Genetic Susceptibility Study Of Breast Cancer In Chinese Population

Background:Breast cancer (BC) is the most common cancer and leading cause of cancer death among women worldwide. It now represents the most commonly diagnosed cancer in both developing and developed countries. Previous epidemiology studies have shown that BC is a highly heterogeneous disease which is caused by complex environmental and inherited factors although the precise pathogenesis is still unclear. Only a fraction of individuals under the same environment could develop BC, indicating that genetic susceptibility factors may play important roles in the etiology of this cancer. Recently, the genome-wide association studies (GWAS) of BC have identified multiple single nucleotide polymorphisms (SNPs) to be associated with BC risk. However, considering the diversity genetic architecture among ethnicities, the findings from other races could not represent the truly genetic susceptibility of BC in Chinese population. Moreover, the multiple interactions among these identified polymorphisms are still not well established.Objectives:(1):To explore the association of10GWAS identified SNPs and BC risk in Chinese Han population.(2):To investigate the interaction effect between significant SNPs and menopausal status on BC susceptibility.(3):To explore the high-order interactions among the ten GWAS identified SNPs to the genetic susceptibility of BC in Chinese people. Methods:A hospital-based case-control study was conducted in Wuhan population. We utilized the multi-analytic strategy combing random forest (RF), multifactor dimensionality reduction (MDR) and logistic regression (LR) approaches to investigate the associations of the polymorphisms recently identified by GWAS and BC risk and high-order interactions among these polymorphisms to the susceptibility of BC in Chinese. The X2test and t test were employed to test the differences in distribution of demographic characteristics between case and control group where appropriate. The odds ratios (ORs) and their95%confidence intervals (CIs) which were calculated by unconditional multivariate Logistic regression when adjusted by age and menopausal status were used to estimate the effect of each polymorphism on BC risk. The linkage disequilibrium (LD) was calculated using the Haploview4.2by determining the r2value.Results:(1):A total of477histopathologically confirmed BC patients and534frequency-matched healthy controls were included in this case-control study. There were no significant difference between cases and controls for the distribution of age and menopausal status with the P value of0.639and0.419, respectively. Among the cases, there were271(56.8%) BC patients were diagnosed as Estrogen Receptor (ER) positive and168(35.2%) ER negative. Similarly,241(50.5%) cases were defined as Progesterone Receptor (PR) positive and198PR (41.5%) negative. In addition,38patients’ ER and PR status were not obtained due to the deficiency of relevant information.(2):Among the ten GWAS identified polymorphisms, six polymorphisms, rs1219648, rs3757318,rs1926657, rs6556756, rs2046210and rs4973768, were found to be significantly associated with BC risk under independent analysis. Even after false discovery rate (FDR) correction, rsl926657, rs3757318, rs2046210and rs4973768still remained significantly associated with BC risk.(3):The interactions among the six significant SNPs and menopausal status were subsequently evaluated. There was significant multiplicative interaction between rs3757318and menopausal status (P=0.001).(4):In Random Forest analysis, rs3757318, rs2046210and rs4973768were ranked as the top three important risk factors and were selected as the best set which taking interactions into consideration. Subsequently, the MDR analysis of the ten variants found that the three-factor model including rs3757318, rs2046210and rs4973768interpret the best interaction model with the maximized testing accuracy (TA) of0.6183and cross-validation consistency (CVC) of10/10. Intriguingly, cumulative effect was observed in the manner of dose-dependent with increasing numbers of risk alleles (Ptrend=9.80×10-5), and the individuals carrying1,2,3and4-6risk alleles had a2or3-fold higher risk of BC than carrying0risk alleles with the OR of2.06(95%CI=1.40-3.01),2.37(95%CI=1.64-3.44),2.28(95%CI=1.48-3.52) and3.27(95%CI=1.96-5.48).Conclusions:(1):The SNPs of rs1926657, rs1219648, rs3757318, rs2046210, rs4973768and rs6556756were significantly associated with BC risk in Chinese population. Among these polymorphisms, rs3757318was the most important susceptibility factor for BC incidence with the lowest P value.(2):There was significant multiplicative interaction between rs3757318and menopausal status.(3): Our findings emphasized the proof of principle that multiple interactions of genetic variants, including rs3757318, rs2046210and rs4973768may play important roles in the susceptibility of BC though the biological mechanisms underlying the observed associations need to be elucidated.Innovations:(1):This current study firstly investigated the associations of rs1926657, rs1978503, rs6556756and rs2075555and BC risk in Chinese population.