Single nucleotide polymorphism 8q24 rs13281615 and risk of breast cancer: meta-analysis of more than 100,000 cases

Genetic association studies using disease liabilities from deep neural networks

The case-control study is a widely used method for investigating the genetic landscape of binary traits. However, the health-related outcome or disease status of participants in long-term, prospective cohort studies such as the UK Biobank are subject to change. Here, we develop an approach for the genetic association study leveraging disease liabilities computed from a deep patient phenotyping framework (AI-based liability). Analyzing 44 common traits in 261,807 participants from the UK Biobank, we identified novel loci compared to the conventional case-control (CC) association studies. Our results showed that combining liability scores with CC status was more powerful than the CC-GWAS in detecting independent genetic loci across different diseases. This boost in statistical power was further reflected in increased SNP-based heritability estimates. Moreover, polygenic risk scores calculated from AI-based liabilities better identified newly diagnosed cases in the 2022 release of the UK Biobank that served as controls in the 2019 version (6.2% percentile rank increase on average). These findings demonstrate the utility of deep neural networks that are able to model disease liabilities from high-dimensional phenotypic data in large-scale population cohorts. Our pipeline of genome-wide association studies with disease liabilities can be applied to other biobanks with rich phenotype and genotype data.

Variants in the 8q24 region associated with risk of breast cancer: Systematic research synopsis and meta-analysis

Breast cancer is a molecularly heterogeneous disorder associated with high lethal malignant tumors among women worldwide. Genetic factors play an important role in breast cancer development. Several single nucleotide polymorphisms in the 8q24 region associated with risk of breast cancer have been identified. Fifteen studies including 32,955 cases and 43,716 controls were collected to conduct a meta-analysis to evaluate the associations between variants in 8q24 region and risk of breast cancer. Our study showed that only rs13281615 is associated with breast cancer risk in this large-scale research synopsis and meta-analysis. Further studies are needed to explore the role of the 8q24 variants in the development of breast cancer.

Association between 8q24 (rs13281615 and rs6983267) polymorphism and breast cancer susceptibility: a meta-analysis involving 117,355 subjects

Published data on the association between 8q24 polymorphism and breast cancer (BC) risk are inconclusive. Thus, we conducted a meta-analysis to evaluate the relationship between 8q24 (rs13281615 and rs6983267) polymorphism and BC risk. We searched PubMed, EMBASE, Web of Science and the Cochrane Library up to August 13, 2015 for relevant studies. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to estimate the strength of associations. Twenty-six studies published from 2008 to 2014, with a total of 52,683 cases and 64,672 controls, were included in this meta-analysis. The pooled results showed that there was significant association between 8q24 rs13281615 polymorphism and BC risk in any genetic model. In the subgroup analysis by ethnicity, the effects remained in Asians and Caucasians. However, no genetic models reached statistical association in Africans. There was no association in any genetic model in rs6983267. This meta-analysis suggests that 8q24 rs13281615 polymorphism is a risk factor for susceptibility to BC in Asians, Caucasians and in overall population, While, there was no association in Africans. The rs6983267 polymorphism has no association with BC risk in any genetic model. Further large scale multicenter epidemiological studies are warranted to confirm this finding.

Expression Study and Clinical Correlations of MYC and CCAT2 in Breast Cancer Patients

Background:

Colon cancer-associated transcript 2 (CCAT2) is a newly recognized lncRNA transcribed from the 8q24 genomic region. It functions as an oncogene in various types of cancers including breast cancer, in which it affects Wnt/β-catenin pathway. Previous studies have shown a putative interaction between this lncRNA and MYC proto-oncogene.

Methods:

In the current study, we evaluated the expression of CCAT2 in breast cancer tissues with regards to the expression of its target MYC. In addition, we assessed the relationship between CCAT2 and MYC expression levels in tumor tissues and the clinical prognostic characteristics of breast cancer patients.

Results:

MYC expression levels were significantly up-regulated in tumor tissues compared with adjacent non-cancerous tissues (ANCTs), while such analysis showed no statistically significant difference between these two tissue types in CCAT2 expression. Starkly increased CCAT2 gene expression levels were found in 12/48 (25%) of cancer tissue samples compared with their corresponding ANCTs. Furthermore, significant inverse correlations were found between CCAT2 expression and stage, as well as lymph node involvement. Besides, a significant inverse correlation was found between the relative MYC expression in tumor tissues compared with their corresponding ANCTs and disease stage.

