Abstract P5-04-27: Investigating the incidence of ESR1 gene amplification in breast cancers resistant to multiple endocrine agents

Background: Around 70% of all breast cancers (BCs) are estrogen receptor positive (ER+), but some do not respond to endocrine therapy (ET) and many eventually develop resistance. ESR amplification (ESRA) linked to an increase in ESR1 gene expression is known to occur in some cancers that are endocrine resistant. However, the incidence of ESRA has been the object of debate and its clinical significance remains unclear. This study aimed to investigate the incidence of ESRA in BCs resistant to multiple sequential ETs and optimise a fluorescence in-situ hybridisation (FISH) methodology to robustly detect ESRA.

Methods: Two unique cohorts have been studied:

(A) 20 post-menopausal women with ER+ BC with acquired resistance to letrozole, subsequently treated with up to 4 different lines of ET. Serial RNA and DNA from 3-5 cancer samples per patient (58 samples from 20 patients) were analysed by Ribo0-RNAseq and DNA exome sequencing;

(B) 18 post-menopausal women who developed ER+ BC recurrences on 1st line adjuvant letrozole, then on 2nd line tamoxifen and subsequently on 3rd line exemestane. Tissues were collected at the time of each surgery.

We have optimised a FISH method to assess ESRA in these tissues.

Results: In cohort A, 6/20 patients developed ESR1 gene amplification (ESRA) at some point during treatment. In 5 of these cases, ESRA was only found while on 2nd or 3rd line exemestane but was not present on acquired resistance to previous letrozole or tamoxifen. 1 patient had ESRA at the time of first recurrence on letrozole.

The FISH method showed concordance with the genomic analysis. This suggests that ESRA may be associated with BCs that are treated with and then become resistant to exemestane.

ESRA is also evident in samples from Cohort B, which includes 18 exemestane resistant cases. The complete analysis is ongoing.

Conclusions:

· ESRA can be seen in ER+ recurrent BCs.

· ESRA may be associated with BCs treated with 2nd or 3rd line exemestane.

· The frequency of ESRA in endocrine and exemestane resistance can now be ascertained using an optimised FISH-based method, which is more cost-effective than alternative genomic and biochemical methods.

Citation Format: Turnbull AK, Martinez-Perez C, Mok S, Tanioka M, Fernando A, Renshaw L, Keys J, Wheless A, Garrett A, Parker J, He X, Sims AH, Carey LA, Perou CM, Dixon JM. Investigating the incidence of ESR1 gene amplification in breast cancers resistant to multiple endocrine agents [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-27.

Abstract P5-04-14: Tracking ESR1 mutation clonal evolution in breast cancer using in situ mutation detection

Background: Approximately 70% of breast cancers (BCs) are estrogen receptor positive (ER+). Not all ER+ cancers respond to endocrine therapy (ET) and many eventually develop acquired resistance. Next-generation sequencing (NGS) has shown ESR1 mutations (ESRMs) are present in 10-50% of recurrent/metastatic cancers treated with aromatase inhibitors (AIs). Many of these mutations are located in the ligand-binding domain of ER, so they can lead to constitutive activation. This suggests ESRMs are a major mechanism of acquired resistance to endocrine therapy (ET) and numerous studies have shown a link between ESRMs and reduced sensitivity to 2nd line ET. The aim of this project was to investigate the incidence and clonal evolution of common ESRMs in BCs resistant to multiple sequential ETs using NGS, as well as novel PCR and in situ mutation detection methods.

Methods: We have optimised an allele-specific real-time PCR (rtPCR) assay and an in situ mutation detection method (ER-ISMD) for the assessment of ESRMs. Both have been designed to identify a missense gain-of-function D538G mutation with a single nucleotide-resolution in formalin-fixed paraffin-embedded (FFPE) BC tissues.

Two unique cohorts have been studied:

(A) 20 post-menopausal women (PMW) with ER+ BC who acquired resistance to letrozole and were treated with up to 4 subsequent lines of ET. Serial RNA and DNA from 3-5 cancer samples per patient (58 samples from 20 patients) were analysed by Ribo0-RNAseq, DNA exome sequencing, rtPCR and ER-ISMD.

(B) 150 PMW with ER+ BC who developed local (n=79), lymph node (n=59) or distant (n=12) recurrences on 1st line adjuvant letrozole, anastrozole or tamoxifen. Of these, 48 patients developed subsequent recurrences on 2nd line ET. Tissue samples from each recurrence and matched primary BC were collected.

Results: In cohort A, 5/20 patients (20%) had expansion of a D538G ESR1 mutation clone at time of resistance 1st line ET (3:letrozole, 1:anastrozole, 1:tamoxifen). The mutant allele frequency (MAF) increased further in the 4 BCs treated with 2nd line ET (2:tamoxifen, 2:exemestane) and further still in the 1 BC who received 3rd line exemestane. 0/6 patients with ESRM responded to subsequent ET. Allele-specific rtPCR and ER-ISMD have been used to validate these findings and also identified low frequency ESRM clones in the sequential samples prior to the development of clinical resistance, that were not reported by NGS. Both methods have also been applied to screen tissues from patients in cohort B, where ESRMs have also been identified in recurrent samples. Complete analysis is currently ongoing.

Conclusions:

· ESRMs develop and expand in some BCs as a mechanism for acquired resistance to ET and are associated with a lack of response to subsequent standard ETs.

· Allele-specific rtPCR can detect ESRMs and is more cost-effective and easier to use than NGS for ER mutation analysis.

· Some ESRMs predate clinical resistance.

· ER-ISMD is a novel approach that allows for identification and visualisation of the distribution of mutant clones in morphologically intact FFPE tissue.

· ER-ISMD has the potential to become a clinically useful tool to help direct the use of 2nd line ET in routine care.

Citation Format: Martinez-Perez C, Turnbull AK, Tanioka M, Fernando A, Renshaw L, Keys J, Wheless A, Garrett A, Parker J, He X, Sims AH, Carey LA, Perou CM, Dixon JM. Tracking ESR1 mutation clonal evolution in breast cancer using in situ mutation detection [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-14.

Abstract P5-18-03: A predictive model for local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS)

Background: Ductal carcinoma in situ (DCIS) is a heterogeneous precursor, non-invasive breast lesion. There is a lack of specific DCIS molecular predictors of in breast tumour recurrence (IBTR) or progression to invasive breast cancer (IBC) after breast conserving surgery (BCS) +/- radiotherapy (RT). The aim of this was to identify novel biomarkers and combine these with clinical parameters to develop a new model to predict IBTR in patients treated by BCS for DCIS.

Methods: A single institution DCIS biomarker discovery study included a case-control matched series of 180 patients (median age 61, range 35-94) treated at the Edinburgh Breast Unit between 2000 and 2010:

· 88 patients with low/intermediate grade DCIS treated with BCS alone; 18 recurred within 10 years.

· 92 patients with high grade DCIS treated by BCS and RT; 22 recurred within 10 years.

Median follow-up was 7.4 years. RNA was extracted from DCIS lesions and whole-genome transcriptomics analysis was performed using Lexogen QuantSeq. Predictive models were generated based upon the most informative genes. Independent validation cohorts are also available and are currently being used for validation.

Results: The models developed predict risk of IBTR in patients with low or intermediate grade DCIS treated with BCS alone and high grade DCIS treated with DCIS plus RT. The models were found to be independent of grade and stratify patients into binary groups of high and low risk of recurrence.

A promising model was developed based on the expression of 5 genes combined with tumour diameter ≤15mm or >15mm.

• In low/intermediate grade DCIS expression levels of a solute carrier family gene, kinetochore associated gene and an immunomodulatory gene are predictive of recurrence.

• In high grade DCIS an additional solute carrier and a glutathione S-transferase related gene are predictive of recurrence.

• In the training sets the models have 96% (high-grade) and 92% (low/intermediate grade) accuracy of prediction of subsequent recurrence and estimates of IBTR-free survival were highly significant in both groups (<0.0001). Validation of the model by RT-PCR and immunohistochemistry is underway in both the training cohort and an independent validation cohort.

Conclusions:

· Promising models to predict risk of IBTR in patients treated for DCIS have been developed.

· Novel biomarkers that predict recurrence have been identified using new technologies that may have clinical potential.

· Independent validation is currently underway.

