Differences in polygenic score distributions in European ancestry populations: implications for breast cancer risk prediction

The 313-variant polygenic risk score (PRS313) provides a promising tool for breast cancer risk prediction. However, evaluation of the PRS313 across different European populations which could influence risk estimation has not been performed. Here, we explored the distribution of PRS313 across European populations using genotype data from 94,072 females without breast cancer, of European-ancestry from 21 countries participating in the Breast Cancer Association Consortium (BCAC) and 225,105 female participants from the UK Biobank. The mean PRS313 differed markedly across European countries, being highest in south-eastern Europe and lowest in north-western Europe. Using the overall European PRS313 distribution to categorise individuals leads to overestimation and underestimation of risk in some individuals from south-eastern and north-western countries, respectively. Adjustment for principal components explained most of the observed heterogeneity in mean PRS. Country-specific PRS distributions may be used to calibrate risk categories in individuals from different countries.

Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel

BACKGROUND

Polygenic risk score (PRS), calculated based on genome-wide association studies (GWASs), can improve breast cancer (BC) risk assessment. To date, most BC GWASs have been performed in individuals of European (EUR) ancestry, and the generalisation of EUR-based PRS to other populations is a major challenge. In this study, we examined the performance of EUR-based BC PRS models in Ashkenazi Jewish (AJ) women.

METHODS

We generated PRSs based on data on EUR women from the Breast Cancer Association Consortium (BCAC). We tested the performance of the PRSs in a cohort of 2161 AJ women from Israel (1437 cases and 724 controls) from BCAC (BCAC cohort from Israel (BCAC-IL)). In addition, we tested the performance of these EUR-based BC PRSs, as well as the established 313-SNP EUR BC PRS, in an independent cohort of 181 AJ women from Hadassah Medical Center (HMC) in Israel.

RESULTS

In the BCAC-IL cohort, the highest OR per 1 SD was 1.56 (±0.09). The OR for AJ women at the top 10% of the PRS distribution compared with the middle quintile was 2.10 (±0.24). In the HMC cohort, the OR per 1 SD of the EUR-based PRS that performed best in the BCAC-IL cohort was 1.58±0.27. The OR per 1 SD of the commonly used 313-SNP BC PRS was 1.64 (±0.28).

CONCLUSIONS

Extant EUR GWAS data can be used for generating PRSs that identify AJ women with markedly elevated risk of BC and therefore hold promise for improving BC risk assessment in AJ women.

Polymorphisms in genes of melatonin biosynthesis and signaling support the light-at-night hypothesis for breast cancer

Light-at-night triggers the decline of pineal gland melatonin biosynthesis and secretion and is an IARC-classified probable breast-cancer risk factor. We applied a large-scale molecular epidemiology approach to shed light on the putative role of melatonin in breast cancer. We investigated associations between breast-cancer risk and polymorphisms at genes of melatonin biosynthesis/signaling using a study population of 44,405 women from the Breast Cancer Association Consortium (22,992 cases, 21,413 population-based controls). Genotype data of 97 candidate single nucleotide polymorphisms (SNPs) at 18 defined gene regions were investigated for breast-cancer risk effects. We calculated adjusted odds ratios (ORs) and 95% confidence intervals (CI) by logistic regression for the main-effect analysis as well as stratified analyses by estrogen- and progesterone-receptor (ER, PR) status. SNP-SNP interactions were analyzed via a two-step procedure based on logic regression. The Bayesian false-discovery probability (BFDP) was used for all analyses to account for multiple testing. Noteworthy associations (BFDP < 0.8) included 10 linked SNPs in tryptophan hydroxylase 2 (TPH2) (e.g. rs1386492: OR = 1.07, 95% CI 1.02-1.12), and a SNP in the mitogen-activated protein kinase 8 (MAPK8) (rs10857561: OR = 1.11, 95% CI 1.04-1.18). The SNP-SNP interaction analysis revealed noteworthy interaction terms with TPH2- and MAPK-related SNPs (e.g. rs1386483R ∧ rs1473473D ∧ rs3729931D: OR = 1.20, 95% CI 1.09-1.32). In line with the light-at-night hypothesis that links shift work with elevated breast-cancer risks our results point to SNPs in TPH2 and MAPK-genes that may impact the intricate network of circadian regulation.

A genome-wide gene-environment interaction study of breast cancer risk for women of European ancestry

BACKGROUND

Genome-wide studies of gene-environment interactions (G×E) may identify variants associated with disease risk in conjunction with lifestyle/environmental exposures. We conducted a genome-wide G×E analysis of ~ 7.6 million common variants and seven lifestyle/environmental risk factors for breast cancer risk overall and for estrogen receptor positive (ER +) breast cancer.

METHODS

Analyses were conducted using 72,285 breast cancer cases and 80,354 controls of European ancestry from the Breast Cancer Association Consortium. Gene-environment interactions were evaluated using standard unconditional logistic regression models and likelihood ratio tests for breast cancer risk overall and for ER + breast cancer. Bayesian False Discovery Probability was employed to assess the noteworthiness of each SNP-risk factor pairs.

RESULTS

Assuming a 1 × 10-5 prior probability of a true association for each SNP-risk factor pairs and a Bayesian False Discovery Probability < 15%, we identified two independent SNP-risk factor pairs: rs80018847(9p13)-LINGO2 and adult height in association with overall breast cancer risk (ORint = 0.94, 95% CI 0.92-0.96), and rs4770552(13q12)-SPATA13 and age at menarche for ER + breast cancer risk (ORint = 0.91, 95% CI 0.88-0.94).

CONCLUSIONS

Overall, the contribution of G×E interactions to the heritability of breast cancer is very small. At the population level, multiplicative G×E interactions do not make an important contribution to risk prediction in breast cancer.

Association of the CHEK2 c.1100delC variant, radiotherapy, and systemic treatment with contralateral breast cancer risk and breast cancer-specific survival

BACKGROUND

Breast cancer (BC) patients with a germline CHEK2 c.1100delC variant have an increased risk of contralateral BC (CBC) and worse BC-specific survival (BCSS) compared to non-carriers.

AIM

To assessed the associations of CHEK2 c.1100delC, radiotherapy, and systemic treatment with CBC risk and BCSS.

METHODS

Analyses were based on 82,701 women diagnosed with a first primary invasive BC including 963 CHEK2 c.1100delC carriers; median follow-up was 9.1 years. Differential associations with treatment by CHEK2 c.1100delC status were tested by including interaction terms in a multivariable Cox regression model. A multi-state model was used for further insight into the relation between CHEK2 c.1100delC status, treatment, CBC risk and death.

RESULTS

There was no evidence for differential associations of therapy with CBC risk by CHEK2 c.1100delC status. The strongest association with reduced CBC risk was observed for the combination of chemotherapy and endocrine therapy [HR (95% CI): 0.66 (0.55-0.78)]. No association was observed with radiotherapy. Results from the multi-state model showed shorter BCSS for CHEK2 c.1100delC carriers versus non-carriers also after accounting for CBC occurrence [HR (95% CI): 1.30 (1.09-1.56)].

CONCLUSION

Systemic therapy was associated with reduced CBC risk irrespective of CHEK2 c.1100delC status. Moreover, CHEK2 c.1100delC carriers had shorter BCSS, which appears not to be fully explained by their CBC risk.

Spectrum and Frequency of Germline FANCM Protein-Truncating Variants in 44,803 European Female Breast Cancer Cases

FANCM germline protein truncating variants (PTVs) are moderate-risk factors for ER-negative breast cancer. We previously described the spectrum of FANCM PTVs in 114 European breast cancer cases. In the present, larger cohort, we report the spectrum and frequency of four common and 62 rare FANCM PTVs found in 274 carriers detected among 44,803 breast cancer cases. We confirmed that p.Gln1701* was the most common PTV in Northern Europe with lower frequencies in Southern Europe. In contrast, p.Gly1906Alafs*12 was the most common PTV in Southern Europe with decreasing frequencies in Central and Northern Europe. We verified that p.Arg658* was prevalent in Central Europe and had highest frequencies in Eastern Europe. We also confirmed that the fourth most common PTV, p.Gln498Thrfs*7, might be a founder variant from Lithuania. Based on the frequency distribution of the carriers of rare PTVs, we showed that the FANCM PTVs spectra in Southwestern and Central Europe were much more heterogeneous than those from Northeastern Europe. These findings will inform the development of more efficient FANCM genetic testing strategies for breast cancer cases from specific European populations.

Understanding the genetic complexity of puberty timing across the allele frequency spectrum

Pubertal timing varies considerably and has been associated with a range of health outcomes in later life. To elucidate the underlying biological mechanisms, we performed multi-ancestry genetic analyses in ~800,000 women, identifying 1,080 independent signals associated with age at menarche. Collectively these loci explained 11% of the trait variance in an independent sample, with women at the top and bottom 1% of polygenic risk exhibiting a ~11 and ~14-fold higher risk of delayed and precocious pubertal development, respectively. These common variant analyses were supported by exome sequence analysis of ~220,000 women, identifying several genes, including rare loss of function variants in ZNF483 which abolished the impact of polygenic risk. Next, we implicated 660 genes in pubertal development using a combination of in silico variant-to-gene mapping approaches and integration with dynamic gene expression data from mouse embryonic GnRH neurons. This included an uncharacterized G-protein coupled receptor GPR83, which we demonstrate amplifies signaling of MC3R, a key sensor of nutritional status. Finally, we identified several genes, including ovary-expressed genes involved in DNA damage response that co-localize with signals associated with menopause timing, leading us to hypothesize that the ovarian reserve might signal centrally to trigger puberty. Collectively these findings extend our understanding of the biological complexity of puberty timing and highlight body size dependent and independent mechanisms that potentially link reproductive timing to later life disease.

PREDICT validity for prognosis of breast cancer patients with pathogenic BRCA1/2 variants

We assessed the PREDICT v 2.2 for prognosis of breast cancer patients with pathogenic germline BRCA1 and BRCA2 variants, using follow-up data from 5453 BRCA1/2 carriers from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) and the Breast Cancer Association Consortium (BCAC). PREDICT for estrogen receptor (ER)-negative breast cancer had modest discrimination for BRCA1 carrier patients overall (Gönen & Heller unbiased concordance 0.65 in CIMBA, 0.64 in BCAC), but it distinguished clearly the high-mortality group from lower risk categories. In an analysis of low to high risk categories by PREDICT score percentiles, the observed mortality was consistently lower than the expected mortality, but the confidence intervals always included the calibration slope. Altogether, our results encourage the use of the PREDICT ER-negative model in management of breast cancer patients with germline BRCA1 variants. For the PREDICT ER-positive model, the discrimination was slightly lower in BRCA2 variant carriers (concordance 0.60 in CIMBA, 0.65 in BCAC). Especially, inclusion of the tumor grade distorted the prognostic estimates. The breast cancer mortality of BRCA2 carriers was underestimated at the low end of the PREDICT score distribution, whereas at the high end, the mortality was overestimated. These data suggest that BRCA2 status should also be taken into consideration with tumor characteristics, when estimating the prognosis of ER-positive breast cancer patients.

