literature in Egyp-tian women with BC (CHI3L1-rs4950928, VDR FokI-rs2228570, and VDR BsmI-rs1544410); however, the single-locus effects of the other 3 SNPs (RANKL-rs9533156, OPG-rs2073618, and OPG-rs2073617) on BC susceptibility in Egyptian women were published.23 All selected SNPs were functional and were observed/ predicted to affect transcription, translation, or structure of their corresponding proteins.30-36 SNPs chromosome and genomic po-sition, alteration site, function, and biological process are listed in Table 1.
Genotyping of RANKL, OPG, and VDR SNPs was determined using a PCR restriction fragment length polymorphism assay after DNA extraction from whole blood as previously described.23,26 CHI3L1-rs4950928 was genotyped in a Qiaplex real-time PCR system using the TaqMan SNP genotyping assay (Applied Biosystems, Thermo Fisher Scientific, Waltham, MA).
SNP-SNP Interactions
Table 1 SNP Position, Function, Biologic Processes, and Effect on Breast Cancer Susceptibility
dbSNP, Chromosome
Breast
Major/Minor and Genomic
Cancer Selected
Gene Allelesa Position Alteration Function Association Biologic Process
2 kb upstream transcription factor binding sites or RNA
TNF-mediated signaling pathway,
secondary structure thus could affect
cytokine activity, cytokineecytokine
RANKL gene expression.
receptor interaction, osteoclast
differentiation, immune response,
positive regulation of MAPK signaling
third amino acid from lysine (basic) to
cytokine activity, cytokineecytokine
asparagine (uncharged polar) thus
receptor interaction, osteoclast
influences OPG secretion from cells.
differentiation, immune response,
CC genotype is associated with
inflammatory response, apoptosis,
lower OPG level.30
positive regulation of MAPK signaling
2 kb upstream transcription and translation of OPG by
altering secondary structure.31
CHI3L1 rs4950928 1:203186754 UTR variant 50 Promoter SNP located within binding site No25 Hydrolyzing O-glycosyl compounds,
2 kb upstream for MYC and MAX transcription factors;
positive regulation of PKB,
minor G allele disrupts binding of MAX
inflammatory response, apoptosis,
and MYC, and is associated with
positive regulation of MAPK signaling,
reduced transcription and reduced
response to TNF
circulating YKL-40 protein level.32
Conversely, C allele was associated with
increased serum YKL-40 levels.33
site that leads to production of shorter no28,29 polymerase II transcription factor
protein receptor, with higher