Citation Format: Martinez-Perez C, Turnbull AK, Fernando A, Ekatah GE, Arthur LM, Cartlidge CW, Johns N, Sims AH, Thomas JS, Dixon JM. A predictive model for local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-18-03.

Abstract P3-11-13: On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer

Purpose: Neo-Adjuvant chemotherapy treatment is increasingly being used in breast cancer to preoperatively shrink tumour volumes and facilitate surgical plans. These datasets however, are still scarce, making it difficult to assess the relative value of multiple time point biopsies compared to diagnostic only sampling. This study aims to identify sequential samplings intrinsic value.

Method: A total of 97 samples from a cohort of 50 neoadjuvant chemotherapy treated primary breast cancer patients (aged 29-76 at diagnosis, Allred status 47:53% +/-, Her2 status 80:20% +/-, mixed grade and menopausal status) taken pre- treatment, at 2 weeks on-treatment, mid chemotherapy and at resection were sequenced with Ion Ampliseq transcriptome yielding expression values for 12,635 genes. Differential expression analysis was performed across response groups (16 Responders, 34 Non-Responders) as defined by Pathological Complete Response and over treatment time to identify significantly differentially expressed genes, pathways and markers indicative of response status.

Results: An on-treatment marker for response was identified (AAGAB), which resulted in a testing accuracy of 100% and a validation accuracy of 78% in the I-SPY 1 Trial. AAGAB was predictive of long term survival (p = 0.048 testing, p = 0.031 validation) in both chemotherapy cohorts at the same expression level as defined for treatment response. The single gene on-treatment biomarker, AAGAB proves more performant than established prognostic tests, Mammaprint (Edinburgh NEO trial, pre-treatment 61%, on-treatment 63%. I-SPY 1 trial, pre-treatment 60%, on-treatment 66%) and Pam50 RORS (neo trial pre-treatment 50%, on treatment 58%, Magbanua trial pre-treatment 56%, on-treatment 64%)

Conclusion: Changes in gene expression of on-treatment chemotherapy breast cancer resulted in the identification of a novel gene marker that was as effective in predicting prognostic status as established prognostic tests. These results support the use of on-treatment testing in breast cancer to improve the accuracy of tumour response prediction.

Citation Format: Bownes RJ, Turnbull AK, Cameron D, Sims AH, Oikonomidou O. On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-11-13.

Abstract P5-04-03: Molecular characterisation of ER+ breast cancer dormancy and acquired resistance using a clinical model: Potential involvement of epigenetic regulation

Background: The risk of recurrence for oestrogen receptor positive (ER+) breast cancer patients treated with 5 years of adjuvant endocrine therapy persists for many years or even decades following surgery and apparently successful adjuvant therapy. This period of dormancy and acquired resistance is inherently difficult to investigate. Therefore, previous efforts have been limited to in vitro or in vivo approaches. In this study sequential tumour samples from patients receiving extended neoadjuvant endocrine treatment were characterised as a novel clinical model of ER+ breast cancer dormancy and acquired resistance.

Methods: Consecutive tumour samples from 62 patients undergoing extended (4-45 months) neoadjuvant letrozole therapy were subjected to transcriptomic and proteomic analysis, representing pre- (before treatment), early-on (13-120 days) and long-term (>120 days) neoadjuvant letrozole treatment. Patients with at least a 40% initial reduction in tumour size by 4 months of treatment were included. Of these, 42 patients with no subsequent progression were classified as “dormant”, and the remaining 20 patients as “acquired resistant”. Expression analysis was performed by using Illumina BeadChips. R and BioConductor packages were used for analysis. Differentially expressed genes were determined by using paired Rank Products (FDR, 5%).

Results: Multidimensional scaling using most variant 500 genes demonstrated that long-term treated dormant samples clustered separately from their matched pre- and early-on samples whereas long-term treated resistant samples were indistinguishable from their pre-treatment counterparts. Therapy-induced changes in resistant tumours were common features of treatment, rather than being specific to resistant phenotype. Comparative analysis of long-term treated dormant and resistant tumours highlighted changes in epigenetics pathways including DNA methylation and histone acetylation. DNA methylation marks 5-methylcytosine and 5-hydroxymethylcytosine were significantly reduced in resistant tumours compared to dormant tissues after extended letrozole treatment. Decrease in 5-hydroxymethylcytosine were significant early-on.

Conclusions: This is the first patient-matched gene expression study investigating long-term aromatase inhibitor-induced dormancy and acquired resistance in breast cancer. Dormant tumors exhibit distinct molecular changes under extended treatment whereas acquired resistant tumors are more similar to matched diagnostic samples supporting the molecular concordance between primary tumors and metastases. Global loss of DNA methylation was observed in resistant tumours under extended treatment which can be predicted within first 4 months of therapy. Epigenetic alterations may lead to escape from dormancy and drive acquired resistance in a subset of patients supporting a potential role for therapy targeted at these epigenetic alterations in the management of endocrine resistant breast cancer.

Funding: This work was supported by Marie Skłodowska-Curie Individual Fellowship [H2020-MSCA-IF, 658170] and Welcome Trust Institutional Fund (ISSF3) to CS and AHS, Breast Cancer Now to AHS.

Citation Format: Selli C, Turnbull AK, Pearce D, Fernando A, Renshaw L, Thomas JS, Dixon MJ, Sims AH. Molecular characterisation of ER+ breast cancer dormancy and acquired resistance using a clinical model: Potential involvement of epigenetic regulation [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-03.

Abstract P3-10-26: Predicting benefit from HER2-targeted therapies in patients with ER+/HER2+ breast cancer

Background: ER+/HER2+ accounts for up to 10% of all breast cancers (BCs) and most are treated with endocrine therapy (ET) after surgery to reduce the recurrence risk. We developed and validated an immunohistochemistry (IHC) based test (EA2Clin) that incorporates baseline IL6ST, clinical variables and on-treatment measurement of MCM4. Responders (Rs) and non-responders (NRs) to ET are identified and it accurately estimates recurrence-free survival (RFS) and BC-specific overall survival (BCSS). The aim was to determine if EA2Clin could accurately predict ER+/HER2+ patients likely to benefit from ET and to determine if it can identify those for whom HER2-targeted therapies are required.

Methods: 3 cohorts were studied:

A: 32 post-menopausal women (PMW) with large ER+/HER2+ BC treated with neoadjuvant (3-6 months) then adjuvant letrozole. 5 also received adjuvant chemotherapy plus Herceptin. Neoadjuvant clinical response was assessed by changes in tumour volume. Tumour core biopsies were taken at 0, 14 days and 3 months. Gene expression analysis using Illumina HT12 whole-genome beadarrays was performed on a subset (n=17) where fresh tissue was available.

B: 13 PMW with ER+/HER2+ BC who were treated by surgery without neoadjuvant therapy. RNA was extracted from excision tissues and analysed using whole-genome Affymetrix U133A microarrays.

C: 15 PMW with ER+/HER2+ BC treated with 2-weeks of pre-operative letrozole (n=7) or anastrozole (n=8). All received adjuvant letrozole. Tissues were collected at pre-treatment and at surgery. None received Herceptin or chemotherapy.

All patients were followed-up after surgery (median follow-up = 6.4 years).

Results: In cohort A, half (16/32) of the patients responded to ET with tumour volume reductions of >70% with neoadjuvant treatment. Innate resistance was apparent in 3 patients with continued tumour growth on ET, whereas 13 patients developed resistance after a period of response. EAClin2 predicted neoadjuvant response with a 92% accuracy. There was increased expression of phospho-AKT and phospho-ERK in NRs, not seen in Rs. Half (8/16) of the NR cancers expressed phospho-ER; but was not seen in any responsive cancer. Gene expression analysis in 17 patients showed increased MAPK and PI3K pathway activity in the 9 NR compared with the 8 R tumours. These results were recapitulated in cohort B where MAPK and PI3K activity were associated with low levels of IL6ST.

In the 16/32 patients who responded well to neoadjuvant ET the actuarial recurrence rate was 0% at 5 and 10 years. The rate of recurrence in the NR was 30% at both 5 and 10 years. Of the 5 patients who received chemotherapy plus Herceptin, none recurred despite a poor response to neoadjuvant letrozole (median length to last follow-up was 6.1 years). Initial data suggest that in cohort B EA2Clin identifies a group of ER+/HER2+ cancers that can be managed by ET alone.

Conclusions:

· The EA2Clin test identifies ER+/HER2+ BCs who respond well to ET alone and those with a poor clinical response who have higher risk of recurrence.

