Meta-analysis of three genome-wide association studies identifies two loci that predict survival and treatment outcome in breast cancer

Genetic variations in inflammation-and angiogenesis-related genes may alter the coded protein level and impact the pathogenesis of breast cancer (BC). The present study investigated the association of functional single nucleotide polymorphisms (SNPs) in the VEGFA, IL-1β, IL-1α and IL-6 genes with the early-stage BC phenotype and survival. Genomic DNA and clinical data were collected for 202 adult Eastern European (Lithuanian) women with primary I-II stage BC. Genotyping of the SNPs was performed using TaqMan SNP genotyping assays. Nine VEGFA, IL-1β, IL-1α and IL-6 polymorphisms were analysed. The VEGFA and IL-6 haplotypes were inferred using Phase software. Patients were prospectively followed-up for recurrence, occurrence of metastasis and mortality until April 30, 2019. All studied genotypes were in Hardy-Weinberg equilibrium and had the same distribution as the 1,000 Genomes project Phase 3 dataset for European population. Significant associations of the studied SNPs with clinicopathologic variables were observed between IL-1α rs1800587 C allele and larger primary tumour size; IL-6 rs1800797 A allele, rs1800797 GA genotype, rs1800795 C allele, IL-6 (rs1800797-re1800795) AC diplotype and hormonal receptor-positive disease; IL-6 rs1800797 A allele and HER2 negative status. In univariate Cox survival analysis, IL-1α rs1800587 CC and IL-6 rs1800797 GG genotype carriers exhibited worse disease-free survival (DFS), metastasis-free survival (MFS) and overall survival (OS). The IL-6 rs1800795 GG genotype was associated with worse OS. IL-6 (rs1800797, rs1800795) GG/GG diplotype carriers had shorter MFS and OS. Multivariate Cox survival analysis revealed that the IL-1α rs1800587 CC genotype was an independent negative prognostic factor for DFS, MFS and OS, and the IL6 GG/GG diplotype was an independent negative prognostic factor for MFS and OS. According to the present study, functional SNPs in the IL-1α and IL-6 genes may contribute to the identification of patients at higher risk of BC recurrence, development of metastases and worse OS among early-stage patients with BC.

1 Background: The relationship between germline genetic variation and breast cancer 2 survival is largely unknown, especially in understudied minority populations who often 3 have poorer survival. Genome-wide association studies (GWAS) have interrogated 4 breast cancer survival but often are underpowered due to subtype heterogeneity and 5 many clinical covariates and detect loci in non-coding regions that are difficult to interpret. 6 Transcriptome-wide association studies (TWAS) show increased power in detecting 7 functionally-relevant loci by leveraging expression quantitative trait loci (eQTLs) from 8 external reference panels in relevant tissues. However, ancestry-or race-specific 9 reference panels may be needed to draw correct inference in ancestrally-diverse cohorts. 10 Such panels for breast cancer are lacking. 12Results: We provide a framework for TWAS for breast cancer in diverse populations, 13 using data from the Carolina Breast Cancer Study (CBCS), a North Carolina population-14 based cohort that oversampled black women. We perform eQTL analysis for 406 breast 15 cancer-related genes to train race-stratified predictive models of tumor expression from 16 germline genotypes. Using these models, we impute expression in independent data from 17 CBCS and TCGA, accounting for sampling variability in assessing performance. These 18 models are not applicable across race, and their predictive performance varies across 19 tumor subtype. Within CBCS (ܰ = 3,828), at a false discovery-adjusted significance of 20 0.10 and stratifying for race, we identify associations in black women near AURKA, 21 CAPN13, PIK3CA, and SERPINB5 via TWAS that are underpowered in GWAS. 22Conclusions: We show that carefully implemented and thoroughly validated TWAS is an 24 efficient approach for understanding the genetics underpinning breast cancer outcomes 25 in diverse populations. 26 27 Keywords: transcriptome-wide analysis (TWAS); breast cancer; expression quantitative 28 trait loci (eQTL); survival; polygenic traits 29 4 Background 30 Breast cancer remains the most common cancer among women in the world [1]. Breast 31 cancer tends to be more aggressive in young women and African American women, 32 though underlying germline determinants of poor outcomes are not well-studied. Cohorts 33 that represent understudied minority populations, like the Carolina Breast Cancer Study 34 (CBCS), have identified differences in healthcare access, socioeconomics, and 35 environmental exposures associated with disparities in outcome [2-4], but more targeted 36 genomic studies are necessary to interrogate these disparities from a biologic and genetic 37 perspective. 38 39 Few genome-wide association studies (GWAS) have studied the relationship between 40 germline variation and survival outcomes in breast cancer, with most focusing instead on 41 genetic predictors of risk [5,6]. Recently, GWAS have shown evidence of association 42 between candidate common germline variants and breast cancer survival, but these 43 studies are often underpow...

RAD50 is commonly depleted in basal-like breast cancer with concomitant absence of INPP4B and several tumor suppressors such as BRCA1 and TP53. Our previous study revealed that INPP4B and RAD50 interact and such an interaction is associated with breast cancer survival at the transcriptional, translational and genomic levels. In the present study, we explored single nucleotide polymorphisms (SNPs) of these two genes that have synergistic effects on breast cancer survival to decipher mechanisms driving their interactions at the genetic level. The Cox’s proportional hazards model was used to test whether SNPs of these two genes are interactively associated with breast cancer survival, following expression quantitative trait loci (eQTL) analysis and functional investigations. Our study revealed two disease-associating blocks, each encompassing five and two non-linkage disequilibrium linked SNPs of INPP4B and RAD50, respectively. Concomitant presence of any rare homozygote from each disease-associating block is synergistically prognostic of poor breast cancer survival. Such synergy is mediated via bypassing pathways controlling cell proliferation and DNA damage repair, which are represented by INPP4B and RAD50. Our study provided genetic evidence of interactions between INPP4B and RAD50, and deepened our understandings on the orchestrated genetic machinery governing tumor progression.