Abstract S1-05: In-depth genomic analysis of ER+ breast cancers during development of endocrine resistance
Authors: Dixon J Michael , Turnbull Arran K , Fan Chris , Parker Joel S , He Xiaping , Arthur Laura , Martinez-Perez Carlos , Renshaw Lorna , Perou Charles 
Published: May 2015

Abstract
Background: Aromatase inhibitors (AIs) have an established role in the treatment of estrogen receptor alpha positive (ER+) post-menopausal breast cancer. Response rates are only 50-70% in the neoadjuvant setting and up to 40-50% of all adjuvantly treated patients will eventually relapse. Mutations in certain genes have been previously shown to confer resistance to therapy, and molecular subtype has associations with poor outcome (i.e. LumB and HER2E). In order to improve the outcomes of non-responders or patients who become resistant to endocrine treatment, the identification of key mutations, and their interaction with subtype, is crucial. Dynamic profiling of the same tumour demonstrating de novo or developing resistance after responding to one or more lines of endocrine treatment in the neoadjuvant setting provides a unique opportunity to identify such genomic changes.
Methods: This series is unique in that it includes 17 post-menopausal women with ER+ breast cancer treated with neoadjuvant letrozole. 13 of these patients progressed on treatment or initially responded to treatment and then developed acquired resistance and 4 responded well. Dynamic clinical response was assessed for each patient using periodic 3D ultrasound measurements performed during treatment. Fresh tissue was taken before treatment and when the tumor was resistant to treatment (4 patients had 2 biopsies, 9 patients had 3 and 4 patients had 4 available biopsies taken). RNA and DNA were extracted from tumour and normal DNA obtained from either matched blood or normal lymphatic tissue. In total, 51 tumour samples were available and have completed RNA-Seq, with exome sequencing shortly to be completed.
Results: From the RNA-seq data, the intrinsic subtype distribution was 9 LumA, 7 LumB, and 1 HER2-enriched; when stratified according to response, the "progressors" were 7 LumB, 5 LumA and 1 HER2-enriched, while "responders" were 3 LumA and 1 LumB. When examined in an unsupervised hierarchical clustering analysis along with &gt;800 TCGA Breast tumor samples, 13/17 patients had all of their samples grouped immediately together, suggesting that the overall tumor phenotype was maintained. Interestingly, the most dominant change in gene expression was the observation that there were 5 "progressor" patients where the pre-treatment sample was LumB and all subsequent samples were LumA; we only observed one instance of a patient starting as LumA and changing to a LumB, who was also labelled as a "progressor". Full exome sequencing is underway and these results will be presented.
Conclusion: Genomic analysis of progression suggests that an apparent "subtype shift" appears in a number of patients where a shift to LumA is seen; this apparent change may be reflective of decreased proliferation rates caused by therapy, or the acquisition of a true LumA phenotype. We cannot differentiate between these two hypotheses at this time, but expect that the exome sequencing will help to differentiate between these two hypotheses given the large number of mutations and copy number alterations that can differentiate between LumA vs. LumB.
Citation Format: J Michael Dixon, Arran K Turnbull, Chris Fan, Joel S Parker, Xiaping He, Laura Arthur, Carlos Martinez-Perez, Lorna Renshaw, Charles Perou. In-depth genomic analysis of ER+ breast cancers during development of endocrine resistance [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr S1-05.