· NR to ET have increased expression of PI3K and MAPK pathways, consistent with active HER2 signalling.

· There is potential role for EA2Clin in selecting ER+/HER2+ patients that require and benefit from HER2-targeted therapies.

Citation Format: Turnbull AK, Webber V, McStay D, Arthur L, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Clarke R, Sims AH, Dixon JM. Predicting benefit from HER2-targeted therapies in patients with ER+/HER2+ breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-10-26.

Abstract P3-06-17: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis

Background: Transcriptomic analyses of clinical samples can help improve our understanding of disease aetiology, drug effectiveness, assign molecular subtypes and derive prognostic signatures for clinical decision-making. The success of early microarray studies relied heavily on sample quality and predominantly fresh frozen (FF) tissues to generate reliably robust data. The emergence of next-generation microarray and sequencing-based technologies from formalin-fixed paraffin-embedded (FFPE) tissues provides an opportunity to study archival clinical tissues with long-term follow-up. Here we assess 9 technologies, which vary in resolution, cost and RNA requirements, with matched FF and FFPE tissues from the same patient.

Methods: Sequential tumour biopsies were taken pre-treatment and on-treatment (at 14-days and 3-months) from 11 postmenopausal patients with oestrogen receptor positive breast cancer treated with 3 months of neoadjuvant letrozole. Half of each sample was snap frozen in liquid nitrogen and half was FFPE, RNA was extracted from both. Transcriptomic analyses were performed using 9 technologies: Illumina Beadarray, Affymetrix U133A, Affymetrix Clariom S, NanoString nCounter, AmpliSeq Transcriptome, Lexogen QuantSeq and IonXpress RNAseq, Tempo-Seq BioSpyder and Qiagen UPX3'.

Results: Success rates for generating robust expression profiles from FFPE tissues were 100% all except the Illumina BeadChip (22%) and AmpliSeq Transcriptome (83%) , which varied by the age of tissue. With the total number and position of probes/primers/counts varying widely between approaches, in total 7305 genes were represented across all of the whole-genome technologies tested.

Clear batch effects were evident when comparing data from FF and FFPE tissues and when comparing between different technologies. Standard batch correction approaches such as XPN and ComBat minimised technical bias effect and increased the correlations between matched samples (FF and FFPE) to R>0.9, irrespective of the technology used.

When analysed by multi-dimensional scaling following batch correction, samples clustered by treatment time-point. When ranked by expression of 60 proliferation genes, reported by us to change with letrozole treatment, samples ordered again by time-point, consistent with our previous findings, and paired samples clustered together.

Conclusions:

· Robust gene expression profiles can be reliably generated from FFPE tissues and are comparable to those derived from FF tissue using established transcriptomic approaches.

· A range of new technologies are available for the study of FFPE tissues; these vary in cost, resolution and RNA requirements to fit the user's needs.

· Gene expression data from biologically similar studies, generated using different technologies, can be reliably integrated for robust meta-analysis, subject to appropriate batch correction analysis.

Citation Format: Turnbull AK, Selli C, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Figueroa JD, He X, Tanioka M, Munro A, Murphy L, Fawkes A, Clark R, Coutts A, Perou CM, Carey LA, Dixon JM, Sims AH. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-17.

Abstract P5-11-03: Measurement of on-treatment proliferation biomarkers in nodal metastasis improves prediction of endocrine therapy response using the EA2CliN test

Background: The majority of patients with early-stage estrogen receptor positive (ER+) breast cancer (BC) are treated with adjuvant endocrine therapy (ET) after surgery to reduce the risk of recurrence. Recently, we have developed and validated an immunohistochemistry (IHC) based assay (EndoAdjuvant2 Clinical; EA2Clin) that measures pre-treatment IL6ST level together with clinical variables and on-treatment MCM4 to assess proliferation. We have previously shown that it can accurately identify responders and non-responders to ET and predicts recurrence-free survival (RFS) and BC-specific overall survival (BCSS). We postulated that measuring on-treatment proliferation in lymph node metastases (LN+) rather in the primary cancer might further improve the accuracy of the test for these patients. The aim was to test and validate this in cohorts of pre- and post-menopausal women (preMW & PMW) treated with preoperative ET (tamoxifen (T), fulvestrant (F), letrozole (L) or anastrozole (A)) and subsequent adjuvant ET.

Methods: Cohorts: (1) 137 PMW with ER+ BC, 59 were LN+, treated with neoadjuvant L (median duration 4.8 months, range 1-33), then surgery followed by adjuvant L (n=109) or other ET (n=28); (2) 148 PMW with ER+ BC, 55 were LN+, treated with 2 weeks of preoperative L (n=76) or A (n=72), then surgery followed by adjuvant L (n=69) or T (n=79); (3) 52 preMW with ER+ BC, 24 were LN+, treated with 2 weeks of preoperative T (n=26) or 1x750mg dose of F (n=26), then surgery followed by adjuvant T. All LN+ patients had sentinel node biopsies or clearance. The median follow-up was 6.5 years (cohort 1), 6.3 years (cohort 2) and 10.2 years (cohort 3).

EA2Clin: Patients are classified as:

· Low risk: ER+ and LN-negative and <2cm or pre-treatment IL6ST 2+/3+ (IHC) and post-treatment MCM4 in the primary has <20% positive nuclear staining.

· High risk: ER+ LN+ grade 3 BCs >2cm or pre-treatment IL6ST is 0 or 1+, or IL6ST is 2+ or 3+ and MCM4 in the primary has >10% positive nuclear staining.

EA2CliN uses the post-treatment level of MCM4 in the nodes, rather than the primary cancer.

Results: In cohort 1, EA2Clin (using primary tumour MCM4) was significantly associated with both RFS (P=0.0003, HR=13.17, 95%CI=5.48-13.61) and BCSS (P=0.005, HR=11.91, 95%CI=8.73-31.42). The 5 and 10 year actuarial recurrence rates were 5%/5% and 48%/64% for the low and high-risk groups respectively.

In the same cohort, using the MCM4 level in the node (EA2CliN) there was an even more significant association with both RFS (P<0.00009, HR=18.16, 95%CI=12.59-19.46) and BCSS (P=0.002, HR=12.93, 95%CI=5.43-25.62). The 5 and 10 year actuarial recurrence rates were 0%/0% and 48%/72% for the low and high-risk groups respectively. Further validation of EA2CliN in cohorts 2 and 3 is underway.

Discussion:

· Direct measurement of on-treatment proliferation biomarkers in LN metastases improves prediction of outcomes to ET in women with BC.

· This tests identifies a group of low risk women that are node negative and node positive with a 100% RFS and BCSS.

· This is the most impressive predictive test for patients with ER+ breast cancer yet developed.

Citation Format: Turnbull AK, Mok S, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Sims AH, Dixon JM. Measurement of on-treatment proliferation biomarkers in nodal metastasis improves prediction of endocrine therapy response using the EA2CliN test [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-11-03.

Abstract P4-08-03: EA2Clin: A novel immunohistochemical prognostic and predictive test for patients with estrogen receptor-Positive breast cancer

Background: The majority of patients with early-stage estrogen receptor positive (ER+) breast cancer (BC) are treated with adjuvant endocrine therapy (ET) after primary surgery to reduce the risk of recurrence. A variety of tests are available to predict outcomes on ET but most require gene-level measurements and are expensive. Recently, we developed an immunohistochemistry (IHC) based test (EA2Clin) using levels of pre-treatment IL6ST together with clinical variables and on-treatment proliferation. The aim was to validate this test in cohorts of both pre- and post-menopausal women treated with two weeks of a variety of endocrine treatments (tamoxifen, fulvestrant or an aromatase inhibitor) prior to surgery.

Methods: The cohorts are: (A) 186 post-menopausal women (PMW) with ER+ BC treated with at least 2 weeks of preoperative or neoadjuvant letrozole or anastrozole, then surgery followed by adjuvant letrozole (n=132) or tamoxifen (n=54); (B) 51 pre-menopausal women (preMW) with ER+ BC treated with 2 weeks of either neoadjuvant tamoxifen (n=24) or one 750mg dose of faslodex (n=27), then surgery followed by adjuvant tamoxifen. The median follow-up was 5.4 years for cohort A and 10.2 years for cohort B. IHC analysis was performed using a Leica BOND III autostainer and the EA2Clin algorithm was used to stratify patients in binary high or low-risk groups.