Conclusions:

These results highlight the significance of MYC and CCAT2 expressions in the early stages of breast cancer development and suggest a potentially significant role for CCAT2 in a subset of breast cancer patients, which could be applied as a potential therapeutic target in these patients.

Associations of Genetic Variants at Nongenic Susceptibility Loci with Breast Cancer Risk and Heterogeneity by Tumor Subtype in Southern Han Chinese Women

Current understanding of cancer genomes is mainly “gene centric.” However, GWAS have identified some nongenic breast cancer susceptibility loci. Validation studies showed inconsistent results among different populations. To further explore this inconsistency and to investigate associations by intrinsic subtype (Luminal-A, Luminal-B, ER−&PR−&HER2+, and triple negative) among Southern Han Chinese women, we genotyped five nongenic polymorphisms (2q35: rs13387042, 5p12: rs981782 and rs4415084, and 8q24: rs1562430 and rs13281615) using MassARRAY IPLEX platform in 609 patients and 882 controls. Significant associations with breast cancer were observed for rs13387042 and rs4415084 with OR (95% CI) per-allele 1.29 (1.00–1.66) and 0.83 (0.71–0.97), respectively. In subtype specific analysis, rs13387042 (per-allele adjusted OR = 1.36, 95% CI = 1.00–1.87) and rs4415084 (per-allele adjusted OR = 0.82, 95% CI = 0.66–1.00) showed slightly significant association with Luminal-A subtype; however, only rs13387042 was associated with ER−&PR−&HER2+ tumors (per-allele adjusted OR = 1.55, 95% CI = 1.00–2.40), and none of them were linked to Luminal-B and triple negative subtype. Collectively, nongenic SNPs were heterogeneous according to the intrinsic subtype. Further studies with larger datasets along with intrinsic subtype categorization should explore and confirm the role of these variants in increasing breast cancer risk.

Association of polymorphisms with a family history of cancer and the presence of germline mutations in the BRCA1/BRCA2 genes

Introduction

Breast cancer (BC) is an important public health problem worldwide. In Brazil, breast cancer is the most frequently diagnosed tumor and the leading cause of cancer death in women. Hereditary cancer represents approximately 5 to 10 % of BC cases. Even outside the hereditary cancer context, the presence of polymorphisms acting as genetic modifiers may contribute to a better or worse prognosis. Not much is known about the hereditary BC epidemiology in Brazil or about the influence of polymorphisms on hereditary predisposition.

Objective

This study examined the role of five different polymorphisms in four groups of women with BC: Group 1: women with a germline mutation in the BRCA1/2 genes; Group 2: women with variants of uncertain significance in BRCA1/2 and Group 3: women with no mutations in BRCA1/2.

Patients and methods

The women included in groups 1, 2 and 3 were patients from the Department of Oncogenetics of the Barretos Cancer Hospital who had undergone genetic testing because of a clinical suspicion of hereditary predisposition syndrome. The constitutive DNA was analyzed for the presence of polymorphisms at rs2981582 (FGFR2 gene); rs3803662 (TNRC9); rs889312 (MAP3K1); rs3817198 (LSP1 gene); and rs13281615 (8q24). The analyses were performed using PCR amplification and bi-directional sequencing.

Results

No differences were identified in the frequency of the polymorphisms that were analyzed among the three groups. However, some associations were identified, such as the occurrence of bilateral breast cancer and homozygosity for the G allele in rs13281615 as well as the correlation between the SNPs rs2981582 and rs13281615 and the number of cancer cases in the family. Regarding the G allele of rs13281615, we observed that the proportion of individuals who were homozygous for this allele increased with the number of generations affected by cancer, regardless of the group where the patients were included. Concerning the rs2981582 we could observe that individuals from group 1 and homozygous CC had fewer cancer (and also fewer breast cancer) cases. Regarding the hormone receptors, we observed an increased frequency in C homozygotes (rs3803662) among estrogen receptor-negative individuals from groups 1 and 3. For rs2981582 (FGFR2), we observed an increased frequency of the T allele in women who were positive for the estrogen and progesterone receptors regardless of the BRCA1/2 mutational status (p = 0.020 and p = 0.014, respectively).

Conclusion

The results presented here provide interesting data on the modifying effect of polymorphisms on a family history of cancer; this may be a variable to consider in the analysis of tumor diversity, and of the family history observed in families with hereditary breast cancer (even in those harboring the same type of genetic alteration).