The impact of coding germline variants on contralateral breast cancer risk and survival

Evidence linking coding germline variants in breast cancer (BC)-susceptibility genes other than BRCA1, BRCA2, and CHEK2 with contralateral breast cancer (CBC) risk and breast cancer-specific survival (BCSS) is scarce. The aim of this study was to assess the association of protein-truncating variants (PTVs) and rare missense variants (MSVs) in nine known (ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53) and 25 suspected BC-susceptibility genes with CBC risk and BCSS. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated with Cox regression models. Analyses included 34,401 women of European ancestry diagnosed with BC, including 676 CBCs and 3,449 BC deaths; the median follow-up was 10.9 years. Subtype analyses were based on estrogen receptor (ER) status of the first BC. Combined PTVs and pathogenic/likely pathogenic MSVs in BRCA1, BRCA2, and TP53 and PTVs in CHEK2 and PALB2 were associated with increased CBC risk [HRs (95% CIs): 2.88 (1.70-4.87), 2.31 (1.39-3.85), 8.29 (2.53-27.21), 2.25 (1.55-3.27), and 2.67 (1.33-5.35), respectively]. The strongest evidence of association with BCSS was for PTVs and pathogenic/likely pathogenic MSVs in BRCA2 (ER-positive BC) and TP53 and PTVs in CHEK2 [HRs (95% CIs): 1.53 (1.13-2.07), 2.08 (0.95-4.57), and 1.39 (1.13-1.72), respectively, after adjusting for tumor characteristics and treatment]. HRs were essentially unchanged when censoring for CBC, suggesting that these associations are not completely explained by increased CBC risk, tumor characteristics, or treatment. There was limited evidence of associations of PTVs and/or rare MSVs with CBC risk or BCSS for the 25 suspected BC genes. The CBC findings are relevant to treatment decisions, follow-up, and screening after BC diagnosis.

Association of the CHEK2 c.1100delC variant, radiotherapy, and systemic treatment with contralateral breast cancer risk and breast cancer-specific survival

Breast cancer (BC) patients with a germline CHEK2 c.1100delC variant have an increased risk of contralateral BC (CBC) and worse BC-specific survival (BCSS) compared to non-carriers. We aimed to assess the associations of CHEK2 c.1100delC, radiotherapy, and systemic treatment with CBC risk and BCSS. Analyses were based on 82,701 women diagnosed with invasive BC including 963 CHEK2 c.1100delC carriers; median follow-up was 9.1 years. Differential associations of treatment by CHEK2 c.1100delC status were tested by including interaction terms in a multivariable Cox regression model. A multi-state model was used for further insight into the relation between CHEK2 c.1100delC status, treatment, CBC risk and death. There was no evidence for differential associations of therapy with CBC risk by CHEK2 c.1100delC status The strongest association with reduced CBC risk was observed for the combination of chemotherapy and endocrine therapy [HR(95%CI): 0.66 (0.55-0.78)]. No association was observed with radiotherapy. Results from the multi-state model showed shorter BCSS for CHEK2 c.1100delC carriers versus non-carriers also after accounting for CBC occurrence [HR(95%CI) :1.30 (1.09-1.56)]. In conclusion, systemic therapy was associated with reduced CBC risk irrespective of CHEK2 c.1100delC status. Moreover, CHEK2 c.1100delC carriers had shorter BCSS, which appears not to be fully explained by their CBC risk. (Main MS: 3201 words).

FANCM missense variants and breast cancer risk: a case-control association study of 75,156 European women

Evidence from literature, including the BRIDGES study, indicates that germline protein truncating variants (PTVs) in FANCM confer moderately increased risk of ER-negative and triple-negative breast cancer (TNBC), especially for women with a family history of the disease. Association between FANCM missense variants (MVs) and breast cancer risk has been postulated. In this study, we further used the BRIDGES study to test 689 FANCM MVs for association with breast cancer risk, overall and in ER-negative and TNBC subtypes, in 39,885 cases (7566 selected for family history) and 35,271 controls of European ancestry. Sixteen common MVs were tested individually; the remaining rare 673 MVs were tested by burden analyses considering their position and pathogenicity score. We also conducted a meta-analysis of our results and those from published studies. We did not find evidence for association for any of the 16 variants individually tested. The rare MVs were significantly associated with increased risk of ER-negative breast cancer by burden analysis comparing familial cases to controls (OR = 1.48; 95% CI 1.07-2.04; P = 0.017). Higher ORs were found for the subgroup of MVs located in functional domains or predicted to be pathogenic. The meta-analysis indicated that FANCM MVs overall are associated with breast cancer risk (OR = 1.22; 95% CI 1.08-1.38; P = 0.002). Our results support the definition from previous analyses of FANCM as a moderate-risk breast cancer gene and provide evidence that FANCM MVs could be low/moderate risk factors for ER-negative and TNBC subtypes. Further genetic and functional analyses are necessary to clarify better the increased risks due to FANCM MVs.

Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry

BACKGROUND

Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes.

METHODS

We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry.

RESULTS

In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 × 10-6) and AC058822.1 (P = 1.47 × 10-4), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C.

CONCLUSIONS

Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 × 10-5), demonstrating the importance of diversifying study cohorts.

Distinct Reproductive Risk Profiles for Intrinsic-Like Breast Cancer Subtypes: Pooled Analysis of Population-Based Studies

BACKGROUND

Reproductive factors have been shown to be differentially associated with risk of estrogen receptor (ER)-positive and ER-negative breast cancer. However, their associations with intrinsic-like subtypes are less clear.

METHODS

Analyses included up to 23 353 cases and 71 072 controls pooled from 31 population-based case-control or cohort studies in the Breast Cancer Association Consortium across 16 countries on 4 continents. Polytomous logistic regression was used to estimate the association between reproductive factors and risk of breast cancer by intrinsic-like subtypes (luminal A-like, luminal B-like, luminal B-HER2-like, HER2-enriched-like, and triple-negative breast cancer) and by invasiveness. All statistical tests were 2-sided.

RESULTS

Compared with nulliparous women, parous women had a lower risk of luminal A-like, luminal B-like, luminal B-HER2-like, and HER2-enriched-like disease. This association was apparent only after approximately 10 years since last birth and became stronger with increasing time (odds ratio [OR] = 0.59, 95% confidence interval [CI] = 0.49 to 0.71; and OR = 0.36, 95% CI = 0.28 to 0.46 for multiparous women with luminal A-like tumors 20 to less than 25 years after last birth and 45 to less than 50 years after last birth, respectively). In contrast, parous women had a higher risk of triple-negative breast cancer right after their last birth (for multiparous women: OR = 3.12, 95% CI = 2.02 to 4.83) that was attenuated with time but persisted for decades (OR = 1.03, 95% CI = 0.79 to 1.34, for multiparous women 25 to less than 30 years after last birth). Older age at first birth (Pheterogeneity < .001 for triple-negative compared with luminal A-like breast cancer) and breastfeeding (Pheterogeneity < .001 for triple-negative compared with luminal A-like breast cancer) were associated with lower risk of triple-negative breast cancer but not with other disease subtypes. Younger age at menarche was associated with higher risk of all subtypes; older age at menopause was associated with higher risk of luminal A-like but not triple-negative breast cancer. Associations for in situ tumors were similar to luminal A-like.

CONCLUSIONS

This large and comprehensive study demonstrates a distinct reproductive risk factor profile for triple-negative breast cancer compared with other subtypes, with implications for the understanding of disease etiology and risk prediction.

Physical activity, sedentary time and breast cancer risk: a Mendelian randomisation study

OBJECTIVES

Physical inactivity and sedentary behaviour are associated with higher breast cancer risk in observational studies, but ascribing causality is difficult. Mendelian randomisation (MR) assesses causality by simulating randomised trial groups using genotype. We assessed whether lifelong physical activity or sedentary time, assessed using genotype, may be causally associated with breast cancer risk overall, pre/post-menopause, and by case-groups defined by tumour characteristics.

METHODS

We performed two-sample inverse-variance-weighted MR using individual-level Breast Cancer Association Consortium case-control data from 130 957 European-ancestry women (69 838 invasive cases), and published UK Biobank data (n=91 105-377 234). Genetic instruments were single nucleotide polymorphisms (SNPs) associated in UK Biobank with wrist-worn accelerometer-measured overall physical activity (nsnps=5) or sedentary time (nsnps=6), or accelerometer-measured (nsnps=1) or self-reported (nsnps=5) vigorous physical activity.

RESULTS

Greater genetically-predicted overall activity was associated with lower breast cancer overall risk (OR=0.59; 95% confidence interval (CI) 0.42 to 0.83 per-standard deviation (SD;~8 milligravities acceleration)) and for most case-groups. Genetically-predicted vigorous activity was associated with lower risk of pre/perimenopausal breast cancer (OR=0.62; 95% CI 0.45 to 0.87,≥3 vs. 0 self-reported days/week), with consistent estimates for most case-groups. Greater genetically-predicted sedentary time was associated with higher hormone-receptor-negative tumour risk (OR=1.77; 95% CI 1.07 to 2.92 per-SD (~7% time spent sedentary)), with elevated estimates for most case-groups. Results were robust to sensitivity analyses examining pleiotropy (including weighted-median-MR, MR-Egger).

CONCLUSION

Our study provides strong evidence that greater overall physical activity, greater vigorous activity, and lower sedentary time are likely to reduce breast cancer risk. More widespread adoption of active lifestyles may reduce the burden from the most common cancer in women.

Breast cancer risks associated with missense variants in breast cancer susceptibility genes

BACKGROUND

Protein truncating variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2 are associated with increased breast cancer risk, but risks associated with missense variants in these genes are uncertain.

METHODS

We analyzed data on 59,639 breast cancer cases and 53,165 controls from studies participating in the Breast Cancer Association Consortium BRIDGES project. We sampled training (80%) and validation (20%) sets to analyze rare missense variants in ATM (1146 training variants), BRCA1 (644), BRCA2 (1425), CHEK2 (325), and PALB2 (472). We evaluated breast cancer risks according to five in silico prediction-of-deleteriousness algorithms, functional protein domain, and frequency, using logistic regression models and also mixture models in which a subset of variants was assumed to be risk-associated.

