Abstract A38: Effects on epigenomic, transcriptomic, and genomic landscape of neoadjuvant tamoxifen in estrogen receptor alpha breast cancer
Authors: Severson Tesa M. , Nevedomskaya Ekaterina , Peeters Justine , Rossum Annelot van , Kuilman Thomas , Krijgsman Oscar , Koornstra Rutger , Peeper Daniel , Wesseling Jelle , Simon Iris M. , Wessels Lodewyk , Zwart Wilbert , Linn Sabine C. 
Published: May 2016

Abstract
Background: The Anastrozole, Fulvestrant or Tamoxifen Exposure—Response in molecular profile (AFTER study, NCT00738777) aims to investigate the molecular basis of therapy response to neoadjuvant treatment in Estrogen Receptor alpha (ERα) breast cancer patients. ERα breast cancer makes up the majority of breast cancer diagnosed in the world each year. In these patients, tumor cell proliferation is driven by transcriptional activation through ERα binding DNA at specific genomic locations. To block this proliferation, endocrine therapies such as tamoxifen have been developed. While endocrine therapy is considered a successful targeted treatment, resistance is common. Patients who recur are typically given a different type of endocrine therapy and frequently respond well, suggesting ERα breast cancer is a heterogeneous disease made up of subtypes responsive to different treatments. We hypothesize drug exposure induces molecular changes in the tumor and the basis for these alterations may provide insight into the phenomenon of therapy resistance.
Study Design and Methods: In the AFTER study ERα breast cancer patients are randomized for treatment arm in a multi-institutional study. Male and pre-menopausal patients receive tamoxifen. The primary endpoint is decreased tumor cell proliferation assessed by Ki67 gene expression. Tumor samples are taken at the time of diagnosis (biopsy) and surgery (primary tumor) for molecular and clinical assays. Treatment occurs during the pre-operative window after diagnosis. All data are collected at both timepoints. Molecular data collected include gene expression and ERα/DNA binding patterns and DNA copy number profiles. Clinical data comprise ERα/PR/HER2 and Ki67 immunohistochemical staining (IHC) and lymphnode status.
Results: 67 patients are currently enrolled in the study. We examined the subset of tamoxifen treated patients (n=28). All tumors were HER2-negative. ERα/PR showed no significant difference between pre- and post-treatment levels. Tumor cell proliferation was significantly lower in post-treatment samples (Ki67 gene expression P &lt; 0.01). ERα/DNA interaction regions were more frequently overlapping in the post-treatment samples compared with the pre-treatment samples. Change in published gene expression proliferation signatures was significantly correlated with change in Ki67 gene expression (ρ = 0.7, P &lt;0.001). In addition, we observed a significant decrease in proliferation signature gene expression variability in post-treatment samples (P &lt;0.001). By testing clustering of DNA copy number data, we observed no evidence for subclone selection after treatment. Using the ‘IntClust’ R package to perform joint clustering on DNA copy number and gene expression data we determined the majority of samples retained their classification after treatment. All samples were classified in clusters that are typically representative of luminal A and/or luminal B disease.
Conclusions: Substantial synchronization in ERα/DNA binding and gene expression pattern was observed after treatment, while DNA copy number patterns remained stable. Our results indicate neoadjuvant tamoxifen induces molecular changes in a heterogeneous group of breast cancers associated with change in proliferation and ERα/DNA binding landscape. Importantly, while most tumors show these changes, some do not. Follow-up data will demonstrate whether taking samples after treatment exposure may be a powerful tool to help understand response to treatment.
Citation Format: Tesa M. Severson, Ekaterina Nevedomskaya, Justine Peeters, Annelot van Rossum, Thomas Kuilman, Oscar Krijgsman, Rutger Koornstra, Daniel Peeper, Jelle Wesseling, Iris M. Simon, Lodewyk Wessels, Wilbert Zwart, Sabine C. Linn. Effects on epigenomic, transcriptomic, and genomic landscape of neoadjuvant tamoxifen in estrogen receptor alpha breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A38.