Electronic supplementary material

The online version of this article (doi:10.1186/s13053-015-0042-1) contains supplementary material, which is available to authorized users.

CD44 single nucleotide polymorphism and isoform switching may predict gastric cancer recurrence

BACKGROUND AND OBJECTIVES

The clinical implications of single nucleotide polymorphisms (SNPs) in CD44 remain unclear. This study examined the relationships of CD44 SNPs with clinicopathological parameters and prognosis in Japanese gastric cancer patients.

METHODS

The CD44 SNPs were analyzed in 11 gastric cancer cell lines and 517 clinical specimens. The expression of CD44 standard (CD44s) and CD44 variant 9 isoform (CD44v9) transcripts were measured by quantitative real-time polymerase chain reaction.

RESULTS

The CD44 rs187116 A/A, A/G, and G/G genotypes were present in 10.3%, 45.1%, and 44.7% of patients, respectively. The presence of CD44 rs187116 A/G or G/G genotypes was significantly associated with positive peritoneal washing cytology (P = 0.012). Disease-free survival of patients with these genotypes was significantly worse than in those with the A/A genotype (P = 0.039). Multivariate analysis showed that the CD44 rs187116 was independently prognostic of disease-free survival (P = 0.047). The CD44s/CD44v9 ratio was significantly lower in patients with the CD44 rs187116 A/A genotype than in those with the A/G (P = 0.046) and G/G (P = 0.047) genotypes.

CONCLUSIONS

The CD44 rs187116 genotype could predict disease recurrence in Japanese gastric cancer patients, and the SNP was associated with CD44 isoform switching.

Replication study for the association of seven genome- GWAS-identified Loci with susceptibility to ovarian cancer in the Polish population

We investigated the previously-demonstrated association of seven genome-wide association studies (GWAS) single nucleotide polymorphisms (SNPs), including rs2072590 (HOXD-AS1), rs2665390 (TIPARP), rs10088218 and rs10098821 (8q24), rs3814113 (9p22), rs9303542 (SKAP1) and rs2363956 (ANKLE1), as risk factors of epithelial ovarian tumors (EOTs). These SNPs were genotyped in two hundred seventy three patients with EOTs and four hundred sixty four unrelated healthy females from the Polish population. We observed the lowest p values of the trend test for the 9p22 rs3814113 and 8q24 rs10098821 SNPs in patients with all subtypes of ovarian cancer (p(trend) = 0.010 and p(trend) = 0.014, respectively). There were also significant p values for the trend of the 9p22 rs3814113 and the 8q24 rs10098821 SNPs for serous histological subtypes of ovarian cancer (p(trend) = 0.006, p(trend) = 0.033, respectively). Moreover, stratification of the patients based on their histological type of cancer demonstrated, in the dominant hereditary model, a significant association of the 9p22 rs3814113 SNP with serous ovarian carcinoma OR = 0.532 (95% CI = 0.342 - 0.827, p = 0.005, p(corr) = 0.035). Despite the relatively small sample size of cases and controls, our studies confirmed some of the previously-demonstrated GWAS SNPs as genetic risk factors for EOTs.

CCAT2, a novel long non-coding RNA in breast cancer: expression study and clinical correlations

The clinical outcome of BC patients receiving the same treatment is known to vary considerably and thus, there is a compelling need to identify novel biomarkers that can select the patients that would benefit most from a given therapy and can predict the clinical outcome. The aim of this study was to determine the prognostic value of CCAT2, a novel long ncRNA recently characterized by our group and overlapping SNP rs6983267, in BC patients. We first evaluated by RT-qPCR and ISH the expression of CCAT2 in normal breast tissue and BC tissue and further analyzed CCAT2 expression in an independent set of 997 primary BC with regard to clinical, histological, pathological and other biological factors. Also, we explored the possibility of CCAT2 adding to the prognostic value of multivariate models that already included the traditional prognostic factors. Finally, we identified in in vitro models the impact of CCAT2 expression and SNP rs6983267 genotype on cell migration and chemoresistance. Our results revealed that although overexpressed in BCs in two out of three sets of patients, and having the highest expression in lymph node negative (LNN) disease, CCAT2 expression levels are informative solely for a subgroup of BC patients, namely for patients with LNP disease that have received adjuvant CMF chemotherapy. For this subgroup high levels of CCAT2 suggest the patients will not benefit from CMF containing adjuvant chemotherapy (shorter MFS and OS). Additionally, we found that CCAT2 upregulates cell migration and downregulates chemosensitivity to 5'FU in a rs6983267-independent manner.