RESULTS

The most predictive in silico algorithms were Helix (BRCA1, BRCA2 and CHEK2) and CADD (ATM). Increased risks appeared restricted to functional protein domains for ATM (FAT and PIK domains) and BRCA1 (RING and BRCT domains). For ATM, BRCA1, and BRCA2, data were compatible with small subsets (approximately 7%, 2%, and 0.6%, respectively) of rare missense variants giving similar risk to those of protein truncating variants in the same gene. For CHEK2, data were more consistent with a large fraction (approximately 60%) of rare missense variants giving a lower risk (OR 1.75, 95% CI (1.47-2.08)) than CHEK2 protein truncating variants. There was little evidence for an association with risk for missense variants in PALB2. The best fitting models were well calibrated in the validation set.

CONCLUSIONS

These results will inform risk prediction models and the selection of candidate variants for functional assays and could contribute to the clinical reporting of gene panel testing for breast cancer susceptibility.

Genome-wide interaction analysis of menopausal hormone therapy use and breast cancer risk among 62,370 women

Use of menopausal hormone therapy (MHT) is associated with increased risk for breast cancer. However, the relevant mechanisms and its interaction with genetic variants are not fully understood. We conducted a genome-wide interaction analysis between MHT use and genetic variants for breast cancer risk in 27,585 cases and 34,785 controls from 26 observational studies. All women were post-menopausal and of European ancestry. Multivariable logistic regression models were used to test for multiplicative interactions between genetic variants and current MHT use. We considered interaction p-values < 5 × 10-8 as genome-wide significant, and p-values < 1 × 10-5 as suggestive. Linkage disequilibrium (LD)-based clumping was performed to identify independent candidate variants. None of the 9.7 million genetic variants tested for interactions with MHT use reached genome-wide significance. Only 213 variants, representing 18 independent loci, had p-values < 1 × 105. The strongest evidence was found for rs4674019 (p-value = 2.27 × 10-7), which showed genome-wide significant interaction (p-value = 3.8 × 10-8) with current MHT use when analysis was restricted to population-based studies only. Limiting the analyses to combined estrogen-progesterone MHT use only or to estrogen receptor (ER) positive cases did not identify any genome-wide significant evidence of interactions. In this large genome-wide SNP-MHT interaction study of breast cancer, we found no strong support for common genetic variants modifying the effect of MHT on breast cancer risk. These results suggest that common genetic variation has limited impact on the observed MHT-breast cancer risk association.

A genome-wide gene-based gene-environment interaction study of breast cancer in more than 90,000 women

Background

Genome-wide association studies (GWAS) have identified more than 200 susceptibility loci for breast cancer, but these variants explain less than a fifth of the disease risk. Although gene-environment interactions have been proposed to account for some of the remaining heritability, few studies have empirically assessed this.

Methods

We obtained genotype and risk factor data from 46,060 cases and 47,929 controls of European ancestry from population-based studies within the Breast Cancer Association Consortium (BCAC). We built gene expression prediction models for 4,864 genes with a significant (P<0.01) heritable component using the transcriptome and genotype data from the Genotype-Tissue Expression (GTEx) project. We leveraged predicted gene expression information to investigate the interactions between gene-centric genetic variation and 14 established risk factors in association with breast cancer risk, using a mixed-effects score test.

Results

After adjusting for number of tests using Bonferroni correction, no interaction remained statistically significant. The strongest interaction observed was between the predicted expression of the C13orf45 gene and age at first full-term pregnancy (PGXE=4.44×10-6).

Conclusion

In this transcriptome-informed genome-wide gene-environment interaction study of breast cancer, we found no strong support for the role of gene expression in modifying the associations between established risk factors and breast cancer risk.

Impact

Our study suggests a limited role of gene-environment interactions in breast cancer risk.

Pathology of Tumors Associated With Pathogenic Germline Variants in 9 Breast Cancer Susceptibility Genes

IMPORTANCE

Rare germline genetic variants in several genes are associated with increased breast cancer (BC) risk, but their precise contributions to different disease subtypes are unclear. This information is relevant to guidelines for gene panel testing and risk prediction.

OBJECTIVE

To characterize tumors associated with BC susceptibility genes in large-scale population- or hospital-based studies.

DESIGN, SETTING, AND PARTICIPANTS

The multicenter, international case-control analysis of the BRIDGES study included 42 680 patients and 46 387 control participants, comprising women aged 18 to 79 years who were sampled independently of family history from 38 studies. Studies were conducted between 1991 and 2016. Sequencing and analysis took place between 2016 and 2021.

EXPOSURES

Protein-truncating variants and likely pathogenic missense variants in ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53.

MAIN OUTCOMES AND MEASURES

The intrinsic-like BC subtypes as defined by estrogen receptor, progesterone receptor, and ERBB2 (formerly known as HER2) status, and tumor grade; morphology; size; stage; lymph node involvement; subtype-specific odds ratios (ORs) for carrying protein-truncating variants and pathogenic missense variants in the 9 BC susceptibility genes.

RESULTS

The mean (SD) ages at interview (control participants) and diagnosis (cases) were 55.1 (11.9) and 55.8 (10.6) years, respectively; all participants were of European or East Asian ethnicity. There was substantial heterogeneity in the distribution of intrinsic subtypes by gene. RAD51C, RAD51D, and BARD1 variants were associated mainly with triple-negative disease (OR, 6.19 [95% CI, 3.17-12.12]; OR, 6.19 [95% CI, 2.99-12.79]; and OR, 10.05 [95% CI, 5.27-19.19], respectively). CHEK2 variants were associated with all subtypes (with ORs ranging from 2.21-3.17) except for triple-negative disease. For ATM variants, the association was strongest for the hormone receptor (HR)+ERBB2- high-grade subtype (OR, 4.99; 95% CI, 3.68-6.76). BRCA1 was associated with increased risk of all subtypes, but the ORs varied widely, being highest for triple-negative disease (OR, 55.32; 95% CI, 40.51-75.55). BRCA2 and PALB2 variants were also associated with triple-negative disease. TP53 variants were most strongly associated with HR+ERBB2+ and HR-ERBB2+ subtypes. Tumors occurring in pathogenic variant carriers were of higher grade. For most genes and subtypes, a decline in ORs was observed with increasing age. Together, the 9 genes were associated with 27.3% of all triple-negative tumors in women 40 years or younger.

CONCLUSIONS AND RELEVANCE

The results of this case-control study suggest that variants in the 9 BC risk genes differ substantially in their associated pathology but are generally associated with triple-negative and/or high-grade disease. Knowing the age and tumor subtype distributions associated with individual BC genes can potentially aid guidelines for gene panel testing, risk prediction, and variant classification and guide targeted screening strategies.

Abstract P1-07-08: Endoxifen predicts early recurrence in breast cancer: A Brazilian prospective study

Tamoxifen is widely used in adjuvant therapy for breast cancer patients, but up to one-third of patients recur within 15 years after surgery even with its regular use. Low plasma levels of (Z)-endoxifen, the most active tamoxifen metabolite, have been studied as a possible predictor of treatment failure. Here, we evaluated plasma (Z)-endoxifen as a predictor of response to adjuvant treatment in breast cancer patients. Methods: One hundred forty nine patients were selected from a prospective cohort of consecutive newly diagnosed breast cancer patients recruited at a national referral center for treatment of cancer in Curitiba, Southern Brazil. Inclusion criteria were breast cancer women on stage I - III, positive hormone receptor tumors, operable, undergoing or not (neo)adjuvant chemotherapy, and signed for adjuvant tamoxifen for at least five years. At diagnosis, peripheral blood samples were collected for CYP2D6 genotyping for *1 *2, *3, *4, *5, *6, *7, *8, *9, *10, *17, *29 and *41 and subsequent metabolic activity scores according to phenotypes assigned for each allele (poor metabolizer PM; intermediate, IM; extensive, EM and ultrarapid metabolizer, UM). After the tamoxifen initiation, patients were evaluated at months 3, 6, and 12 for adherence and drug interactions, and plasma (Z)-endoxifen quantification. They were followed from April 2014 to April 2019. The study's primary objective was to evaluate whether (Z)-endoxifen plasma levels predict early recurrence in patients on adjuvant tamoxifen. The secondary aim was to evaluate an association between (Z)-endoxifen levels and clinical and phenotypic CYP2D6 metabolism variables. A Cox model estimated hazard ratios (HR) comparing recurrence free survival (RFS) according to (Z)-endoxifen plasma levels. The survival was compared using the Kaplan-Meier method and the log-rank test. Results: The median follow-up period was 52.3 months and at that point, there were 20 recurrences of 149 patients. At 3 months there were no cases of low adherence to tamoxifen. The (Z)-endoxifen levels were established by quartiles, with the first lower quartile being used as a cutoff (14.72nM). High (Z)-endoxifen levels at 3 months (&gt;14.72nM) were detected in 75.8% (n = 113) of cases and low levels (≤14.72nM) in 24.2% (n = 36). There was no statistically significant difference between the groups with low or high (Z)-endoxifen levels regarding clinical and pathological variables, but there was a higher CYP2D6 PM/IM frequency in the low (Z)-endoxifen levels group (p&lt;0.001). High (Z)-endoxifen levels were associated with lower RFS compared to low (Z)-endoxifen levels (HR 2.5, 95% CI 1.00-6.22, p=0.041). Low (Z)-endoxifen levels increased the recurrence risk even when adjusted for staging and molecular subtypes (HR 2.55, 95% CI 1.00-6.48, p&lt;0.001) or staging and CYP2D6 phenotype (UM/EM vs IM/PM; HR 4.38, 95% CI 1.66-11.59, p=0.003), or prior chemotherapy exposure (HR 2.65, 95% CI 1.06-6.61, p=0.036). Conclusion: This is the first Brazilian prospective trial evaluating the association of plasma (Z)-endoxifen levels, with the clinical outcome in breast cancer women treated with adjuvant tamoxifen, controlled by predictable confounding factors of plasma (Z)-endoxifen levels, such as tamoxifen adherence, and drug interaction with CYP2D6 inhibitors. In our study, a low plasma level of (Z)-endoxifen (≤ 14.72nM) after 3 months of tamoxifen treatment was a predictor of early recurrence in patients under adjuvant tamoxifen (p=0.041). A longer follow-up and a larger cohort may be needed to confirm the (Z)-endoxifen cutoff value that is a predictor of long-term recurrence.

Citation Format: Thais Almeida, Werner Schroth, Jeanine Marie Nardin, Thomas Mürdter, Solane Picolotto, Reiner Hoppe, Jenifer Primon Kogin, Elisa Daniele Gaio, Angela Dasenbrock, Raquel Cristina Skrsypcsak, Lucia Noronha, Hiltrud Brauch, José Claudio Casali-da-Rocha. Endoxifen predicts early recurrence in breast cancer: A Brazilian prospective study [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-07-08.

