Abstract 2934: Genomic alterations associated with resistance to antiestrogens identified by multiplatform molecular analysis in operable ER+ breast cancer
Authors: Giltnane Jennifer M. , Balko Justin , Mu Jasmine , Christiansen Jason , Murphy Danielle , Mayer Ingrid , Meszoely Ingrid 
Published: May 2015

Abstract
Breast cancer proliferation measured by Ki67 immunohistochemistry after short-term antiestrogen therapy has been shown to correlate with disease-free survival. This suggests the use of biomarkers of the early effects of endocrine therapy on ER+ tumors to identify cancers that are resistant to antiestrogens. Thus, we hypothesized that by profiling operable ER+ tumors after short term treatment with an aromatase inhibitor, we would discover actionable molecular alterations causally associated with resistance to estrogen deprivation.
We performed whole exome sequencing (WES), RNA-Seq and quantitative immunofluorescence (QIF; AQUA) in tumor biopsies from 130 patients with an operable ER+/HER2- breast cancer that had received letrozole for 10-21 days prior to surgery. Tumors were categorized by the natural log (ln) of post-letrozole Ki67 as sensitive (ln ≤1 or ≤2.7% Ki67+ cells; n=68) or resistant (ln ≥2 or ≥7.4%; n=18).
Higher post-treatment HER2 AQUA protein scores (without HER2 gene amplification), as measured by QIF, correlated with resistance to letrozole (p=0.004). RNA-Seq data in 50 tumors revealed 5 putative ESR1 fusion transcripts, including a novel ESR1-USP36 transcript in a resistant tumor and two ESR1:CCDC170/c6orf97 fusions in the intermediate Ki67 cohort (&gt;2.7% and &lt;7.4% Ki67+ cells). WES was performed in 61 tumors and paired germline DNA; of these, 11 were resistant and 34 were sensitive. PI3KCA, CDH1, TP53, CCND1, FGFR1, TBX3, and GATA3 genes were among those frequently altered (≥15%). Copy number analysis uncovered 8 focal amplifications and 9 focal deletions; including amplifications at 8p12 (FGFR1) and/or 11q13 (CCND1) identified in 6/11 (55%) resistant versus 5/34 sensitive tumors (p=0.006). Nine of 11 resistant tumors (82%) harbored one or more mutations in cell cycle regulatory genes, including TP53 (4), ARID1A (2), DYRK2 (2), ATM, BRCA1, BRCA2, CCNT1, CCND1, CCNF and CCNG1, whereas only 41% (14 of 34) of the sensitive tumors did so (p=0.03).
Conclusions: This is one of the largest primary tumor cohorts treated with letrozole with pharmacodynamic, RNA-Seq and WES data combined. ER+/HER2- tumors resistant to estrogen deprivation exhibited higher post-treatment HER2 protein levels detected by AQUA. The role of novel ESR1 fusions in antiestrogen resistance is currently under active investigation and will be reported at the meeting. Amplification of FGFR1 and CCND1 were more frequent in tumors that retained a high Ki67 upon treatment. Several actionable somatic alterations were identified in resistant tumors, suggesting this approach may lead to the identification of patients with ER+ breast cancer in whom rational combinations of targeted therapies should be investigated.
Citation Format: Jennifer M. Giltnane, Justin Balko, Jasmine Mu, Jason Christiansen, Danielle Murphy, Ingrid Mayer, Ingrid Meszoely. Genomic alterations associated with resistance to antiestrogens identified by multiplatform molecular analysis in operable ER+ breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2934. doi:10.1158/1538-7445.AM2014-2934