Results: In the cohort of PMW, EA2Clin was highly significantly associated with both recurrence-free survival (RFS) (P<0.0001, HR=13.26, 95%CI=5.59-13.46) and breast cancer specific survival (BCSS) (P<0.0001, HR=12.93, 95%CI=4.43-37.72). The 5 and 10 year actuarial recurrence rates were 7%/22% and 46%/73% for the low and high risk groups, respectively. The actuarial breast cancer-related death rate for the low risk group was 5% at both 5 and 10 years, whereas for the high risk group was 33%/38%. Confounding factors were not found to be significant.

In the cohort of preMW, our test was significantly associated with both RFS (P=0.002, HR=5.71, 95%CI=1.91-17.05) and BCSS (P=0.016, HR=4.81, 95%CI=1.34-17.26). The 5 and 10 year actuarial recurrence rates were 12%/29% and 27%/77% for the low and high risk groups, respectively. The 5 and 10 year actuarial breast cancer-related death rates were 7%/19% and 9%/58% for low and high risk groups, respectively.

Discussion:

· This study has validated EA2Clin as the first predictive tool to incorporate clinical data with pre and on-treatment immunohistochemical biomarkers to predict accurately the outcome of patients with ER positive breast cancer treated with adjuvant ET.

· This test predicts both RFS and BCSS in pre- and PMW treated with a variety of endocrine agents.

· Because this test incorporates clinical variables with simple IHC, it can be performed locally in any pathology lab.

Citation Format: Turnbull AK, Fernando A, Renshaw L, Keys J, Thomas JS, Sims AH, Dixon JM. EA2Clin: A novel immunohistochemical prognostic and predictive test for patients with estrogen receptor-Positive breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-08-03.

Abstract P5-11-02: Predicting local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS)

Background: Ductal carcinoma in situ (DCIS) of the breast represents a heterogeneous group of precursor, non-invasive breast lesions. Currently we lack accurate tools to stratify DCIS patients according to inherent risk of in breast tumour recurrence (IBTR) or progression to invasive breast cancer (IBC).Most DCIS patients are treated by breast-conversing surgery (BCS), followed by whole-breast radiotherapy (RT) for the majority of high-grade DCIS. The aim of this study was to identify novel biomarkers which predict recurrence after BCS +/- RT.

Methods: A single institution study of 466 consecutive patients (median age 61, range 35-94) with DCIS treated by BCS between 2000 and 2010 was carried out. 271 patients with grade 3 DCIS received RT and 155 with grade 1/2 DCIS did not receive RT.

For biomarker discovery, a case-control matched series of 200 patients (mean age = 61, range = 36-84) from the above audit that met the following criteria was selected:

· 120 with low/intermediate-grade DCIS treated with BCS alone: 30 have recurred, 90 patients matched 3:1 have not recurred by 10 years.

· 80 with high-grade DCIS treated by BCS plus RT: 20 have recurred, 60 patients matched 3:1 have not recurred by 10 years.

Median follow-up was 7.4 years. RNA has been extracted and Affymetrix Clariom S whole-genome analysis has been performed and is currently being analysed.

Results:

In the cohort of 466 patients, 271 patients with high grade DCIS had BCS plus RT. Actuarial IBTR and IBC-IBTR in this group were 10% and 4% at 5 years and 18% and 6% at 10 years, respectively. 155 patients with low/intermediate grade DCIS had BCS alone. Actuarial overall IBTR and IBC-IBTR in this group were 6% and 2% at 5 years and 13% and 2% at 10 years respectively.

In the high-grade, RT treated group, lesion size (P<0.001, P=0.003), presence of comedo necrosis (P=0.018, P=0.025) and the Van Nuys Prognostic Index (VNPI) (P=0.02, P=0.004) were significantly associated with overall IBTR and DCIS-IBTR. No factor was significantly associated with IBS-IBTR in the high grade group and no factor predicted for any IBTR in the low/intermediate group.

Full genomic analysis of the 240 patient case-control matched cohort is underway and will be presented.

Discussion:

· This is the first DCIS biomarker discovery study using whole genome analysis and the matched cohort design looking separately at BCS + RT for high-grade DCIS and BCS only for low/intermediate grade DCIS.

· Clinical parameters alone may have insufficient sensitivity to identify high-grade, RT-treated patients at risk of developing IBC-IBTR.

· While recurrence rates in the low/intermediate grade DCIS group are lower than in the high-grade group, some patients do recur and there is a need to develop new tools which can identify low grade patients with a sufficiently high risk of recurrence to warrant additional treatment.

Citation Format: Martinez-Perez C, Turnbull AK, Ekatah GE, Arthur LM, Fernando A, Sims AH, Thomas JS, Dixon JM. Predicting local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS) [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-11-02.

Abstract P4-08-02: Understanding the mechanisms of action underlying the role of IL6ST, a key biomarker for prediction of response to endocrine therapy

Introduction: IL6ST is regarded as a putative ER target gene. Recently it has been recognised as a key biomarker for prediction of response to endocrine therapy (ET), having been included as the primary biomarker in our EA2Clin test and as an ER-signalling gene in the EndoPredict test. In both tests higher IL6ST expression is associated with a better response to ET and better prognosis. Despite its importance as a biomarker, little is known about its functional role in breast cancer (BC).

Methods: Pre- and on-treatment (at 14-days and at surgery) samples were collected from 102 post-menopausal women with ER+ BC, treated with 3-6 months of neoadjuvant ET. RNA was extracted for whole-genome expression analysis. From a subset with available fresh frozen tissue (28 patients, 83 samples) protein was extracted and proteome analysis using mass spectrometry is currently underway – results available for SABCS 2017. Immunohistochemistry was performed on FFPE tissue microarrays (TMAs) comprising pre-treatment samples from 102 patients. Cytoplasmic/membrane staining was scored using a graduated scale (0-3+) and nuclear staining was graded using an Immunoscore.

Results: IL6ST exists in membrane-bound and soluble forms of varying size. The full-length membrane bound molecule comprises 8 domains: 6 extracellular, 1 transmembrane and 1 cytoplasmic. In the EA2Clin test, pre-treatment BC tissues are stained for IL6ST with an antibody specific for a region spanning the transmembrane and cytoplasmic domains. TMAs were stained for IL6ST with both this and a second antibody binding the extracellular part, detecting both full-length and most soluble isoforms. Levels of both were correlated (R=0.82, P<0.0001).

IL6ST is known to mediate the action of cytokines including IL6, OSM and LIF via downstream regulation of pathways such as JAK/STAT. TMAs were stained for antibodies against IL6ST, OSM, IL6, total STAT3, pSTAT3 (Tyr705) and pSTAT3 (Ser727). IL6ST was scored as low (0/1+) or high (2+/3+). There was a positive association between levels of IL6ST and IL6 (P=0.02) and total STAT3 (P=0.003). There was no association between IL6ST and OSM or either pSTAT3.

Supervised gene expression analysis comparing pre-treatment samples with high and low IL6ST levels revealed increased levels of STAT3-regulated genes: cell cycle (CEBPD, CDKN1B), apoptosis (NFIL3, ATF3, BCL2), extracellular matrix remodelling (ADM, SEPRINE1-3) and interferon signalling (IFIT1, IFI44, IFI27). Unsupervised gene enrichment analysis revealed increased expression of genes involved with JAK/STAT, PI3K, mTOR and ERBB1 signalling in tumours expressing higher IL6ST levels. Lower levels were associated with increased energy generation, cellular metabolism and epithelial-mesenchymal transition.

Conclusions:

• This is the first matched whole-genome and mass spectrometry proteome analysis of sequential ET-treated BC patients

• IL6ST predicts response to ET – it is used in2 independent assays

• Levels of full-length IL6ST appear to be the most important for ET response prediction

• IL6ST may have an active role in BC cells, mediating signalling of cytokines such as IL6 through the JAK/STAT pathway and subsequent downstream transcriptional regulation.

Citation Format: Turnbull AK, Fernando A, Martinez-Perez C, Finch AJ, von Kriegsheim A, Wills J, Quinn N, Selli C, Mosley D, Langdon SP, Sims AH, Dixon JM. Understanding the mechanisms of action underlying the role of IL6ST, a key biomarker for prediction of response to endocrine therapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-08-02.