Rare germline copy number variants (CNVs) and breast cancer risk

Germline copy number variants (CNVs) are pervasive in the human genome but potential disease associations with rare CNVs have not been comprehensively assessed in large datasets. We analysed rare CNVs in genes and non-coding regions for 86,788 breast cancer cases and 76,122 controls of European ancestry with genome-wide array data. Gene burden tests detected the strongest association for deletions in BRCA1 (P = 3.7E-18). Nine other genes were associated with a p-value < 0.01 including known susceptibility genes CHEK2 (P = 0.0008), ATM (P = 0.002) and BRCA2 (P = 0.008). Outside the known genes we detected associations with p-values < 0.001 for either overall or subtype-specific breast cancer at nine deletion regions and four duplication regions. Three of the deletion regions were in established common susceptibility loci. To the best of our knowledge, this is the first genome-wide analysis of rare CNVs in a large breast cancer case-control dataset. We detected associations with exonic deletions in established breast cancer susceptibility genes. We also detected suggestive associations with non-coding CNVs in known and novel loci with large effects sizes. Larger sample sizes will be required to reach robust levels of statistical significance.

Germline variants and breast cancer survival in patients with distant metastases at primary breast cancer diagnosis

Breast cancer metastasis accounts for most of the deaths from breast cancer. Identification of germline variants associated with survival in aggressive types of breast cancer may inform understanding of breast cancer progression and assist treatment. In this analysis, we studied the associations between germline variants and breast cancer survival for patients with distant metastases at primary breast cancer diagnosis. We used data from the Breast Cancer Association Consortium (BCAC) including 1062 women of European ancestry with metastatic breast cancer, 606 of whom died of breast cancer. We identified two germline variants on chromosome 1, rs138569520 and rs146023652, significantly associated with breast cancer-specific survival (P = 3.19 × 10-8 and 4.42 × 10-8). In silico analysis suggested a potential regulatory effect of the variants on the nearby target genes SDE2 and H3F3A. However, the variants showed no evidence of association in a smaller replication dataset. The validation dataset was obtained from the SNPs to Risk of Metastasis (StoRM) study and included 293 patients with metastatic primary breast cancer at diagnosis. Ultimately, larger replication studies are needed to confirm the identified associations.

Association of germline genetic variants with breast cancer-specific survival in patient subgroups defined by clinic-pathological variables related to tumor biology and type of systemic treatment

BACKGROUND

Given the high heterogeneity among breast tumors, associations between common germline genetic variants and survival that may exist within specific subgroups could go undetected in an unstratified set of breast cancer patients.

METHODS

We performed genome-wide association analyses within 15 subgroups of breast cancer patients based on prognostic factors, including hormone receptors, tumor grade, age, and type of systemic treatment. Analyses were based on 91,686 female patients of European ancestry from the Breast Cancer Association Consortium, including 7531 breast cancer-specific deaths over a median follow-up of 8.1 years. Cox regression was used to assess associations of common germline variants with 15-year and 5-year breast cancer-specific survival. We assessed the probability of these associations being true positives via the Bayesian false discovery probability (BFDP < 0.15).

RESULTS

Evidence of associations with breast cancer-specific survival was observed in three patient subgroups, with variant rs5934618 in patients with grade 3 tumors (15-year-hazard ratio (HR) [95% confidence interval (CI)] 1.32 [1.20, 1.45], P = 1.4E-08, BFDP = 0.01, per G allele); variant rs4679741 in patients with ER-positive tumors treated with endocrine therapy (15-year-HR [95% CI] 1.18 [1.11, 1.26], P = 1.6E-07, BFDP = 0.09, per G allele); variants rs1106333 (15-year-HR [95% CI] 1.68 [1.39,2.03], P = 5.6E-08, BFDP = 0.12, per A allele) and rs78754389 (5-year-HR [95% CI] 1.79 [1.46,2.20], P = 1.7E-08, BFDP = 0.07, per A allele), in patients with ER-negative tumors treated with chemotherapy.

CONCLUSIONS

We found evidence of four loci associated with breast cancer-specific survival within three patient subgroups. There was limited evidence for the existence of associations in other patient subgroups. However, the power for many subgroups is limited due to the low number of events. Even so, our results suggest that the impact of common germline genetic variants on breast cancer-specific survival might be limited.

Abstract 1946: Synergistic cell death induction in breast cancer cell lines by combining ABT-199 and cisplatin irrespective of estrogen receptor and p53 expression

50 Years after the generation of the most studied human breast cancer cell line, MCF-7, many research results fundamentally changed patient outcomes for the better. The mortality of breast cancer in women has decreased significantly, especially in the last 30 years. But the total number of deaths is rising again in the last ten years. Considering that breast cancer is the most common cancer in women and the second most common cancer overall, with incidences of 24,2% and 11,6%, respectively, total numbers of new cases are in the millions every year.

First line drugs for the treatment of breast cancer often target microtubules (e.g. Vinblastine and Paclitaxel) or induce DNA damage (e.g. Carboplatin and Cisplatin (CisPt)). In addition to these classic therapeutic drugs new compounds that specifically target cancer-driving molecular alterations have been developed. Among these is the group of BH3-mimetics. The efficacy of several BH3-mimetics is investigated in numerous clinical trials while the BCL-2 specific inhibitor ABT-199 (Venetoclax) is already approved for clinical application in chronic lymphatic leukemia (CLL), acute myeloid leukemia (AML) and small lymphocytic lymphoma (SLL). BH3-mimetics target the apoptosis machinery by interacting with anti-apoptotic Bcl-2 proteins, mimicking the function of pro-apoptotic BH3-only proteins. In turn, the pro-apoptotic potential of pore-forming BCL-2 effectors BAX, BAK and BOK is released inducing mitochondrial outer membrane permeabilization and cell death.

Recently we reported synergistic cell death induction by ABT-199 in combination with the proteasome inhibitor Bortezomib (BOZ) in soft tissue sarcoma (STS) cells. ABT-199 and BOZ induce accumulation of BOK and the BH3-only protein NOXA (Muenchow et al. 2020). Here, we combined ABT-199, CisPt and Nutlin-3 in breast cancer cell lines that differ in expression of the estrogen receptor (ER) and p53 activity. Similar to the results in STS cells synergistic induction of apoptotic cell death was observed by FACS analysis of the mitochondrial membrane potential (TMRM) and exposure of phosphatidyl serine (Annexin-V). Western blot analysis revealed that ABT-199 induced accumulation of NOXA and MCL-1, irrespective of the ER status or p53 mutation. Simultaneous treatment with ABT-199 and CisPt or Nutlin-3 further increased expression of NOXA and MCL-1. Interestingly, qRT-PCR revealed enhanced expression of NOXA and MCL-1 mRNA in ABT-199 treated cells indicating transcriptional regulation. However, transcriptional induction of NOXA was also detected independent of p53 activity. Thus, combined therapeutic approaches using CisPt and ABT-199 should be effective irrespective of ER and p53 expression. Nevertheless, in p53 proficient tumors Nutlins might increase therapeutic efficacy.

Citation Format: Benjamin Schaefer, Sandra Weller, Tobias Beigl, Kathrin Boepple, Reiner Hoppe, Klaus Schulze-Osthoff, Hans-Georg Kopp, Walter E. Aulitzky, Frank Essmann. Synergistic cell death induction in breast cancer cell lines by combining ABT-199 and cisplatin irrespective of estrogen receptor and p53 expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1946.

Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element

A combination of genetic and functional approaches has identified three independent breast cancer risk loci at 2q35. A recent fine-scale mapping analysis to refine these associations resulted in 1 (signal 1), 5 (signal 2), and 42 (signal 3) credible causal variants at these loci. We used publicly available in silico DNase I and ChIP-seq data with in vitro reporter gene and CRISPR assays to annotate signals 2 and 3. We identified putative regulatory elements that enhanced cell-type-specific transcription from the IGFBP5 promoter at both signals (30- to 40-fold increased expression by the putative regulatory element at signal 2, 2- to 3-fold by the putative regulatory element at signal 3). We further identified one of the five credible causal variants at signal 2, a 1.4 kb deletion (esv3594306), as the likely causal variant; the deletion allele of this variant was associated with an average additional increase in IGFBP5 expression of 1.3-fold (MCF-7) and 2.2-fold (T-47D). We propose a model in which the deletion allele of esv3594306 juxtaposes two transcription factor binding regions (annotated by estrogen receptor alpha ChIP-seq peaks) to generate a single extended regulatory element. This regulatory element increases cell-type-specific expression of the tumor suppressor gene IGFBP5 and, thereby, reduces risk of estrogen receptor-positive breast cancer (odds ratio = 0.77, 95% CI 0.74-0.81, p = 3.1 × 10-31).

Gene-Environment Interactions Relevant to Estrogen and Risk of Breast Cancer: Can Gene-Environment Interactions Be Detected Only among Candidate SNPs from Genome-Wide Association Studies?

In this study we aim to examine gene-environment interactions (GxEs) between genes involved with estrogen metabolism and environmental factors related to estrogen exposure. GxE analyses were conducted with 1970 Korean breast cancer cases and 2052 controls in the case-control study, the Seoul Breast Cancer Study (SEBCS). A total of 11,555 SNPs from the 137 candidate genes were included in the GxE analyses with eight established environmental factors. A replication test was conducted by using an independent population from the Breast Cancer Association Consortium (BCAC), with 62,485 Europeans and 9047 Asians. The GxE tests were performed by using two-step methods in GxEScan software. Two interactions were found in the SEBCS. The first interaction was shown between rs13035764 of NCOA1 and age at menarche in the GE|2df model (p-2df = 1.2 × 10-3). The age at menarche before 14 years old was associated with the high risk of breast cancer, and the risk was higher when subjects had homozygous minor allele G. The second GxE was shown between rs851998 near ESR1 and height in the GE|2df model (p-2df = 1.1 × 10-4). Height taller than 160 cm was associated with a high risk of breast cancer, and the risk increased when the minor allele was added. The findings were not replicated in the BCAC. These results would suggest specificity in Koreans for breast cancer risk.

Breast Cancer Risk Factors and Survival by Tumor Subtype: Pooled Analyses from the Breast Cancer Association Consortium

BACKGROUND

It is not known whether modifiable lifestyle factors that predict survival after invasive breast cancer differ by subtype.

METHODS

We analyzed data for 121,435 women diagnosed with breast cancer from 67 studies in the Breast Cancer Association Consortium with 16,890 deaths (8,554 breast cancer specific) over 10 years. Cox regression was used to estimate associations between risk factors and 10-year all-cause mortality and breast cancer-specific mortality overall, by estrogen receptor (ER) status, and by intrinsic-like subtype.

RESULTS

There was no evidence of heterogeneous associations between risk factors and mortality by subtype (P adj > 0.30). The strongest associations were between all-cause mortality and BMI ≥30 versus 18.5-25 kg/m2 [HR (95% confidence interval (CI), 1.19 (1.06-1.34)]; current versus never smoking [1.37 (1.27-1.47)], high versus low physical activity [0.43 (0.21-0.86)], age ≥30 years versus <20 years at first pregnancy [0.79 (0.72-0.86)]; >0-<5 years versus ≥10 years since last full-term birth [1.31 (1.11-1.55)]; ever versus never use of oral contraceptives [0.91 (0.87-0.96)]; ever versus never use of menopausal hormone therapy, including current estrogen-progestin therapy [0.61 (0.54-0.69)]. Similar associations with breast cancer mortality were weaker; for example, 1.11 (1.02-1.21) for current versus never smoking.

