Abstract P3-07-20: A validated test for neoadjuvant clinical response to endocrine therapy in breast cancer that estimates accurately recurrence-free and overall survival

Background: Aromatase inhibitors (AIs) have an established role in the treatment of estrogen receptor alpha positive post-menopausal breast cancer. Recently we have developed and validated a microarray-derived 4-gene test (Edinburgh EndoResponse4) to predict response to AIs in the neoadjuvant setting. We have also demonstrated the translational potential of this test in predicting accurately clinical response when mRNA is measured for these genes by polymerase chain reaction (PCR) or the gene protein is measured by immunohistochemistry (IHC). There is a major clinical need for biomarkers to predict which patients are likely to recur on adjuvant endocrine therapy so alternative or additional treatments can be provided to reduce recurrence and improve outcome. The aim of this study was to determine if Endoresponse4 and IHC of these gene proteins could do this.

Methods: The original microarray assay used pre- and on-treatment (14-days) biopsies from 73 post-menopausal women with ER-rich breast cancer receiving 3 months of neoadjuvant letrozole prior to surgery with 10 years follow-up after adjuvant letrozole. Matched formalin-fixed paraffin embedded (FFPE) tissue sections from 42 of these patients were used for IHC and antibodies were optimised against 3 of the 4 proteins (where validated antibodies were available) using Envision technology. The ability of our test to estimate recurrence-free (RFS) and breast cancer specific overall survival (OS) using both PCR and IHC was then tested in a unique validation cohort of 140 post-menopausal women with ER-rich breast cancer treated with 2 weeks of neoadjuvant letrozole or anastrozole prior to surgery followed by adjuvant endocrine therapy and 10 years of follow up..

Results: Within our training cohort (n=73) using Kaplan-Meier analysis our 4-gene test predicted neoadjuvant clinical response and demonstrated a significant association with both RFS (P=0.029) and OS (P=0.009). This approach predicts outcomes within 2-weeks rather than 4-months of treatment required in other studies such as P024. Using IHC in the training cohort (n=42), two gene markers in combination (IL6ST at diagnosis and MCM4 after 2-weeks treatment) predicted both RFS (P=0.017) and OS (P=0.009) with great accuracy. The 140 patient group is being analysed and the findings are so far are consistent with the initial training cohort and indicate a significant association with outcomes.

Conclusion:

• A 4 gene model with clinical potential has been developed and validated to predict response to neoadjuvant aromatase inhibitors.

• This 4 gene model predicts for response and also predicts relapse free and overall survival.

• Proteins encoded by 2 of these 4 genes measured by IHC in an initial test set of 42 patients predict accurately both EFS and OS

• A validation cohort (n=140) with over 10-years of follow-up will be available at SABCS 2015 to determine if this 2 biomarker test can predict outcome on adjuvant endocrine therapy.

Citation Format: Turnbull AK, Arthur LM, Webber V, Thomas J, Uddin S, Webb H, Dunbier A, Dowsett M, Renshaw L, Sims AH, Dixon JM. A validated test for neoadjuvant clinical response to endocrine therapy in breast cancer that estimates accurately recurrence-free and overall survival. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-20.

Abstract PD3-2: Accurate and robust prediction of clinical response to aromatase inhibitors by two weeks of neoadjuvant breast cancer treatment

Background: Aromatase inhibitors (AIs) have an established role in the treatment of estrogen receptor alpha positive (ER+) post-menopausal breast cancer. Response rates are 50-70% in the neoadjuvant setting and lower in advanced disease. There is a need to identify biomarkers to predict response that outperform those currently available, to be able to offer more stratified treatments and improved patient care.

Methods: Pre- and on-treatment (at 14 days and 3-months) biopsies were obtained from 89 post-menopausal women with ER+ breast cancer receiving 3 months of neoadjuvant Letrozole. Illumina Beadarray gene expression data (n = 34) were combined with Affymetrix GeneChip data (n = 55) and cross-platform integration approaches developed as part of this study were implemented to combine data. Dynamic clinical response was assessed for each patient using periodic 3D ultrasound measurements performed during treatment. A gene classifier was developed from pre and 14 day gene array expression data to predict response. An independent series from the Royal Marsden was used to validate the classifier.