Abstract P4-04-02: Characterising the effects of neoadjuvant endocrine therapy on primary cancers and nodal metastasis

Background: Approximately 40% of ER+ breast cancer present with nodal metastasis. To date, there has been no comparison of the molecular response of primary cancers and metastases to ET. Recent evidence suggests that nodal metastases have different clones and subclones compared to the primary tumour. The aim of this study is to characterise the molecular response of primaries and nodal metastases to ET.

Methods: A unique set of 7 post-menopausal women with ER-positive breast cancer had biopsies taken from the primary tumour and a positive lymph node at diagnosis and at surgery following 3-12 months of neoadjuvant letrozole. 14-day and 3-6 month on-treatment biopsies from the primary tumour and involved nodes were also taken from the same patients, giving a total of 75 samples. Lymph node FFPE blocks were stained for cytokeratin and macro-dissected to enrich for tumour tissue. RNA and DNA were extracted and Ribo0-RNAseq, DNA exome sequencing and somatic mutation detection using UNCeqR performed. Whole-transcriptome AmpliSeq targeted-sequencing has been analysed for 4 patients.

Results: Multi-dimensional scaling and hierarchical clustering analysis based on all transcripts and the 500 most variably expressed genes revealed that primaries and nodal metastases are strongly associated at diagnosis but some nodes diverge during ET treatment. Analysis of estrogen-responsive proliferation-associated genes (n=60) in nodal metastasis revealed a reduction in expression of the majority of genes with ET. However, the expression levels of some remained high in the on-treatment node samples in all 4 patients analysed compared with the matched primary tumour on treatment. In particular, expression of genes involved in DNA replication and regulation of cell cycle including MCM6 and RRM2 (DNA replication), ASPM and CEP55 (mitosis) and CDKN3 (regulation of cell cycle) persisted at high levels in nodal metastases, but reduced in the primary cancers. Similarly, primary tumours had increased levels of ECM remodeling genes (n=60) as treatment continued, while levels in the nodal metastasis were heterogeneous on-treatment. Full genome sequencing results will be available by December 2017.

Discussion

· This is the first study to investigate genomic and transcriptomic changes with ET in both primary cancers and nodal metastases.

· On-treatment changes in nodal disease are heterogeneous between patients and within the same patient.

· Nodal metastases do respond to ET with reduced levels of proliferation-associated genes.

· Some proliferation-associated genes appear to maintain higher expression in nodal disease.

· Patterns of gene expression observed in some nodal metastases are consistent with profiles previously described by us for ET resistance and recurrent disease.

· Nodal metastases may accumulate mutations during treatment with ET and on-going analysis will clarify this.

Citation Format: Dixon JM, Turnbull AK, Tanioka M, Parker J, He X, Fernando A, Renshaw L, Keys J, Thomas JS, Sims AH, Carey LA, Perou CM. Characterising the effects of neoadjuvant endocrine therapy on primary cancers and nodal metastasis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-04-02.

Abstract P4-03-01: Causes of endocrine therapy resistance: An in-depth genomic analysis of resistant multidrug ER+ breast cancers

Background: 70% of all breast cancers (BCs) are ER+. Not all ER+ cancers respond to endocrine therapy (ET) and many eventually develop resistance. The aim was to perform in-depth genomic analysis of both primary resistant BCs, that do not respond to ET, and cancers which progress (>40% increase in size) after an initial response as they acquire resistance (AQR) to ET.

Methods: A unique series of 48 post-menopausal women with ER+ BC received neoadjuvant ET using letrozole (L) or anastrozole (A) (mean treatment duration 17 months, range 3-67). 13/48 received up to 4 lines of ET.

12/48 responded to A or L, 16/48 had primary resistance and 20/48 had AQR.

Of 20 with AQR, 13 had 2nd line ET with A or tamoxifen (T). 6 had 3rd line ET with exemestane (E) and 1 had 4th line megestrol acetate (MA). Serial RNA & DNA from 3-5 cancer samples/patient (226 samples) had Ribo0-RNAseq, DNA exome sequencing and somatic mutation detection using UNCeqR. We have data so far on 29 patients: 5 responders, 4 with primary resistance and 20 AQR, the full cohort will be complete shortly.

Results:

ESR1 Mutations (ESRM): 1/5 responders had an ESRM (E380Q) at diagnosis. This clone disappeared with response to L. 5/20 patients with AQR (25%) had clonal expansion of an ESRM during 1st line ET (L:4, A:1). 4 had a chr6:152419926[lowbar]A:G (D538G) ESRM and 1 had a novel ESRM. Of the 5 with ESRM acquired during 1st line ET, the mutant allele fraction (MAF) increased further in the 4 who had 2nd ET (3:T, 1:E) and increased further for the 2 who had 3rd line E.

ESR1 Amplification (ESRA):

5 patients developed ESRA. 3/5 developed ESRA on 2nd or 3rd line E that was not present on AQR to 1st line L or A and 2nd line T. The other 2 developed ESRA on L. 2/5 with ESRA had concomitant CYP19A1 amplification. One patient with ESRA that developed on 3rd line E subsequently responded to MA. No patients with primary resistance to 1st line ET had an ESRM or ESRA.

PIK3CA mutations (PIK3M): 5/20 with AQR had PIK3M (25%). 3/7 had PIK3M at diagnosis and in 3 MAF increased between 1st and 2nd line ET. 2/7 developed PIK3M when resistant to 2nd line ET, 1 of the 2 had ESRA. 2 patients responsive to L had PIK3M at diagnosis and MAF decreased with therapy.

Other Mutations: Unique mutations with limited commonality developed and new clones expanded in the remaining cancers during primary and acquired resistance. Clonality analysis of AQR samples to different ETs showed proliferation of specific clones, characterised by novel sets of mutations, which typically became the dominant clone at the time of resistance to a particular agent.

Summary: 13/20 with acquired resistance had ESRM, ESRA, or PIK3M in resistant tumours: 1 had all 3, 2 ERSM + ESRA, 1 ERSA + PIK3CA, 4 ESRM only, 2 ESRA only and 3 had PIK3M only.

Conclusions:

• Endocrine resistance is complex

• ESRM or ESRA is uncommon at diagnosis and does not explain primary ET resistance

• ESRM (in particular the D538G mutation) occurs in one-third of patients with acquired resistance. 2nd line ET results in clonal selection and expansion of ESRM cells. Assessing recurrences for ESRM by in situ detection has clinical utility

• ESRA is only seen in heavily ET-pre-treated tumours, with its significance being unknown.

Citation Format: Dixon JM, Turnbull AK, Tanioka M, Wheless A, Garrett A, Martinez-Perez C, Parker J, He X, Sims AH, Thomas JS, Carey LA, Perou CM. Causes of endocrine therapy resistance: An in-depth genomic analysis of resistant multidrug ER+ breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-03-01.

Abstract P1-06-04: Molecular characterisation, subtype concordance and prognostic group assignment between patient-matched primary breast tumours and axillary lymph node metastases

Introduction

Currently the primary breast tumour is used for prognostic profiling and as a monitor of response to therapy but how often does the molecular profile of the primary cancer reflect the molecular profile of nodal metastases? No previous study has investigated in detail the genomic profile of matched primary breast cancer (P) and nodal metastases (N) and correlated these with outcome. The aim of this study was to investigate whether the mRNA profiles of matched P and N differ significantly.

Methods

RNA was extracted from core biopsies from primary breast tumours and paired metastatic axillary lymph node samples from both FFPE blocks and fresh frozen samples. RNA was labelled and hybridised to Illumina HT-12 BeadChips to create a dataset consisting of one primary and one or two matched nodal metastasis, totalling 68 samples from 31 patients. Data was processed and corrected for batch effects, then analysed using the statistical programming language R. Clinical data on progression free and overall survival was collected from electronic and medical case note review.

Results

Unsupervised hierarchical clustering of the 500 most variable genes in each sample grouped only 12 of 31 P&Ns (39%) together, meaning in the majority of patients their P or N more resembled a cancer from another patient than its own paired P or N.

The number of genes with greater than 2 fold change (>2FC) between P&N was used to categorise paired samples into 'least changed' (<130 genes with >2 FC) and 'most changed' (>370 genes with >2FC) groups. Multidimensional scaling of the 500 most variable genes in the most changed group (n-=10) showed consistently that nodal metastases differed molecularly from the primary cancer.