CONCLUSIONS

We confirm associations between modifiable lifestyle factors and 10-year all-cause mortality. There was no strong evidence that associations differed by ER status or intrinsic-like subtype.

IMPACT

Given the large dataset and lack of evidence that associations between modifiable risk factors and 10-year mortality differed by subtype, these associations could be cautiously used in prognostication models to inform patient-centered care.

Downregulation of 15-hydroxyprostaglandin dehydrogenase during acquired tamoxifen resistance and association with poor prognosis in ERα-positive breast cancer

Aim:

Tamoxifen (TAM) resistance remains a clinical issue in breast cancer. The authors previously reported that 15-hydroxyprostaglandin dehydrogenase (HPGD) was significantly downregulated in tamoxifen-resistant (TAMr) breast cancer cell lines. Here, the authors investigated the relationship between HPGD expression, TAM resistance and prediction of outcome in breast cancer.

Methods:

HPGD overexpression and silencing studies were performed in isogenic TAMr and parental human breast cancer cell lines to establish the impact of HPGD expression on TAM resistance. HPGD expression and clinical outcome relationships were explored using immunohistochemistry and in silico analysis.

Results:

Restoration of HPGD expression and activity sensitised TAMr MCF-7 cells to TAM and 17β-oestradiol, whilst HPGD silencing in parental MCF-7 cells reduced TAM sensitivity. TAMr cells released more prostaglandin E₂ (PGE₂) than controls, which was reduced in TAMr cells stably transfected with HPGD. Exogenous PGE₂ signalled through the EP4 receptor to reduce breast cancer cell sensitivity to TAM. Decreased HPGD expression was associated with decreased overall survival in ERα-positive breast cancer patients.

Conclusions:

HPGD downregulation in breast cancer is associated with reduced response to TAM therapy via PGE₂-EP4 signalling and decreases patient survival. The data offer a potential target to develop combination therapies that may overcome acquired tamoxifen resistance.

Gene Expression Signatures of BRCAness and Tumor Inflammation Define Subgroups of Early-Stage Hormone Receptor-Positive Breast Cancer Patients

PURPOSE

Patients with estrogen receptor- and/or progesterone receptor-positive, early breast cancer benefit from hormonal treatment, yet high global death burdens due to high prevalence and long-term recurrence risk call for biomarkers to guide additional treatment approaches.

EXPERIMENTAL DESIGN

From a prospective, observational study of postmenopausal early breast cancer patients treated with tamoxifen or aromatase inhibitors, gene expression analyses of 612 tumors was performed using the NanoString Breast Cancer 360 panel to interrogate 23 breast cancer pathways. Candidate signatures associated with disease subtype and event-free survival (EFS) were obtained by cluster analysis, Cox modeling, and conditional inference trees, and were independently tested in 613 patients from BreastMark. Tumor-infiltrating lymphocytes (TIL) were assessed on tissue sections, and mutational burden was assessed in 36 tumors by whole-exome sequencing.

RESULTS

PAM50-derived classification distinguished lower-risk (Luminal A) from higher-risk subtypes (Luminal B, P = 0.04; HER2, P = 0.006; Basal, P = 0.008). In higher-risk patients, shorter EFS was associated with low androgen receptor [HR = 3.61; 95% confidence interval (CI), 1.72-7.56; P = 0.001] or high BRCAness signature expression (HR = 3.58; 95% CI, 1.19-10.7; P = 0.023). BRCAness was independently confirmed as a predictor of shorter EFS (HR = 2.64; 95% CI, 1.31-5.34; P = 0.007). About 13%-15% of patients, enriched for high-grade, higher-risk subtypes (P ≤ 0.0001), had strong expression of the Tumor Inflammation Signature (TIS) suggestive of an inhibited antitumor immune response. TIS scores were strongly associated with TIL numbers (P < 1e-30) but not with tumor mutation status.

CONCLUSIONS

BRCA-related DNA repair deficiency and suppressed tumor immune responses may be clinically relevant predictors of endocrine therapy complementing treatment options in subgroups of hormone-sensitive early breast cancer.

Abstract 144: Genome-wide DNA methylation changes in AI-resistant breast cancer models during E2-treatment

Disruption of estrogen signaling with tamoxifen or aromatase inhibitors (AI) is the clinical standard for the treatment of estrogen receptor-positive breast cancer, yet resistance to antiestrogen therapies is inevitable. The long-term E2-deprived breast cancer models MCF-7:5C and MCF-7:2A mimic AI resistance and moreover are vulnerable to E2-induced apoptosis due to the reconfiguration of their survival signaling. E2-induced apoptosis which results from the accumulation of endoplasmic reticulum (ER), oxidative, and inflammatory stresses, is a new paradigm to subvert endocrine resistance, with sensors of the unfolded protein response (UPR) being important mediators of ER stress (Ariazi et al. 2011; Fan et al. 2013, 2015). Here we asked whether epigenetic modifications may play a role in this and investigated genome-wide changes of 5C and 2A DNA methylation patterns that occurred during E2 stimulation during a 72h time course with WS8 cells as a reference. Methylation patterns were established using the Illumina Infinium HumanMethylation450 BeadChip (Service XS, Leiden, NL), and raw intensities were normalized and filtered using the bioconductor minfi package. A linear model (bioconductor limma package) has been built to detect differentially methylated CpGs. F-statistics were calculated by empirical Bayes moderation of standard errors with "trend" and "robust" set “on”. We also performed whole-genome bisulfite sequencing (WGBS) in untreated cells using the Illumina HiSeq platform (GATC Biotech, Konstanz, DE) to obtain maximum baseline CpG coverage. Trimmed WGBS reads were aligned to the hg38 genome (Bismarck, PMC3102221), duplicates removed, and methylation levels extracted with MethylDackel (https://github.com/dpryan79/MethylDackel) with a 3x coverage threshold (Wreczycka et al. 2017). Raw methylation levels were smoothed and differential methylation called using the bsseq package (Hansen et al. 2012). At baseline, WGBS-derived profiles showed a 2-fold higher degree of hypomethylation (beta &lt;0.2) in 5C compared to 2A and WS8. In time course E2-treatments we identified 134 dynamic CpGs across all three models (Padj &lt; 0.05). Methylation status mainly decreased, with few specific changes in 5C and 2A. Among 120 affected CpG sites matching to GeneHancer regulatory elements 23 locate to ERE sites suggesting a direct control of inferred target genes (UCSC genome browser). Their matching to ER stress-, UPR- and apoptosis-related gene sets identified among others ATF6B, EIF2AK4, HSPB1, TNF, GANAB and PPIA. Currently, we are performing functional enrichment analyses and E2-responsive CpGs are being correlated with respective transcriptome signatures. Our preliminary data suggest that E2-triggered methylation changes in cell models vulnerable to E2-induced apoptosis may aid the identification of potential therapeutic targets towards overcoming endocrine resistance.

Citation Format: Reiner Hoppe, Siarhei Kandabarau, Ping Fan, Stefan Winter, Balkees Abderrahman, Heather Cunliffe, Werner Schroth, V. Craig Jordan, Hiltrud B. Brauch. Genome-wide DNA methylation changes in AI-resistant breast cancer models during E2-treatment [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 144.

Subunits of BK channels promote breast cancer development and modulate responses to endocrine treatment in preclinical models

BACKGROUND AND PURPOSE

Pore-forming α subunits of the voltage- and Ca²⁺ -activated K⁺ channel with large conductance (BKα) promote malignant phenotypes of breast tumour cells. Auxiliary subunits such as the leucine-rich repeat containing 26 (LRRC26) protein, also termed BKγ1, may be required to permit activation of BK currents at a depolarized resting membrane potential that frequently occur in non-excitable tumour cells.

EXPERIMENTAL APPROACH

Anti-tumour effects of BKα loss were investigated in breast tumour-bearing MMTV-PyMT transgenic BKα knockout (KO) mice, primary MMTV-PyMT cell cultures, and in a syngeneic transplantation model of breast cancer derived from these cells. The therapeutic relevance of BK channels in the context of endocrine treatment was assessed in human breast cancer cell lines expressing either low (MCF-7) or high (MDA-MB-453) levels of BKα and BKγ1, as well as in BKα-negative MDA-MB-157.

KEY RESULTS

BKα promoted breast cancer onset and overall survival in preclinical models. Conversely, lack of BKα and/or knockdown of BKγ1 attenuated proliferation of murine and human breast cancer cells in vitro. At low concentrations, tamoxifen and its major active metabolites stimulated proliferation of BKα/γ1-positive breast cancer cells, independent of the genomic signalling controlled by the oestrogen receptor. Finally, tamoxifen increased the relative survival time of BKα KO but not of wild-type tumour cell recipient mice.

CONCLUSION AND IMPLICATIONS

Breast cancer initiation, progression, and tamoxifen sensitivity depend on functional BK channels thereby providing a rationale for the future exploration of the oncogenic actions of BK channels in clinical outcomes with anti-oestrogen therapy.