Results: Response to endocrine therapy in the neoadjuvant setting based on the expression of 4 genes has been developed. The classifier comprises baseline expression of an immune signalling gene and an apoptosis related gene, together with 14 day expression of two proliferation genes. Early on-treatment gene changes in combination with pre-treatment gene expression significantly improve predictive power compared to pre-treatment gene expression alone. The classifier had a 96% accuracy in a training dataset (n = 73) and 91% accuracy in an independent validation dataset (n = 44) dataset.

Table 1 AccuracySensitivitySpecificityPPVNPVAUC (ROC)Training0.960.890.980.890.960.96Validation0.910.80.970.920.9NASensitivity and specificity of model in training and validation datasets

Expression of the pre-treatment immune signalling gene alone predicted for response with 85% and 82% accuracy in training and validation datasets respectively. Higher pre-treatment levels of this gene were associated with a significantly better 1 year progression free survival (PFS) (P = 0.0001). In a larger series of patients treated with neoadjuvant Letrozole (n = 129) higher expression of this gene alone was associated with a significantly improved 10 year RFS (p = 0.0359). In a separate tamoxifen treated cohort (n = 212) higher expression of this gene at diagnosis was associated with a significantly improved 5 year (p = 0.0015) and 10 year (p = 0.04) recurrence free survival (RFS).

Conclusion:

• A 4 gene classifier has been developed and validated to predict response to neoadjuvant Letrozole.

• One of the genes identified is a significant predictor in independent data sets of long term RFS in endocrine treated patients.

• This new classifier has the potential to predict accurately the benefit of endocrine therapy and has huge potential clinical value.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr PD3-2.

An in vitro model showing adaptation to long-term oestrogen deprivation highlights the clinical potential for targeting kinase pathways in combination with aromatase inhibition

Aromatase inhibitors (AI) have improved the treatment of oestrogen receptor positive (ER+) breast cancer. Despite the efficacy of these agents over 40% of patients relapse with endocrine resistant disease. Here we describe an in vitro model of acquired resistance to long-term oestrogen deprivation (LTED). The LTED cells retain expression of the ER and appear hypersensitive to oestrogen as a result of altered kinase activity. Furthermore analysis of temporal changes in gene expression during the acquisition of resistance highlight growth factor receptor pathways as key mediators of this adaptive process.

A Breast Cancer-Associated SNP Adjacent to ESR1 Correlates with Oestrogen Receptor-α (ERα) Level in Invasive Breast Tumours

Aim: To identify whether breast cancer-associated SNP rs2046210 is associated with ERα level in invasive breast tumours.BackgroundA recent genome-wide association study identified SNP rs2046210 at 6q25.1 as having a strong association with breast cancer risk1. The SNP is located 29kb upstream of the first untranslated exon of ESR1 and 180kb upstream of the transcription start site2. Rs2046210 is not in linkage disequilibrium (LD) with two of the most widely studied polymorphisms in ESR1. We test here the hypothesis that rs2046210 may be associated with altered ESR1 expression.MethodsPatients with both leukocyte DNA and invasive breast tumour paraffin blocks available were identified from two of our ongoing tissue collections: Femara Anastrazole Clinical Evaluation (FACE) and the British Breast Cancer (BBC) study. Germline DNA was extracted from bloods using the QIAamp DNA Blood Mini Kit. PCR was performed with primers spanning the SNP site, with a single basepair mismatch in the reverse sequence to generate an HhaI restriction site in the presence of the C allele. PCR product was run on a 3% agarose gel to confirm presence of a single 120bp band. Restriction digest with HhaI was then performed and products run on a 4% Metaphor agarose gel. Genotype was assigned as follows: 97bp band only = wild-type (C/C); 97bp and 120bp band = heterozygote (C/T); 120bp band only = variant (T/T). From corresponding invasive breast tumour, ERα was assessed on 4μm whole sections using clone 6F11 (Vector Labs) and quantified by H-score. Mean H-scores (left and right invasive breast tumours) were used for the BBC group. ERα- samples (H-score≤1.0) were excluded. Analysis was by ANOVA using non-parametric bias-corrected and accelerated 95% bootstrap confidence intervals (2000 replications), with genotype fitted as a score and study as a stratifying co-variate.ResultsH-score (mean) by genotypeStudyWild-typeHeterozygoteVariantFACE (n=280)171.8180.9184.9BBC (n=46)180.0178.9194.1Fitted mean172.6179.7186.7(% samples)(45)(44)(11) Minor allele frequency was 33%, which is similar to the 38% previously reported in patients of European ancestry1. Within FACE, increased ERα was seen with presence of variant SNP. In the BBC group, variant SNP patients had higher ERα than both wild-type and heterozygote. Overall, there was a significant difference in ERα score per genotype group of 7.05, (95% CI 0.7-13.5, p=0.035). This was circa 4% difference in H-score per variant allele.ConclusionThe variant genotype of SNP rs2046210 is associated with increased ERα expression. While the increase contributed by the variant allele is relatively modest, this may partly explain why the SNP is associated with increased breast cancer risk. Similar studies should be conducted in normal breast tissue.1Zheng et al. (2009) Nat. Gen. 41(3): 324-3282Kos et al. (2001) Mol. Endocrinol. 15: 2057-2063