When categorised by Sorlie centroid, 12 of 31 patients (39%) had a different molecular subtype in N compared with P. N tended to be a poorer prognostic subtype than P. 50% had luminal A primaries paired with luminal B nodes. The remaining 50% changed in other non-consistent patterns.

6 patients had 2 N samples to analyse alongside P. 4 of these (67%) had the same subtype in all 3 samples, and a further 1 the same 2Ns (luminal B) which differed from P (luminal A). The final had luminal A P paired with 1 luminal A and 1 luminal B Ns.

There was no evident correlation between the least changed and most changed groups and progression free and overall survival. This may however reflect the short term follow up.

Discordance between P and N in expression of ESR1 was 32%; PGR 19% and ERBB2 16%.

Conclusions

This study of gene expression change in matched primary breast cancers and synchronous metastatic paired axillary lymph nodes shows that molecular subtype differs in 39%. 50% of nodes had a poorer prognostic subtype than their primary. Expression of ESR, PGR and ERBB2 differs in up to 32%

Classifying cancer molecular phenotype and estimating prognosis based only on the primary cancer misclassifies significant numbers of patients. Classification of prognosis, and treatment based on the nodal metastasis may provide better information on which to base treatment.

Citation Format: Arthur LM, Turnbull AK, Pearce DA, Renshaw L, Thomas JS, Sims AH, Dixon JM. Molecular characterisation, subtype concordance and prognostic group assignment between patient-matched primary breast tumours and axillary lymph node metastases [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-06-04.

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 P4-05-05: Molecular effects of initial core biopsies in neoadjuvant window studies

Background

A growing number of studies are assessing the effects of drugs on breast cancers by investigating the molecular changes in tumours between the initial core biopsy taken at diagnosis and the excision specimen removed at surgery 2-3 weeks later. It is imperative to know if molecular profiles of tumours change over time without treatment and to assess whether the core biopsy itself influences the molecular profile. This study aimed to investigate changes in molecular profiles of breast cancer between the initial core biopsy and the excision specimen in patients who had no intervening treatment.

Methods

83 patients with paired fresh frozen tissue specimens from an initial diagnostic core biopsy and the later surgical excision biopsy have been studied. Following RNA extraction and processing, Illumina HT-12 BeadArrays were used for gene expression profiling. Samples were analysed for significant changes in gene expression and compared with a large dataset of patients treated with neoadjuvant letrozole.

Results

Analysis is on-going and results from all patients will be available by December 2013. Pairwise Rank Product analysis (false discovery rate 0.01) of the first 12 patients representing all subtypes of breast cancer (6 ER+, 4 HER2+, 2 triple negative) with a mean interval of 22.9 days (range 15 - 33 days) between specimens, identified 346 down regulated genes. Functional processes represented by these genes were; ribosomes, regulation of cell death and apoptosis, and protein complex biogenesis. Up-regulated processes (236 genes) included functions relating to regulation of transcription, mRNA processing/splicing and ECM remodelling.

No consistent changes in a 60 gene immune signature were seen across these 12 patients. Integration of this dataset with a large letrozole-treated dataset, demonstrated that less than 1% of genes that changed on-treatment with letrozole, changed without treatment.

Conclusions

This is the largest study investigating molecular profiles of the same breast cancer sampled at different times. It has shown:

· No consistent changes in expression of genes associated with wound healing and immune response 15-33 days after core biopsy

· Stability of the genetic profile of individual tumours despite multiple biopsies

· Stability in the genes that are changed by two weeks of treatment with daily letrozole.

This study provides definitive evidence of the validity of preoperative or window of opportunity molecular studies and has major implications for investigating the effects of new therapeutic drugs.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-05-05.

Abstract P5-09-01: Comprehensive gene assessment of estrogen receptor positive breast cancer reveals that HER2 plays an important role in resistance to neoadjuvant letrozole

Background

10% of all breast cancers are HER2+/ER+ and these cancers exhibit both intrinsic and acquired resistance to endocrine therapy. They have a worse prognosis than HER2-/ER+ cancers.

Aims

1. To investigate the role of HER2 in response to neoadjuvant Letrozole.

2. To predict which HER2+ cancers do not respond to Letrozole.

Methods

23 postmenopausal women with large, operable, locally advanced HER2+/ER+ breast cancer treated with neoadjuvant Letrozole had response assessed by periodic 3D ultrasound. Core biopsies taken at 0, 14 days and 3 months of treatment. RNA were extracted, amplified, labelled and hybridised to Illumina HT-12 whole genome beadarrays. A group of patients with ER+/HER2- disease were identified to compare clinical and molecular response.

Results

13 (57%) HER2+/ER+ patients responded (R) and 10 (43%) patients did not (NR). HER2 expression was significantly higher at baseline in the NR group (p = 0.005). There were differences in gene expression between HER2+/ER+ R and NR and between the HER2+/ER+ and HER2-/ER+ NR groups. In the HER2+/ER+ NR group, there was virtually no change in gene expression during treatment with Letrozole.

Table 1  Up Regulated GenesDown Regulated Genes n0-14 days14 days-3 months0-3 months0-14 days14 days-3 months0-3 monthsHER2-ve Responders43122833505127213HER2-ve Non Responders1588361432340129HER2+ve Responders13541272703831125HER2+ve Non Responders10851117106

Considerable gene changes with overlap in the genes that changed most was evident in HER2+/ER+ and HER2-/ER+ responders.

Analysis of 55 estrogen sensitive proliferation genes revealed significantly less reduction in the HER2+/ER+ NR group than in the HER2+/ER+ R group (AUC = 10.57 vs 27.93 respectively; p<0.0001). This difference was apparent by 14 days (AUC = 25.55 vs 17.94; p = 0.005).

The HER2+/ER+ NR group had significantly less reduction in these 55 estrogen sensitive proliferation genes when compared to the HER2-/ER+ NR group at 14 days (AUC = 17.94 vs 18.05 respectively; p = 0.0007) and by 3 months (AUC = 10.57 vs 26.26; p<0.0001).

In logistic regression analysis, HER2 status was predictive of disease progression (p = 0.048). A single gene classifier predicted response to endocrine therapy in the ER+/HER2+ group. This was accurate in 94% of patients in the test set (n = 23). This classifier was also predictive of progression free survival (p = 0.006) in HER2+/ER+ patients.

Conclusions

In this large cohort of patients treated with neoadjuvant letrozole:

• HER2+/ER+ cancers have a low rate of response.

• Changes in gene expression are similar in HER2+/ER+ and HER2-/ER+ responders.

• HER2+/ER+ cancers that do not respond to letrozole have few gene changes and little reduction in estrogen signalling pathways.

• In contrast HER2-/ER+ non responders show significant gene changes and reduced expression of estrogen sensitive proliferation genes.

• A single gene classifier at diagnosis in ER+/HER2+ has been identified which predicts response to Letrozole with 94% accuracy.

• Validation continues. This single gene classifier may provide a simple test to predict which HER2+/ER+ cancers are endocrine resistant.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-09-01.

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.

Abstract P6-04-09: Lack of response to aromatase inhibitors involves distinct mechanisms

Background: Estrogen is a key hormone involved in cancer cell development. It forms a complex with estrogen receptor alpha (ER) which binds to estrogen response elements (EREs) in the promoter regions of genes under its transcriptional control. Letrozole inhibits local production of estrogen. Despite the prevalent use of such drugs little is known about their effect at molecular and transcriptomic level. A better understanding of the molecular mechanisms underlying why approximately 75% of ER rich cancers respond might help to elucidate the mechanisms characterising a lack of response in some patients.

Methods: A new gene expression dataset was generated from sequential core biopsy/theatre samples (before treatment, 10–14 days on treatment and at surgery) taken from ER+ patients undergoing neo-adjuvant letrozole treatment. Clinical response to treatment was assessed by changes in tumour volume based on 3D ultrasound (performed by a single operator).

Results: On letrozole the majority of ER+ tumours respond with dramatic early transcriptomic changes. A significant reduction in proliferation is seen through down-regulation of key cell cycle control genes such as CyclinD1, CyclinA, CyclinB1, CyclinB2 and CDK2, and genes involved with the initiation phase of DNA replication such as the MCM complex. Several of these (including CyclinD1, CyclinB2 and MCM2) have been shown to contain candidate ERE sequences in their promoter region and therefore down-regulation of these would be concordant with deprivation of estrogen. There is also a significant up-regulation of genes including collagens, lamanins, integrins and others involved with intra-cellular adhesion and extra-cellular matrix (ECM) remodelling. Preliminary analysis suggests the involvement of a local immune response as a potential mechanism for tumour cell death, as genes involved with antigen presentation, leukocyte trans-endothelial mediation, natural killer cell mediated cytotoxicity and T-cell mediated cell death are significantly up-regulated within the clinically responding group.