Abstract P2-11-12: The influences of adherence to tamoxifen and CYP2D6 pharmacogenetics on plasma concentrations of the active metabolite (Z)-endoxifen in breast cancer

One-third of early breast cancer patients with estrogen receptor (ER) positive tumors treated with the selective estrogen receptor modulator tamoxifen either relapse or die from the disease in the following decade. Improvement of tamoxifen efficacy requires a better knowledge of factors determining outcome of which the medication-taking behavior, i.e. adherence, is a strong suspect. Discontinuation and non-adherence to tamoxifen are frequent and result in increased mortality. Commonly used methods to assess drug adherence such as prescription-refill patterns infer that the medication is taken exactly as prescribed yet, partial adherence or actual use of the medication cannot be controlled. An objective surrogate of tamoxifen adherence is the monitoring of drug concentrations in the patients’ plasma including the parent drug and its active metabolite (Z)-endoxifen (endoxifen), however individual concentrations depend on pharmacogene polymorphisms particularly those of the liver enzyme cytochrome P450 2D6 (CYP2D6). Patients without CYP2D6 variants have normal enzyme function (extensive metabolizer, EM) and achieve high endoxifen concentrations compared to patients with variants conferring absent activity (poor metabolizer, PM) or reduced activity (intermediate metabolizer, IM) who have significantly lower plasma concentrations of the active metabolite. A putative threshold of 5.9 ng/mL endoxifen has been proposed suggesting that patients with endoxifen concentration above or below threshold have lower or higher risk for recurrence, assuming that low endoxifen exposure in the tumor likely results in incomplete inhibition of ER-dependent growth signaling. During tamoxifen treatment it is therefore important that patients achieve clinically relevant endoxifen levels while at the same time avoid confounders of which adherence is a prime candidate. To this end, we investigated patients’ ability to achieve relevant plasma concentrations during tamoxifen treatment in relation to their CYP2D6 metabolizer status and their tamoxifen adherence behavior. Our prospective study included 192 Brazilian breast cancer patients treated with 20 mg tamoxifen daily. Two-thirds of the patients were premenopausal. Plasma levels of tamoxifen and its metabolites were measured by LC-MS/MS at 3, 6 and 12 months of treatment. Adherence to tamoxifen was evaluated by the questionnaire-based Morisky medication adherence scale. CYP2D6 polymorphisms were determined by MALDI-TOF mass spectrometry and real-time PCR. Adherence to tamoxifen decreased from 74% at month 3 to 64% at month 12, and explained 47% of the variability of tamoxifen plasma concentrations (P&lt;.001). Accordingly, plasma monitoring of tamoxifen is useful to inform on tamoxifen adherence. Endoxifen concentrations were associated with CYP2D6 status and adherence. While CYP2D6 explained 26.4% of endoxifen variability at 12 months, the combination with adherence explained 40% (P&lt;.001). The influence of low adherence to not achieving therapeutic endoxifen levels was highest in patients with non-compromised CYP2D6 function (EM phenotype, RR 3.65; 95% CI: 1.48-8.99). we conclude that for patients with intact CYP2D6 function adherence to tamoxifen is critical to achieve therapeutic endoxifen plasma levels. CYP2D6 phenotyping and endoxifen plasma monitoring may help to guide EM (and IM) patients to adhere to tamoxifen which is particularly relevant for premenopausal women who are at higher risk to not adhere to tamoxifen.

Citation Format: Jose Claudio Casali da Rocha, Jeanine M Nardin, Werner Schroth, Thais A Almeida, Thomas Mürdter, Solange Picolotto, Evelyn CL Vendramini, Reiner Hoppe, Jenifer P Kogin, Diandra Miqueleto, Silvia DR Moraes, Matthias Schwab, Roberto F Pecoits-Filho, Hiltrud Brauch. The influences of adherence to tamoxifen and CYP2D6 pharmacogenetics on plasma concentrations of the active metabolite (Z)-endoxifen in breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-11-12.

The Influences of Adherence to Tamoxifen and CYP2D6 Pharmacogenetics on Plasma Concentrations of the Active Metabolite (Z)-Endoxifen in Breast Cancer

Tamoxifen efficacy in breast cancer is suspected to depend on adherence and intact drug metabolism. We evaluated the role of adherence behavior and pharmacogenetics on the formation rate of (Z)-endoxifen. In 192 Brazilian patients, we assessed plasma levels of tamoxifen and its metabolites at 3, 6, and 12 months of treatment (liquid-chromatography tandem mass spectrometry), adherence behavior (Morisky, Green, and Levine medication adherence scale), and cytochrome P450 2D6 (CYP2D6) and other pharmacogene polymorphisms (matrix-assisted laser-desorption-ionization time of flight) mass spectrometry, real-time polymerase chain reaction). Adherence explained 47% of the variability of tamoxifen plasma concentrations (P < 0.001). Although CYP2D6 alone explained 26.4%, the combination with adherence explained 40% of (Z)-endoxifen variability at 12 months (P < 0.001). The influence of low adherence to not achieving relevant (Z)-endoxifen levels was highest in patients with noncompromised CYP2D6 function (relative risk 3.65; 95% confidence interval 1.48-8.99). As a proof-of-concept, we demonstrated that (Z)-endoxifen levels are influenced both by patient adherence to tamoxifen and CYP2D6, which is particularly relevant for patients with full CYP2D6 function.

Abstract 1689: Comparative whole genome analyses of breast cancer aromatase inhibitor resistance models

One third of breast cancer patients treated with Aromatase Inhibitors (AI) or Tamoxifen acquire resistance leading to disease recurrence and death. The clinically observed AI resistance is mimicked by in vitro models MCF-7:5C and MCF-7:2A that are susceptible to apoptosis upon E2-treatment. These models have been instrumental to the current understanding of underlying mechanisms such as the reconfiguration of survival signaling, alterations of stress-related pathways (Ariazi et al. 2011; Fan et al. 2013, 2015), and changes in miRNA expression profiles (Hoppe et al. 2016). How the model phenotypes relate to a specific genomic background is poorly understood. In order to identify somatic variants indicative of AI resistance and potentially useful as novel therapeutic targets we performed NGS analyses of the 5C and 2A clones compared to the non-resistant WS8 and MCF-7 (ATCC). Whole genome/exome libraries were sequenced on Illumina HiSeq/NovaSeq platforms, respectively. Previously we reported first results from a preliminary analysis of gains and losses of variants in both resistant derivatives (Hoppe at al. AACR 2018). Here we report an updated analysis of raw reads trimmed and aligned to GRCh38 reference using BWAkit v 0.7.15. Duplicates were removed by Picard MarkDuplicates. Base quality scores were recalibrated using GATK4 BQSR. WGS and WES alignments were merged and tested for somatic variants using GATK4 Mutect2 (Tumor-only mode) with population variation data from gnomAD as a germline source. Called and filtered variants were uploaded to IVA for functional and clinical annotation. Copy number segments were modeled using both read- and allele-counts from WGS alignments by Gaussian-kernel binary-segmentation algorithm applied in GATK4 ModelSegments tool. To interpret copy number events causative for LOH we recovered germline variants and annotated CNVs that led to loss of the corresponding wild-type allele. In line with the COSMIC database we confirmed 461 mutated loci of which 228 were lost in both resistant derivatives. Examples of 5C-specific coding mutations classified as pathogenic include splice site alterations (i.e. SEMA3A), frameshifts (i.e. ARID1A), and stop gains (i.e. CACNA1S, CDH2, NOTCH4). 2A-specific mutations include for example a stop gain affecting ADGRV1. Copy number variation analyses revealed that both resistance models share prominent genetic defects such as amplified regions at Chr6q25.1 and Chr21q22.2. A 5C-specific aberration is a large Chr18 deletion affecting most of the q-arm, and a 2A-specific aberration is the amplification of most parts of Chr6q23.3-q24.3. We will present the status of this currently ongoing comparative genome analysis of AI resistance models and discuss the putative effects of homozygous mutations at loci with copy number aberrations within the context of AI resistance.

Citation Format: Reiner Hoppe, Siarhei Kandabarau, Ping Fan, V. Craig Jordan, Heather Cunliffe, Hiltrud B. Brauch. Comparative whole genome analyses of breast cancer aromatase inhibitor resistance models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1689.

Abstract 3432: Evolving genomes of breast cancer aromatase inhibitor resistance models

Acquired endocrine resistance is a severe barrier in the anti-hormonal treatment of breast cancer and is responsible for its failure in about half of the treated patients. In vitro models of long-term estrogen deprived breast cancer cells serve as laboratory tools to explore new therapeutic strategies. The models MCF-7:5C and MCF-7:2A mimic clinical AI resistance but regress with E2 due to the reconfiguration of survival signaling known as E2-inducible apoptosis (5C rapid, 2A delayed reaction). Alterations of stress related pathways including the accumulation of endoplasmic reticulum stress, oxidative stress, and inflammatory stress that occur prior to E2-induced apoptosis (Ariazi et al. 2011; Fan et al. 2013, 2015; Sweeney et al. 2014) and specific miRNA expression profiles (Hoppe et al Oncotarget 2016) have been linked with these resistance and E2-inducible apoptosis phenotypes. Little is known on their underlying genetic variability. Here we compare the mutational profiles of 5C and 2A clones with those of the estradiol stimulated growth sensitive MCF-7:WS8 and standard MCF-7 (ATCC) cells. Whole genome libraries were sequenced on the Illumina HiSeq platform (2x150bp reads). Alignments were manually inspected (bcftools mpileup) to avoid false negative variant calling in poorly (&lt;20x) covered regions. Loci with at least 10x coverage and absence of any variant reads were classified as wildtype. The coding genome positions defined as mutant or wildtype in all four cell types served as a basis to select candidate mutations for the verification of MCF-7 variants via comparison to the COSMIC database (http://cancer.sanger.ac.uk/cosmic) and identification of novel mutations by variant calling (GATK HaplotypeCaller). Putative protein effects of variants were predicted by the SnpEff tool. We verified 421 point mutations in MCF-7 (COSMIC) of which 203 mutations were lost in our models, with additional specific losses of 4, 4, and 18 mutations in WS8, 2A and 5C, respectively. In 5C cells new mutations affected 261 genes with 31 high impact mutations based on splice site alterations in 7 genes (i.e. CERS2, SEMA3A, TDRD7, ATP5H) and gain of stop codons in 24 genes (i.e. CACNA1S, NOTCH4, SUN1, JPH3, SERPINB2). Similarly, in 2A cells there were 12 high impact mutations among 122 affected genes (e.g. ARHGEF5, ARHGAP35, ARAP2). We will report on the integrative genomic analysis including larger structural variants (short indels and CNVs) towards the evolution of these models for a comprehensive understanding of the biology of E2-inducible apoptosis.

Citation Format: Reiner Hoppe, Siarhei Kandabarau, Ping Fan, V Craig Jordan, Hiltrud B. Brauch. Evolving genomes of breast cancer aromatase inhibitor resistance models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3432.

Profiles of miRNAs matched to biology in aromatase inhibitor resistant breast cancer

Aromatase inhibitor (AI) resistance during breast cancer treatment is mimicked by MCF-7:5C (5C) and MCF-7:2A (2A) cell lines that grow spontaneously. Survival signaling is reconfigured but cells are vulnerable to estradiol (E₂)-inducible apoptosis. These model systems have alterations of stress related pathways including the accumulation of endoplasmic reticulum, oxidative, and inflammatory stress that occur prior to E₂-induced apoptosis. We investigated miRNA expression profiles of 5C and 2A to characterize their AI resistance phenotypes. Affymetrix GeneChip miRNA2.0 arrays identified 184 miRNAs differentially expressed in 2A and 5C compared to E₂-free wild-type MCF-7:WS8. In 5C, 34 miRNAs of the DLK1-DIO3 locus and miR-31 were overexpressed, whereas miR-222 was low. TCGA data revealed poor and favorable overall survival for low miR-31 and miR-222 levels, respectively (HR=3.0, 95% CI:1.9-4.8; HR=0.3, 95% CI:0.1-0.6). Targets of deregulated miRNAs were identified using CLIP-confirmed TargetScan predictions. KEGG enrichment analyses for 5C- and 2A-specific target gene sets revealed pathways associated with cell proliferation including insulin, mTOR, and ErbB signaling as well as immune response and metabolism. Key genes overrepresented in 5C- and 2A-specific pathway interaction networks including EGFR, IGF1R and PIK3R1 had lower protein levels in 5C compared to 2A and were found to be differentially modulated by respective miRNA sets. Distinct up-regulated miRNAs from the DLK1-DIO3 locus may cause these attenuative effects as they are predicted to interact with corresponding 3′ untranslated regions. These new miRNA profiles become an important regulatory database to explore E₂-induced apoptotic mechanisms of clinical relevance for the treatment of resistant breast cancer.