(2):Our study utilized the multi-analytic strategy including random forest, multifactor dimensionality reduction and logistic regression approaches to investigate the high-order interactions among the ten GWAS identified SNPs. Background:P53, one of the most famous and well-studied transcription factors, has been documented to be an important tumor suppressor. As a transcription factor, p53mainly exerted its function by regulating the transcription of numerous target genes, which potentially contribute to cancer susceptibility. It directly binds to a sequence-specific DNA consensus motif which was called p53response element (p53-RE). P53’s ability to bind the p53-RE and subsequently regulate the transcription of target genes was the essence for its tumor suppressor function. Therefore, it was hypothesized that polymorphisms in key nucleotides of functional p53response elements could influence the ability of p53’transcription regulation and thus might lead to different cancer susceptibility.Objectives:(1):To investigate the association of rs4590952and BC risk in Chinese population.(2):To investigate the association of breast tissue specified variants in p53binding sites and BC risk in a Chinese women.Methods:(1) In the part I study, a hospital-based case-control study was performed to explore the association of rs4590952and BC risk in Wuhan population. In part II, the ChIP-seq database about p53binding sites in MCF-7cell lines was extracted to identify the possible variants in p53target genes. Then, the Mach software was used to find the functional variants. At last, a two-stage large sample size hospital-based case-control study was performed to investigate the association of variants in p53binding sites and BC risk in a Chinese population.The genotype of variants were determined by the TaqMan SNP Genotyping Assay (Applied Biosystems, Foster city, CA) using the7900HT Fast Real-Time PCR System. The X2test and t test were employed to test the differences in distribution of classified variable such as menopausal status, smoking status and alcohol use and quantitative variable such as age between case and control group. The odds ratios (ORs) and their95%confidence intervals (CIs) which were calculated by unconditional multivariate logistic regression when adjusted by age, menopausal status, smoking status and alcohol use were used to estimate the effect of rs4590952on breast cancer risk.Results:(1):In the part I case-control study, a total of1241BC cases and1259frequency-matched healthy controls were included. The average age between cases and controls was comparable (P-0.942). In addition, the There were no significant difference between case and control group for the distribution of menopausal status, smoking status and alcohol use with the P value of0.117,0.123and0.721, respectively. After adjusted by age, smoking status, alcohol use and menopausal status, the logistic regression analysis showed that the rs4590952-A allele was not significantly associated with BC risk, with an OR of1.04(95%CI=0.73-1.46) as compared to the G allele. No association between this variant and BC risk were observed for the heterozygote model, homozygote model, dominant model, recessive model and additive model, yet. When performed stratified analysis by the ER and PR status, no significant association of rs4590952and BC risk were found in ER+/PR+and ER-PR-subgroups.(2) In the part II of the stage1study, a total of1274BC cases and1255frequency-matched cancer-free controls were included in this case-control study. The average age was comparable between case and control group with the P value of0.318. Meanwhile, the distribution of menopausal status, smoking and alcohol use between cases and controls were similar with the P value of0.539,0.258and0.131, respectively. Then753BC cases and1199controls were included in the stage2study to further confirm the significant results. The average age and distribution of menopausal status between cases and controls were comparable with the P value of0.397and0.507. In the stage1study, the genotype distribution of rs1295925was significantly different between case and control group. The individuals carrying rs1295925-CT and rs1295925-TT genotypes were significantly associated with increased BC risk when compared with rs1295925-CC genotype after adjustment of age, menopausal status, smoking and alcohol use (OR=1.32,95%CI=1.07-1.62and OR=1.41,95%CI=1.13-1.78, respectively). Positive associations were also observed in allelic model, dominant and additive models. Furthermore, significant association between rsl295925and BC risk were still remained after FDR adjustment. No significant associations of another two SNPs in BCAS1gene and risk of BC were identified in our study. Moreover, significant association of rs1295925and BC risk was confirmed in the stage2. In addition, positive result was also observed when combined the two stage studies. When performed subgroup analysis according to the ER and PR expression of BC patients in the stage1study, significant association between rsl295925and BC risk was identified in ER-PR-subgroup but not in ER+/PR+subgroup.Conclusions:(1):The rs459052was not associated with BC risk in Chinese population. In one hand, the KITLG gene may not exert the high effect on the development of BC risk as we anticipated; in another hand, some other genetic variants which we did not identified in this gene may confer to the susceptibility of BC risk.(2):The result of our study emphasized the potentially tissue-specific role of rs4590952in cancer susceptibility.(3):The rsl295925which located in VMP1gene was associated with increased BC risk in Chinese population.Innovations:(1):This was the first study which explored the association of the functional variant, rs4590952and BC risk in Chinese population.(2):Our study combined bioinformatics and molecular epidemiology to explore the associations of three polymorphisms in p53binding site and BC risk in Chinese population.