Two distinct subsets were seen in non-responders. The first subgroup shows a ‘classical non-response profile’ with very little change in expression of genes involved with cell cycle, ECM remodelling, cellular adhesion and antigen presentation between baseline and 14-days of treatment. The second subgroup have a gene expression profile similar to the responding group with a down-regulation of cell cycle and up-regulation of genes involved with ECM remodelling, cellular adhesion and antigen presentation. Whether these are true non-responders is not clear.

Conclusion: Approximately half of clinically non-responding patients have molecular profiles similar to responding patients whilst the other half have a distinct pattern of expression with significantly less change in genes associated with cell cycle control, ECM remodelling, intra-cellular adhesion and antigen presentation. On-going work will elucidate long term outcomes in these two groups.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-04-09.

Abstract P6-04-10: Comprehensive gene and protein assessment of the role of Her2 in the response to neoadjuvant Letrozole suggests patients without amplification may also benefit from anti-Her2 treatment

Background: Older postmenopausal patients with large operable or locally advanced oestrogen receptor positive, invasive breast cancers are candidates for treatment with neoadjuvant letrozole. HER2 positivity is a potential marker for early endocrine therapy resistance. In this study we have evaluated the effects of HER2 amplification, gene and protein expression at diagnosis and following 14 and 90 days of treatment with neoadjuvant Letrozole.

Methods: 70 postmenopausal women with large operable and locally advanced oestrogen receptor (ER) positive invasive breast cancers were treated with neoadjuvant letrozole. Response was assessed by 3D ultrasound. Sequential core biopsies were taken at 0, 14 days and 3 months of treatment. 12 patients were HER2 positive (either 3+ or 2+ FISH positive), 20 were HER2 2+ FISH negative and 38 were HER2 negative (0 or +).

Results: 43 patients were responders to letrozole and 17 were non-responders. 7 of the 17 non-responders were HER2 positive. Analysing response in two groups (HER2 2+ and 3+ together versus 0 or +) there was a greater difference in response rate between these two groups than when splitting into conventional HER2 positive and negative groups (P < 0.0001). In non-responding patients HER2 gene expression levels from the microarrays taken at baseline were significantly higher than the HER2 expression in responding patients (p = 0.01). There was also an increase in HER2 gene expression seen during the first 14 days of treatment in non-responding but not responding patients (p = 0.08). Rank product analysis of gene expression identified 34 down-regulated genes and 7 up-regulated genes which were shared between the HER2 2+ FISH negative samples and samples which were HER2 3+ or HER2 2+ FISH positive.

Conclusion: This large cohort of patients treated with neoadjuvant letrozole shows that:

HER2 expression correlates with response to letrozole.

A better cut off for prediction of response to letrozole is the split between 0 and + versus 2+ and 3+ rather than the traditional 3+.

Patients with increased MRNA expression at diagnosis for HER2 have a significantly lower response rate to neoadjuvant letrozole.

Endocrine therapy together with anti-HER2 therapies should be considered for patients having neoadjuvant endocrine therapy for cancers which over express HER2.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-04-10.

Defining the molecular response to trastuzumab, pertuzumab and combination therapy in ovarian cancer

BACKGROUND

Trastuzumab and pertuzumab target the Human Epidermal growth factor Receptor 2 (HER2). Combination therapy has been shown to provide enhanced antitumour activity; however, the downstream signalling to explain how these drugs mediate their response is not clearly understood.

METHODS

Transcriptome profiling was performed after 4 days of trastuzumab, pertuzumab and combination treatment in human ovarian cancer in vivo. Signalling pathways identified were validated and investigated in primary ovarian xenografts at the protein level and across a timeseries.

RESULTS

A greater number and variety of genes were differentially expressed by the combination of antibody therapies compared with either treatment alone. Protein levels of cyclin-dependent kinase inhibitors p21 and p27 were increased in response to both agents and further by the combination; pERK signalling was inhibited by all treatments; but only pertuzumab inhibited pAkt signalling. The expression of proliferation, apoptosis, cell division and cell-cycle markers was distinct in a panel of primary ovarian cancer xenografts, suggesting the heterogeneity of response in ovarian cancer and a need to establish predictive biomarkers.

CONCLUSION

This first comprehensive study of the molecular response to trastuzumab, pertuzumab and combined therapy in vivo highlights both common and distinct downstream effects to agents used alone or in combination, suggesting that complementary pathways may be involved.

Abstract P5-05-06: The Role of Sprouty 2 in HER2 Signaling in Breast Cancer; Decreased Expression Is Associated with Poor Outcome Including in Trastuzumab-Treated Patients

Purpose: Resistance to trastuzumab is a frequent clinical problem, in part due to the overriding activation state of the MAPK/PI3K signaling pathways. Sprouty-family proteins are negative regulators of MAPK/PI3K signaling, but their role in HER2 signaling and resistance to therapy is unknown.

Experimental design: The association of Sprouty 2 gene expression with grade, HER2-status, and survival was investigated in a meta-analysis of 1107 breast tumors from six published microarray studies. Sprouty regulation in response to HER2/HER3 signaling was studied using qRT-PCR. Changes in expression of Spry2 and feedback inhibition on trastuzumab-resistance were studied using full-length/dominant-negative transfection or chemical inhibition in SKBr3 and BT474 cell lines in cell viability assays. Finally, expression of Spry2 was measured in a cohort of 122 patients treated with trastuzumab by quantitative fluorescence microscopy (AQUA).

Results: Low Spry2 gene expression was associated with high HER2 protein expression. Spry2 was regulated through HER2/HER3 signaling as a delayed early gene, an effect reversed by treatment with the dimerization inhibitor pertuzumab. Overexpression of Spry2 in the SKBr3 trastuzumab-resistant cell line resulted in synergistic inhibition of cell viability with trastuzumab. Restitution of feedback inhibition with the PI3K-inhibitor LY294002 had a similar effect. Low Spry2 expression was associated with increased risk of death (HR = 2.28, 95% CI 1.22 - 4.26; p=0.008) in trastuzumab-treated patients, including in multivariate analysis (Cox regression analysis, p=0.002).

Conclusions: These results suggest that combinations of negative regulators of growth factor signaling may be an effective therapeutic strategy in breast cancers with deficient feedback inhibition.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P5-05-06.

Abstract P4-07-06: Yes-Associated Protein, a Proposed Tumour Suppressor, Is Inversely Correlated to Cyclin D1 in Breast Tumours and Associated with a Worse Prognosis

Background: In breast cancer, cyclin D1 over-expression and CCND1 (11q13) gene amplification have been linked to a worse prognosis. Conversely, lower levels of cyclin D1 have also been correlated to an unfavourable outcome. In a microarray analysis of cyclin D1 silenced MDA-MB-231 cells we identified Yes-associated protein (YAP), located at 11q22, as one of the most down-regulated genes. As such, we aimed to determine the importance of YAP in relation to cyclin D1 in breast cancer biology.

Material and methods: Validation of cyclin D1, YAP antibodies and protein levels were performed in MDA-MB-231, MDA-MB-468 and MCF-7 by western blot. YAP protein expression was examined by screening 144 breast tumours and gene expression assessed by meta-analysis of six previously published breast cancer datasets totalling 1107 tumours with clinical follow-up. Subsequent data analysis was performed in SPSS. Results: YAP protein levels were down-regulated in cyclin D1 silenced MDA-MB-231, MDA-MB-468 and MCF-7 cell lines as predicted by microarray analysis. Surprisingly, YAP and cyclin D1 were inversely correlated at both protein and gene level in primary tumours (p=0.004 and P<0.001). Amplification of the CCND1 gene was correlated to low YAP protein expression (P<0.001) in the screening tumour material. Low YAP mRNA was an independent prognostic factor of recurrence (HR= 1.30, 95% CI 1.009-1.678, p=0.043) in the gene expression dataset. This effect was particularly pronounced in the luminal A subtype of breast tumours. Discussion: The independent prognostic value of YAP strengthens the notion of this protein as a tumour suppressor in breast cancer. The regulation of YAP by cyclin D1 appears to occur on both the protein level as seen in cell lines, and on the chromosomal level in terms of 11q aberrations. The inverse correlation observed in the tumour materials between cyclin D1 and YAP may be partly explained by chromosomal rearrangements; the amplification of the CCND1 gene (11q13) is often accompanied by loss of the 11q22 region of the chromosome, harbouring the YAP locus. Further studies are ongoing to clarify the link between YAP and cyclin D1 in breast cancer biology.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-07-06.