Ptychographic analysis of the photorefractive effect in LiNbO3:Fe

We present light induced refractive index changes in iron doped lithium niobate detected with a novel microscopy technique called ptychography. This method determines the change of the refractive index together with the intensity distribution of the writing beam from a single scan with a reconstructed spatial resolution of 3 μm and a sensitivity of the refractive index change of 10^-5. We show that the light induced refractive index change is strongly connected to the intensity shape of the writing beam and that it shows the expected nonlocal behaviour. Applying the novel method to the investigation of the photorefractive effect offers an excellent opportunity to study this nonlocal response to the spatial distribution of the writing beam.

Global patterns of care in advanced stage mycosis fungoides/Sezary syndrome: a multicenter retrospective follow-up study from the Cutaneous Lymphoma International Consortium

BACKGROUND

Advanced-stage mycosis fungoides (MF)/Sézary syndrome (SS) patients are weighted by an unfavorable prognosis and share an unmet clinical need of effective treatments. International guidelines are available detailing treatment options for the different stages but without recommending treatments in any particular order due to lack of comparative trials. The aims of this second CLIC study were to retrospectively analyze the pattern of care worldwide for advanced-stage MF/SS patients, the distribution of treatments according to geographical areas (USA versus non-USA), and whether the heterogeneity of approaches has potential impact on survival.

PATIENTS AND METHODS

This study included 853 patients from 21 specialist centers (14 European, 4 USA, 1 each Australian, Brazilian, and Japanese).

RESULTS

Heterogeneity of treatment approaches was found, with up to 24 different modalities or combinations used as first-line and 36% of patients receiving four or more treatments. Stage IIB disease was most frequently treated by total-skin-electron-beam radiotherapy, bexarotene and gemcitabine; erythrodermic and SS patients by extracorporeal photochemotherapy, and stage IVA2 by polychemotherapy. Significant differences were found between USA and non-USA centers, with bexarotene, photopheresis and histone deacetylase inhibitors most frequently prescribed for first-line treatment in USA while phototherapy, interferon, chlorambucil and gemcitabine in non-USA centers. These differences did not significantly impact on survival. However, when considering death and therapy change as competing risk events and the impact of first treatment line on both events, both monochemotherapy (SHR = 2.07) and polychemotherapy (SHR = 1.69) showed elevated relative risks.

CONCLUSION

This large multicenter retrospective study shows that there exist a large treatment heterogeneity in advanced MF/SS and differences between USA and non-USA centers but these were not related to survival, while our data reveal that chemotherapy as first treatment is associated with a higher risk of death and/or change of therapy and thus other therapeutic options should be preferable as first treatment approach.

Abstract 474: Estrogen-responsive miRNAs as modulators of E2-induced apoptosis in AI-resistant breast cancer

Long-term estrogen deprivation with tamoxifen or aromatase inhibitors (AI) is the basic principle of endocrine treatment of ER-positive breast cancer. Acquired resistance is however a major obstacle in treatment success. Based on clinical observations and in vitro as well as animal in vivo experiments it has been suggested that tumor cell clones evolve over time and become vulnerable to E2-induced apoptosis, thereby potentially providing a promising second line treatment option. In vitro, this vulnerability is mimicked in the AI-resistant breast cancer models MCF-7:5C and MCF-7:2A, which during long-term E2-deprivation reconfigure their survival signaling including endoplasmic reticulum, oxidative and inflammatory stress related pathways. E2-stimulation of these cells initiates an unfolded protein response which in turn triggers apoptosis through the intrinsic and subsequently extrinsic pathway (Jordan VC 2015). Recently, we identified miRNA profiles matching the biology of AI resistance and vulnerability to E2-induced apoptosis (Hoppe R et al. 2016). Here we investigate the modulatory role of miRNAs in E2-induced apoptosis through the identification of their global expression changes in E2-stimulated 5C and 2A models compared to MCF-7:WS8 reference. Each cell line was treated with 10-9 M E2 or vehicle over a 72h time course (6, 12, 24, 72 h). miRNA profiles were generated using Affymetrix GeneChip miRNA2.0 arrays. At each time point relative miRNA expression changes (E2/control) were evaluated resulting in a total of 72 (5C), 104 (2A) and 94 (WS8) differentially expressed miRNAs (FC &gt; 1.5 or &lt; 1/1.5, Pt-test &lt; 0.05). Differential expression analyses between consecutive time points revealed 16 (5C), 43 (2A) and 27 (WS8) miRNAs (maximum absolute FC difference &gt; 1.5, PF-test &lt; 0.05). Differential area under the curve (dAUC) analyses at 6-72, 6-24, and 24-72 h mined the overall, early, and late-responding miRNAs of the different phenotypes (Ppermutation test &lt; 0.05). Representative early down-regulated miRNA candidates potentially modulating E2-induced apoptosis in 5C cells are miR-543 and miR-432 of the DLK1-DIO3 locus on Chr. 14q32.31. Late responding up-regulated miRNA candidates are miR-150* and miR-149* the low expression of which in tumor tissues registered in The Cancer Genome Atlas (miRNA-Seq v. 3.1.17.0) was associated with worse outcome in all PAM50 breast cancer subtypes and Lum B, respectively (HR = 2.1, 95% CI: 1.4-3.2; P = 0.00017; HR = 6.8, 95% CI: 1.5-3.0; P = 0.0036). We are currently in the process to subject respective miRNA sets to functional enrichment analyses (KEGG, GO) and to correlate E2-responsive miRNA candidates with respective transcriptome signatures. In summary, we will present miRNAs matching to the biological processes inherent to E2-induced apoptosis. These may serve as potential targets for the amplification of the apoptotic trigger upon E2-treatment.

Citation Format: Reiner Hoppe, Ping Fan, Stefan Winter, Florian Büttner, V. Craig Jordan, Hiltrud B. Brauch. Estrogen-responsive miRNAs as modulators of E2-induced apoptosis in AI-resistant breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 474. doi:10.1158/1538-7445.AM2017-474

SK4 channels modulate Ca2+ signalling and cell cycle progression in murine breast cancer

Oncogenic signalling via Ca²⁺‐activated K⁺ channels of intermediate conductance (SK4, also known as K_Ca3.1 or IK) has been implicated in different cancer entities including breast cancer. Yet, the role of endogenous SK4 channels for tumorigenesis is unclear. Herein, we generated SK4‐negative tumours by crossing SK4‐deficient (SK4 KO) mice to the polyoma middle T‐antigen (PyMT) and epidermal growth factor receptor 2 (cNeu) breast cancer models in which oncogene expression is driven by the retroviral promoter MMTV. Survival parameters and tumour progression were studied in cancer‐prone SK4 KO in comparison with wild‐type (WT) mice and in a syngeneic orthotopic mouse model following transplantation of SK4‐negative or WT tumour cells. SK4 activity was modulated by genetic or pharmacological means using the SK4 inhibitor TRAM‐34 in order to establish the role of breast tumour SK4 for cell growth, electrophysiological signalling, and [Ca²⁺]_i oscillations. Ablation of SK4 and TRAM‐34 treatment reduced the SK4‐generated current fraction, growth factor‐dependent Ca²⁺ entry, cell cycle progression and the proliferation rate of MMTV‐PyMT tumour cells. In vivo, PyMT oncogene‐driven tumorigenesis was only marginally affected by the global lack of SK4, whereas tumour progression was significantly delayed after orthotopic implantation of MMTV‐PyMT SK4 KO breast tumour cells. However, overall survival and progression‐free survival time in the MMTV‐cNeu mouse model were significantly extended in the absence of SK4. Collectively, our data from murine breast cancer models indicate that SK4 activity is crucial for cell cycle control. Thus, the modulation of this channel should be further investigated towards a potential improvement of existing antitumour strategies in human breast cancer.

Abstract 1073: Modulation of aromatase inhibitor resistance by miRNAs in breast cancer

The blockade of E2 signaling by either tamoxifen or aromatase inhibitors (AI) is the standard treatment of patients with estrogen receptor (ER)-positive breast cancer. However, acquired resistance to antiestrogen therapies remains a big clinical challenge. The in vitro breast cancer models MCF-7:5C and MCF-7:2A mimic clinical AI resistance in that they grow under tamoxifen, but can rapidly regress with E2 due to the reconfiguration of survival signaling known as E2-inducible apoptosis. This principle is currently explored in clinical trials in order to develop strategies to overcome endocrine resistance. To better understand the biology of AI resistance we previously ascertained a wide range of alterations of stress related pathways including the accumulation of endoplasmic reticulum stress, oxidative stress, and inflammatory stress that occur prior to E2-induced apoptosis (Ariazi et al. 2011; Fan et al. 2013, 2015; Sweeney et al. 2014). In this current work we investigated miRNA expression profiles of the 5C and 2A models (both compared to MCF-7:WS8 reference) in order to further elucidate the molecular scenario that characterizes the AI resistance phenotypes and their susceptibility to E2-induced apoptosis. Using Affymetrix GeneChip miRNA2.0 arrays we identified 184 miRNAs differentially expressed between 2A and 5C (FC &gt; 1.5 or &lt; 1/1.5, P &lt; 0.05). Of these, 30 miRNAs were specific for 2A, 99 for 5C, and 55 overlapped. Common miRNAs include upregulated oncogenic miRNAs of the miR-17-92 cluster (Chr. 13q31) and the paralogous 106a-363 cluster (Chr. X), as well as downregulated tumor suppressive miRNAs such as miR-342-5p. Thirty-four miRNAs that cluster at Chr. 14q32 were overexpressed in 5C cells and highly correlate with the downregulated miR-99a and miR-125b (Chr. 21q21). At the clinical level based on data from The Cancer Genome Atlas (miRNA-Seq v. 3.1.17.0), low expression of miR-31 was associated with poor (HR = 3.0, 95% CI: 1.9-4.8; Padj = 8.7E-5), and low miR-222 expression was associated with better outcome (HR = 0.3, 95% CI: 0.1-0.6; Padj. = 4.4E-3). As miR-31 expression is high and miR-222 expression is low in 5C cells compared to the MCF-7:WS8 reference, we suggest protective roles. Functions of miRNAs were deciphered via analyses of their predicted targets (CLIP-confirmed). Using KEGG and GO databases functional enrichment analyses of 5C and 2A specific miRNA sets revealed pathways associated with cell proliferation for both models including insulin, mTOR, and ErbB signaling as well as immune response and metabolism associated pathways. While the 2A specific miRNA set revealed additional metabolic pathways, the 5C specific miRNA set points to pathways involved in apoptosis. Thus, we confirmed the biological processes inherent to AI resistance and provide critical evidence for miRNA profiles as an important regulatory principle in these AI resistance models.

