Abstract P3-06-11: Time-course DNA and RNA profiling of tumors from intra-patient cross-over trial of sequential use of aromatase inhibitors
Authors: Vaske CJ , Parulkar R , Bahrami N , Sauer T , Loeng M , Gravdehaug B , Aljabri B , Bemanian V , Lindstrøm J , Lüders T , Kristensen V , Geisler J 
Published: May 2019

Abstract
Background. The NEO-LET-EXE trial examines the neoadjuvant use of sequential administration of the aromatase inhibitor 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 some patients after switching to the alternative drug and progressing on the first choice, new responses may appear. The mechanism behind this clinical observation is currently not known. The solution may lead to a novel strategy to re-sensitize tumors to hormonal treatment. Prior studies have examined genomics at the four month time point, but not at both two months and four months.
Material. Postmenopausal patients with estrogen receptor (ER) positive (&gt;50%), HER-2 negative locally advanced breast cancer may be enrolled. Age: 18+ (no upper limit). Present accrural and target accrural: 49 out of planned 100 patients have been enrolled so far. The last patient is expected to enter the trial in Q4 2019.
Study design. In the neoadjuvant, randomized, open-label, intra-patient cross-over trial NEO-LET-EXE biopsies are taken before treatment, after two months on one aromatase inhibitor and swap to the other aromatase inhibitor, and at surgery at four months.
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. When grouping both arms together, mutational burden decreased at two months, while clonality of mutations increased, providing evidence of selection. At four months, mutational burden increased from the two month timepoint. In particular, PIK3CA somatic variants present at the first time point were not detected at two months. However, these were detected again at significant variant allele fractions at four months after switch of treatment. The majority of gene expression changes happen in the initial two months, with fewer changes between two and four months. Instead, significant changes in alternative splicing at two months and four months were observed, for example for FGFR1, which does not experience a large fold change in expression between these two points. Our preliminary results show significant DNA and RNA changes in the first two months of aromatase inhibition leading to fewer, more clonal variants. Comparison of the four month to two month time point shows fewer RNA changes than the prior two months and an increase in the number of somatic variants compared to the two month timepoint.
Citation Format: Vaske CJ, Parulkar R, Bahrami N, Sauer T, Loeng M, Gravdehaug B, Aljabri B, Bemanian V, Lindstrøm J, Lüders T, Kristensen V, Geisler J. Time-course DNA and RNA profiling of tumors from intra-patient cross-over trial of sequential use of aromatase inhibitors [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 P3-06-11.