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4138.

Aromatase Inhibitors Reduce the Expression of a Hypoxia Metagene in Oestrogen Receptor Positive Breast Cancer in Postmenopausal Women

Aims: To (1) define the effect of oestrogen deprivation on genes related to hypoxia in oestrogen receptor positive (ER+) breast cancer and (2) identify any link between hypoxia and proliferation.Background: The majority of breast cancer patients are postmenopausal women with ER+ tumours and at some point receive an aromatase inhibitor (AI) as part of their treatment. Hypoxia and proliferation are important factors in the progression of ER+ tumours. Proliferation is profoundly reduced in most ER+ cancers after treatment with AIs[1], however little is known on the effects of AIs on hypoxia.Materials and methods: 81 pre- and 2-week post-treatment core-cut tumor biopsies were obtained from postmenopausal women with ER+ breast cancer who received single agent neoadjuvant anastrozole (AI)[2], and from 20 of these patients after 16 weeks of AI treatment. RNA was extracted and analysed on Illumina 48K microarrays. A hypoxia metagene (MG) was developed by identification of genes whose expression clustered with the expression of classical hypoxia-regulated genes[3]. Genes associated with proliferation were removed from the MG. A proliferation MG was derived by selecting the intersection of proliferation clusters from three public breast cancer datasets.Results: Spearman correlations revealed a strong relationship between the hypoxia and proliferation MGs prior to AI treatment (r =0.61, p<10-3), and persisted after 2 weeks (r =0.77, p<10-3) and after 16 weeks of treatment (r=0.72, p =0.002). Baseline expression of the hypoxia MG was (1) positively correlated with 2-week Ki67 (Spearman r =0.37, p =0.002), (2) showed a trend for a positive correlation with poor 2-week Ki67 change (Spearman r=0.22, p =0.06) and with poor reduction in the mean expression of four classical oestrogen dependant genes (TFF1/pS2, GREB1, PDZK1 and PGR) known as AVERG[4] (Spearman r =0.22, p=0.06). Expression of the hypoxia MG was significantly down-regulated after 2 weeks of oestrogen deprivation using AI treatment (p<10-3). The 2-week change in hypoxia showed a positive correlation with the 2-week change in proliferation (Spearman r=0.58, p<10-3), and with the 2-week change in Ki67 (Spearman r=0.35, p=0.005).Conclusions: The expression of a hypoxia MG decreases after oestrogen deprivation. The hypoxia MG is strongly associated with proliferation prior to and after AI treatment. The data are consistent with hypoxia being a secondary effect of proliferation in ER+ breast cancer and could contribute in understanding the need to combine anti-proliferative drugs with anti-angiogenic agents for these patients. There may be a weak effect of hypoxia on de-novo resistance to AIs.1. Dowsett M, et al., Clin Cancer Res 2006; 12(3): p.1024-302. Smith, I.E, et al., J Clin Oncol 2007; 25(25): p.3816-223. Winter, S.C, et al., Cancer Res 2007; 67(7): p.3441-94. Dunbier, A.K, et al., Cancer Res 2009; 69(Suppl.), 78sSupported by The Mary-Jean Mitchell Green Foundation and Breakthrough Breast Cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 408.

Hereditary diffuse gastric cancer

Hereditary diffuse gastric cancer (HDGC) is a cancer predisposition syndrome caused by germline mutation of the gene for the cell-to-cell adhesion protein E-cadherin. The syndrome is dominated by predisposition to the histologically diffuse, poorly differentiated form of gastric cancer. It is not associated with intestinal-type gastric cancer, but families may have an elevated risk of lobular breast cancer. Here, we review the identified families, mutations, and proposed mechanisms by which E-cadherin loss promotes tumorigenesis.