Citation Format: Reiner Hoppe, Ping Fan, Florian Büttner, Stefan Winter, Heather Cunliffe, V. Craig Jordan, Hiltrud B. Brauch. Modulation of aromatase inhibitor resistance by miRNAs in breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1073.

Abstract 2030: The role of genetic variation in calcium-activated potassium channels in breast cancer patients treated with tamoxifen

Potassium channels control membrane voltage and are essential for cell proliferation. Abnormal regulation and/or expression of these channels have been reported in cancer and result in dysregulated cell cycle progression, cell proliferation and migration. In breast cancer, clinical correlations of potassium channels have been associated with brain metastases, high stage, high grade, high proliferation, nodal status and poor prognosis. Interestingly, they have been associated with increased estrogen receptor (ER) expression. The selective ER modulator, tamoxifen, blocks estrogen from binding to the ER and is commonly used to treat patients with ER-positive breast cancer. However, up to 33% of patients treated with tamoxifen relapse or dies at 15 years of follow up. Both estrogen and tamoxifen have been demonstrated to activate potassium channels which then cause an increase in cell proliferation. In preliminary animal in vivo studies, we observed a better breast cancer prognosis in those with a knockout in potassium channel genes. Therefore, any alterations in the potassium channels may help to explain why patients treated with tamoxifen fail therapy. We hypothesized that genetic variation in potassium channels may affect breast cancer risk as well as tamoxifen treatment outcome. Genotyping was conducted on 45,290 breast cancer patients and 41,880 controls of European ancestry from 41 studies with the custom Illumina Infinium array (iCOGS). More than 200,000 SNPs were genotyped with over 11 million SNPs estimated using genotype imputation with SHAPEIT and IMPUTEv2 and the 1000 Genomes Project March 2012 release as the reference panel (Michailidou et al. Nature Genetics 2015). Variants from 13 potassium channels including KCNMA1, KCNMB1-4, KCNN1-4, LRRC26, LRRC38, LRRC52 and LRRC55 were analyzed. Of these, 3 imputed SNPs from KCNN4 have shown decreased breast cancer risk with GWAS significance (rs12463319, rs12609846, rs1685191; OR 0.94, P &lt; 1.0E-08). In particular, these SNPs were significant in ER-positive breast cancer (OR 0.93, P &lt; 1.0E-09), but was not observed in ER-negative patients (P &gt; 0.05). These findings encouraged us to now further investigate the outcomes of patients with ER-positive breast cancer treated with tamoxifen. Survival data for 49,751 patients with a median follow-up of 8 years has been completed and released in November 2015. Of these, 32,571 were ER-positive and 10,383 have been treated with tamoxifen. Current efforts are underway in order to determine the effects of genetic variations in potassium channels on the survival of patients treated with tamoxifen. Our work will provide a better understanding of the potential clinical relevance of potassium channels in tamoxifen treatment in breast cancer.

Citation Format: Wing-Yee Lo, Corinna Mohr, Friederike Steudel, Marjanka Schmidt, Douglas Easton, Reiner Hoppe, Werner Schroth, Peter Ruth, Robert Lukowski, Hiltrud Brauch, in collaboration with the Breast Cancer Association Consortium. The role of genetic variation in calcium-activated potassium channels in breast cancer patients treated with tamoxifen. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2030.

Abstract 5485: Coactivator PPARGC1B Ala203Pro polymorphism is linked with estrogen-related receptor function and breast cancer outcome

Background

The estrogen-related receptors (ERRs) are orphan nuclear receptors (NRs) with high sequence similarity to the estrogen receptor (ER). Peroxisome proliferator-activated receptor gamma coactivator-1 beta (PERC) specifically activates ER and ERRs, thus providing a link with breast cancer growth. Here we functionally characterized a non-synonymous PERC polymorphism, rs7732671, previously associated with increased risk for familial breast cancer, and tested its clinical relevance for breast cancer progression.

Methods

A mammalian two-hybrid assay was used to identify protein interactions using full-length and truncated NR (ERα, ERRα, ERRγ) and PERC. PERC rs7732671 variant allele (649G&gt;C_A203P) was created by site-directed mutagenesis. Expression of genes involved in cell glycolysis and/or direct ERR targets Eno1, PKM, LDHA and IDH3A, were analyzed in breast cancer cells and in breast tumors (N = 84). Cell supernatants were quantitated for lactate formation using liquid chromatography coupled mass spectrometry. PERC rs7732671 was genotyped in 896 postmenopausal early breast cancer patients treated with adjuvant tamoxifen and clinical outcome was analyzed using Kaplan-Meier and Cox regression analyses.

Results

Truncated PERC (aa129-426) containing the 649G&gt;C_A203P variant did not interact with ERα, but ERRα and ERRγ ligand-binding domains were activated. The PERC129-426-C allele enhanced ERRα activity by 21% and ERRγ by 67%, compared to the PERC129-426-G major allele (P&lt;0.005). Expression of ERR downstream genes Eno1, LDHA, IDH3A and lactate concentrations were increased in MCF7 and MDA-MB-231 overexpressing PERC-C as compared to PERC-G. In breast tumors, glycolytic or ERR target gene expression was increased in patients carrying the PERC-C allele. Patients carrying the PERC-C showed higher distant recurrence rates compared with patients of the G/G genotype (P = 0.01), which was confirmed in Cox regression adjusted to tumor size, nodal status, and grade (Hazard Ratio 2.06; 95% CI 1.26-3.38, P = 0.005 per C allele).

Conclusion

PERC rs7732671 variant 649C_203P enhances ERRα and ERRγ signaling independent of ER. Higher lactate concentrations in cells and increased ERR target gene expression in vitro and in patients with the PERC-C allele point to a modulation of aerobic glycolysis. The ERR/PERC axis is possibly linked with disease progression in breast cancer.

Citation Format: Pilar H. Saladores, Reiner Hoppe, Wing-Yee Lo, Sibylle Cocciardi, Ute Hofmann, Ute Hamann, Peter Fasching, Marcus Schmidt, Hiltrud Brauch, Werner Schroth. Coactivator PPARGC1B Ala203Pro polymorphism is linked with estrogen-related receptor function and breast cancer outcome. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5485. doi:10.1158/1538-7445.AM2015-5485

Abstract 5483: CYP19A1 genetic variation is a potential predictor of outcome in ER-positive postmenopausal early breast cancer patients treated with tamoxifen

Tamoxifen is a selective estrogen receptor modulator which blocks estrogen from binding to the estrogen receptor (ER). Although estrogens are natural hormones vital for development, they are also critical growth factors responsible for cell proliferation and DNA synthesis, thus enhancing the growth of estrogen-responsive breast tumors. With breast cancer being the most frequent cancer in women, the carcinogenic effects of estrogen are mediated by ER which is expressed in approximately 75% of all tumors. Hence tamoxifen is commonly used to treat patients with ER-positive breast cancer. Our group has a long standing interest in the investigation of potential tamoxifen outcome predictors as up to 33% of treated patients relapse or dies at 15 years of follow up. Therefore it is crucial to determine which patient will benefit from tamoxifen or not. In a pilot study of 915 patients, we previously identified a single nucleotide polymorphism (SNP) at the aromatase gene (CYP19A1) which could potentially predict the outcome of postmenopausal patients treated with tamoxifen. Aromatase is a key enzyme in the estrogen biosynthesis pathway and in postmenopausal women, estrogen levels are low with the aromatase being responsible for estrogen synthesis from adipose tissue following the cessation of ovarian function. Therefore any alterations in aromatase function may affect the inhibitory capacity of tamoxifen for estrogen at the ER, resulting in variation of outcome in patients treated with tamoxifen. We hypothesized that genetic variation in CYP19A1 may influence aromatase expression and function, thus affecting the outcome of ER-positive postmenopausal early breast cancer patients treated with tamoxifen. Genotyping was conducted on 55,540 breast cancer patients from 50 studies with the custom Illumina Infinium array (iCOGS) by the Breast Cancer Association Consortium. More than 200,000 SNPs were genotyped of which 89 SNPs are located in the CYP19A1 genomic region. We included patients that are female with European ancestry, available follow up and vital status, invasive breast tumor, ascertained for their first tumor, stage I-III disease, postmenopausal, ER-positive, right truncation at 15 years of follow up, left censoring for study entry and those treated with tamoxifen. Furthermore, studies with less than 10 events for relapse or death were excluded leaving a total of 1313 patients for outcome analyses with distant metastasis-free survival as the endpoint. We identified rs7172156 being associated with poor outcome of which carriers of the minor A allele had a higher risk of distant metastasis or death (P = 0.007). Multivariate Cox regression stratified by study and adjusted for age, node status, tumor size and grade confirmed this observation (HR = 1.30, 95% CI 1.00-1.68, P = 0.049). Our data suggest that rs7172156 could be clinically relevant as a tamoxifen outcome predictor in early breast cancer.

Citation Format: Wing-Yee Lo, Werner Schroth, Reiner Hoppe, Marjanka Schmidt, Montserrat Garcia-Closas, Paul Pharaoh, Per Hall, Douglas Easton, Peter Fasching, Hiltrud Brauch, in collaboration with the Breast Cancer Association Consortium. CYP19A1 genetic variation is a potential predictor of outcome in ER-positive postmenopausal early breast cancer patients treated with tamoxifen. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5483. doi:10.1158/1538-7445.AM2015-5483

Chimerism, graft survival, and withdrawal of immunosuppressive drugs in HLA matched and mismatched patients after living donor kidney and hematopoietic cell transplantation

Thirty-eight HLA matched and mismatched patients given combined living donor kidney and enriched CD34(+) hematopoietic cell transplants were enrolled in tolerance protocols using posttransplant conditioning with total lymphoid irradiation and anti-thymocyte globulin. Persistent chimerism for at least 6 months was associated with successful complete withdrawal of immunosuppressive drugs in 16 of 22 matched patients without rejection episodes or kidney disease recurrence with up to 5 years follow up thereafter. One patient is in the midst of withdrawal and five are on maintenance drugs. Persistent mixed chimerism was achieved in some haplotype matched patients for at least 12 months by increasing the dose of T cells and CD34(+) cells infused as compared to matched recipients in a dose escalation study. Success of drug withdrawal in chimeric mismatched patients remains to be determined. None of the 38 patients had kidney graft loss or graft versus host disease with up to 14 years of observation. In conclusion, complete immunosuppressive drug withdrawal could be achieved thus far with the tolerance induction regimen in HLA matched patients with uniform long-term graft survival in all patients.