Abstract P6-04-07: Time-course DNA and RNA profiling reveals down regulation of all members of the sulfotransferase A1 subfamily during neoadjuvant therapy with aromatase inhibitors
Authors: Vaske Charles , Parulkar Rahul , Bahrami Nazli , Sauer Torill , Lüders Torben , Lorentzen Annika , Gravdehaug Berit , Kristensen Vessela , Geisler Jürgen 
Published: March 2020

Abstract
Background. The NEO-LET-EXE trial examines the neoadjuvant and sequential administration of the aromatase inhibitor (AI) letrozole (Femar/Femara) and the aromatase inactivator exemestane (Aromasin). Although both drugs nearly completely inhibit aromatase, resistance to both is developed with time. However, when used sequentially in patients with metastatic breast cancer (MBC), in some patients after switching to the alternative drug after progressing on the first choice, new responses may appear. The mechanism behind this clinical observation is not known. The solution may lead us potentially to a novel strategy to treat hormonal dependent breast cancer.Material. Postmenopausal patients suffering from strongly estrogen receptor (ER) positive (&gt;50%), HER-2 negative locally advanced breast cancer (LABC) may be enrolled. Age: 18+ (no upper limit). Present accrual and target accrual: 55 out of planned 100 patients have been enrolled so far. The last patient is expected to enter the trial in Q4 2020. We report here results from a scientific subprotocol involving 25 patients.Study design. In the neoadjuvant, randomized, open-label, intra-patient cross-over trial NEO-LET-EXE tumor biopsies are obtained at baseline, after two months on the first AI prior to swap to the other aromatase inhibitor, and, finally, at surgery following at least four months on AIs.Methods. Tumor DNA and RNA were extracted from FFPE samples, and normal DNA was extracted from blood samples. Tumor exome was sequenced to an average of 250x depth, normal exomes was sequenced to an average depth of 125x, and tumor RNA was sequenced with at least 200 million reads. Somatic variants and copy number changes were called, and gene expression was quantified from RNA-seq.Results. In order to explain the phenomenon of a lack of cross-resistance between steroidal and non-steroidal aromatase inhibitors we profiled biopsies at three time points per patient by whole exome and whole transcriptome sequencing from FFPE from 25 patients. A total of 56 DNA whole exomes and 41 RNA-seq transcriptomes were generated from FFPE samples available. Neoadjuvant treatment with sequential use of the two AIs caused a significant downregulation of all four members belonging to the sulfotransferase A1 subfamily (SULT1A1, SULT1A2, SULT1A3 and SULT1A4) following 4 months on AI therapy, irrespectively of the clinically chosen treatment sequence. A significant downregulation of ARSG, ESR1 and PGR was also observed during AI therapy. In addition, a low rate of CYP19A1 copy number changes could be detected in our material. A CYP19A1 deletion occurred in one patient during AI therapy. No DNA or RNA support for hot-spot ESR1 resistance mutations was found at any time point during early neoadjuvant AI therapy.Conclusions. Our findings suggest a significant downregulation of the entire sulfotransferase A1 subfamily during neoadjuvant therapy with AIs in patients with ER-positive LABC. These findings may reflect an early adaptation process caused by the AI-induced estrogen depression. A low rate of CYP19A1 copy number changes could be revealed during the first 4 months of neoadjuvant AI therapy in vivo.
Citation Format: Charles Vaske, Rahul Parulkar, Nazli Bahrami, Torill Sauer, Torben Lüders, Annika Lorentzen, Berit Gravdehaug, Vessela Kristensen, Jürgen Geisler. Time-course DNA and RNA profiling reveals down regulation of all members of the sulfotransferase A1 subfamily during neoadjuvant therapy with aromatase inhibitors [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-04-07.