A gene on the HER2 amplicon, C35, is an oncogene in breast cancer whose actions are prevented by inhibition of Syk

Background:

C35 is a 12 kDa membrane-anchored protein endogenously over-expressed in many invasive breast cancers. C35 (C17orf37) is located on the HER2 amplicon, between HER2 and GRB7. The function of over-expressed C35 in invasive breast cancer is unknown.

Methods:

Tissue microarrays containing 122 primary human breast cancer specimens were used to examine the association of C35 with HER2 expression. Cell lines over-expressing C35 were generated and tested for evidence of cell transformation in vitro.

Results:

In primary breast cancers high levels of C35 mRNA expression were associated with HER2 gene amplification. High levels of C35 protein expression were associated with hallmarks of transformation, such as, colony growth in soft agar, invasion into collagen matrix and formation of large acinar structures in three-dimensional (3D) cell cultures. The transformed phenotype was also associated with characteristics of epithelial to mesenchymal transition, such as adoption of spindle cell morphology and down-regulation of epithelial markers, such as E-cadherin and keratin-8. Furthermore, C35-induced transformation in 3D cell cultures was dependent on Syk kinase, a downstream mediator of signalling from the immunoreceptor tyrosine-based activation motif, which is present in C35.

Conclusion:

C35 functions as an oncogene in breast cancer cell lines. Drug targeting of C35 or Syk kinase might be helpful in treating a subset of patients with HER2-amplified breast cancers.

Bioinformatics and breast cancer: what can high-throughput genomic approaches actually tell us?

High-throughput genomic technology has rapidly become a major tool for the study of breast cancer. Gene expression profiling has been applied to many areas of research from basic science to translational studies, with the potential to identify new targets for treatment, mechanisms of resistance and to improve on current tools for the analysis of prognosis. However, the sheer scale of the data generated along with the number of different protocols, platforms and analysis methods can make these studies difficult for clinicians to comprehend. Similarly, computational scientists and statisticians that may be called upon to analyse the data generated are often unaware of the processes involved in sample collection or the relevance and impact of genetics and pathological characteristics. There is a pressing need for better understanding of the challenges and limitations of microarray approaches, both in experimental design and data analysis. Holistic, whole-genome approaches are still relatively new and critics have been quick to highlight non-overlapping results from groups testing similar hypotheses. However, it is often subtle differences in the experimental design and technology that underpin the variation between these studies. Rather than indicating that the data are meaningless, this suggests that many findings are real, but highly context dependent. This review explores both the current state and potential of bioinformatics to bring meaning to high-throughput genomic approaches in the understanding of breast cancer.

Predicting response to RAD001 treatment in post-menopausal women with ER-positive breast cancer using the breast cancer DSA™ research tool (Almac)

Abstract #2032

Background: RAD001 (everolimus) is a rapamycin derivative that inhibits mTOR and its downstream substrates and has shown promising results in Phase I trials. The aim of this study was to assess the feasibility of predicting patient response to RAD001 treatment from pre-treatment biopsies.
 Materials & Methods: 32 post-menopausal, ER-positive early breast cancer patients received 5mg RAD001 pre-operative treatment daily for 14 days prior to primary surgery. 25 patients completed the regimen, 6 patients withdrew and 1 did not start treatment. Biopsies were taken at diagnosis and at surgery from the RAD001 treated patients. Pre-treatment samples were flash frozen prior to RNA isolation. Patient response status was classified based on the % of Ki-67 positive cells determined by immunohistochemistry in the post-treatment biopsy (Macaskill et al., 2006: Breast Cancer Research & Treatment: 100: S1: S286). RNA from the pre-treatment group was analysed using the Almac Diagnostics Breast Cancer DSATM Research Tool, which represents ∼60,000 normal breast and breast cancer transcripts and Illumina Human Ref.8 chip v2 containing ∼24,500 transcripts representing well-categorised and most commonly known genes, irrespective of disease or tissue. For each array platform, modulated genes were identified using statistically robust gene selection methods. In addition, the sequence content of the two platforms was compared by probe-level analysis using BLAST.
 Results & Discussion: Preliminary assessment of the expression differences between the non-responder and responder groups using the DSA™ Research Tool demonstrated 169 up-regulated and 93 down-regulated genes. This list is comprised of genes involved in chemokine activity, cell adhesion and transport. Cross-platform content comparison demonstrated that the Illumina bead arrays represented 41% of transcripts on the DSA™ Research Tool whilst 82% of the Illumina beadarray transcripts were represented on the DSA™ Research Tool. Genes of interest identified will be validated by quantitative real time PCR and the key pathways reported.
 These datasets have enabled us to begin the identification of tumours most suited to RAD001 treatment and may be used as a guide for the generation of a gene expression classifier for predicting patient response to RAD001.
 Acknowledgements: This work was supported by a grant from Breast Cancer Research Treatment, UK.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2032.

TPD52 and NFKB1 gene expression levels correlate with G2 chromosomal radiosensitivity in lymphocytes of women with and at risk of hereditary breast cancer

PURPOSE

To evaluate a transcriptomic approach to identify healthy women at increased risk of breast cancer due to G2-radiosensitivity and look at transcripts that are differentially expressed between individuals.

MATERIALS AND METHODS

We perform the first study to assess the association of G2 radiosensitivity with basal gene expression in cultured T-lymphocytes from 11 women with breast cancer and 12 healthy female relatives using Affymetrix GeneChips.

RESULTS

Transcripts associated with radiosensitivity and breast cancer risk were predominantly involved in innate immunity and inflammation, such as interleukins and chemokines. Genes differentially expressed in radiosensitive individuals were more similarly expressed in close family members than in un-related individuals, suggesting heritability of the trait. The expression of tumour protein D52 (TPD52), a gene implicated in cell proliferation, apoptosis, and vesicle trafficking was the most strongly correlated with G2 score while nuclear factor (kappa)-B (NFKB1) was highly inversely correlated with G2 score. NFKB1 is known to be activated by irradiation and its inhibition has been previously shown to increase radiosensitivity.

CONCLUSIONS

Gene expression analysis of lymphocytes may provide a quantitative measure of radiation response potential and is a promising marker of breast cancer susceptibility.

Effects of oestrogen on gene expression in epithelium and stroma of normal human breast tissue

Oestrogen (E) is essential for normal and cancer development in the breast, while anti-oestrogens have been shown to reduce the risk of the disease. However, little is known about the effect of E on gene expression in the normal human breast, particularly when the epithelium and stroma are intact. Previous expression profiles of the response to E have been performed on tumour cell lines, in the absence of stroma. We investigated gene expression in normal human breast tissue transplanted into 9-10-week-old female athymic nude (Balb/c nu/nu) mice. After 2 weeks, when epithelial proliferation is minimal, one-third of the mice were treated with 17beta-oestradiol (E2) to give human luteal-phase levels in the mouse, which we have previously shown to induce maximal epithelial cell proliferation. RNA was isolated from treated and untreated mice, labelled and hybridized to Affymetrix HG-U133A (human) GeneChips. Gene expression levels were generated using BioConductor implementations of the RMA and MAS5 algorithms. E2 treatment was found to represent the largest source of variation in gene expression and cross-species hybridization of mouse RNA from xenograft samples was demonstrated to be negligible. Known E2-responsive genes (such as TFF1 and AREG), and genes thought to be involved in breast cancer metastasis (including mammoglobin, KRT19 and AGR2), were upregulated in response to E treatment. Genes known to be co-expressed with E receptor alpha in breast cancer cell lines and tumours were both upregulated (XBP-1 and GREB1) and downregulated (RARRES1 and GATA3). In addition, genes that are normally expressed in the myoepithelium and extracellular matrix that maintain the tissue microenvironment were also differentially expressed. This suggests that the response to oestrogen in normal breast is highly dependent upon epithelial-stromal/myoepithelial interactions which maintain the tissue microenvironment during epithelial cell proliferation.