Frequent mutation of rs13281615 and its association with PVT1 expression and cell proliferation in breast cancer

The q24 band of chromosome 8 (8q24) is frequently amplified in human cancers including breast cancer, and several SNPs (single nucleotide polymorphisms) at 8q24, including rs13281615, have been identified for their association with cancer risks. These SNPs are in a "gene desert" region, and their functions in cancer development remain to be illustrated, although several of the SNPs appear to influence the genes in the "desert" in a long-range manner, including the v-myc avian myelocytomatosis viral oncogene homolog (MYC) and the non-protein coding plasmacytoma variant translocation 1 (PVT1), both of which have been implicated in human cancers. In the current study, we examined rs13281615 for its potential role in breast cancer using normal and cancer tissues from 121 Chinese women with breast cancer. In addition to confirming the association of the GG genotype of rs13281615 with breast cancer risk, we found that germline GG genotype was significantly associated with estrogen receptor (ER) positivity, higher tumor grade and higher proliferation index. We also found frequent somatic mutations (22/121 or 18.2%) of this SNP in breast cancer. Interestingly, the majority of the mutations (17/22 or 77%) involved a G→A change, resulting in a decrease in the number of cancers with the GG risk genotype and subsequent loss of GG association with higher tumor grade and proliferation index in cancers. Furthermore, PVT1 expression was increased in cancers, and the increase was associated with the GG genotype of rs13281615. These results suggest that the GG genotype of SNP rs13281615 plays a role in breast cancer likely by influencing PVT1 expression, and that during oncogenesis, "protective" mutations could occur.

FASLG T844C polymorphism and susceptibility to breast cancer: a meta-analysis

Many studies were published to assess the association between FASLG T844C polymorphism and susceptibility to breast cancer, but the data were controversial. A meta-analysis was performed to assess the association comprehensively. We performed a comprehensive search in PubMed, Embase, and Web of Science to find eligible studies. Six studies with a total of 6,784 participants were finally included into the meta-analysis. There were a total of 3,382 cases with breast cancer and 3,402 controls in those six studies. Odds ratio (OR) with 95 % confidence interval (95 %CI) was used to evaluate the association. Overall, there was an obvious association between FASLG T844C polymorphism and breast cancer under all four contrast models (for C versus T: OR = 1.26, 95 %CI 1.05-1.50, P OR = 0.011; for CC versus TT: OR = 1.42, 95 %CI 1.11-1.81, P OR = 0.005; for CC versus TT/TC: OR = 1.41, 95 %CI 1.06-1.88, P OR = 0.019; for CC/TC versus TT: OR = 1.16, 95 %CI 1.01-1.33, P OR = 0.038). In the subgroup analysis by ethnicity, there was an obvious association between FASLG T844C polymorphism and breast cancer in Asians, but there was no obvious association in Caucasians. The meta-analysis suggests that there is an association between FASLG T844C polymorphism and susceptibility to breast cancer, especially in Asians.

The polymorphism of EGFR 142285G > A exerts no risk effect on breast cancer

The association between the epidermal growth factor receptor (EGFR) 142285G > A polymorphism and the susceptibility to breast cancer is unclear. We conducted a meta-analysis of all published studies to estimate the association of EGFR 142285G > A polymorphism and breast cancer risk. Systematic computerized searching of the PubMed, Web of Science, and Wanfang databases was performed for relevant publications. Overall, there were three eligible case-control studies with 1,360 cases and 1,522 controls included into our study. The pooled ORs showed that the EGFR 142285G > A variant genotypes did not increase or decrease the risk of breast cancer under the following gene models: A vs. G, OR = 1.07, 95% CI 0.96-1.19, P OR = 0.240; AA vs. GG, OR = 1.14, 95% CI 0.91-1.42, P OR = 0.239; GA vs. GG, OR = 0.99, 95% CI 0.83-1.17, P OR = 0.892; GA + AA vs. GG, OR = 1.03, 95% CI 0.87-1.21, P OR = 0.727; AA vs. GG + GA, OR = 1.17, 95% CI 0.97-1.42, P OR = 0.096. The between-study heterogeneity was not significant among all studies. The current meta-analysis showed no evidence for significant association between EGFR 142285G > A polymorphism and breast cancer risk. Subsequent studies with large sample size are needed for further elucidation.