Abstract P4-03-01: Causes of endocrine therapy resistance: An in-depth genomic analysis of resistant multidrug ER+ breast cancers
Authors: Dixon JM , Turnbull AK , Tanioka M , Wheless A , Garrett A , Martinez-Perez C , Parker J , He X , Sims AH , Thomas JS , Carey LA , Perou CM 
Published: February 2018

Abstract
Background: 70% of all breast cancers (BCs) are ER+. Not all ER+ cancers respond to endocrine therapy (ET) and many eventually develop resistance. The aim was to perform in-depth genomic analysis of both primary resistant BCs, that do not respond to ET, and cancers which progress (&gt;40% increase in size) after an initial response as they acquire resistance (AQR) to ET.
Methods: A unique series of 48 post-menopausal women with ER+ BC received neoadjuvant ET using letrozole (L) or anastrozole (A) (mean treatment duration 17 months, range 3-67). 13/48 received up to 4 lines of ET.
12/48 responded to A or L, 16/48 had primary resistance and 20/48 had AQR.
Of 20 with AQR, 13 had 2nd line ET with A or tamoxifen (T). 6 had 3rd line ET with exemestane (E) and 1 had 4th line megestrol acetate (MA). Serial RNA & DNA from 3-5 cancer samples/patient (226 samples) had Ribo0-RNAseq, DNA exome sequencing and somatic mutation detection using UNCeqR. We have data so far on 29 patients: 5 responders, 4 with primary resistance and 20 AQR, the full cohort will be complete shortly.
Results:
ESR1 Mutations (ESRM): 1/5 responders had an ESRM (E380Q) at diagnosis. This clone disappeared with response to L. 5/20 patients with AQR (25%) had clonal expansion of an ESRM during 1st line ET (L:4, A:1). 4 had a chr6:152419926[lowbar]A:G (D538G) ESRM and 1 had a novel ESRM. Of the 5 with ESRM acquired during 1st line ET, the mutant allele fraction (MAF) increased further in the 4 who had 2nd ET (3:T, 1:E) and increased further for the 2 who had 3rd line E.
ESR1 Amplification (ESRA):
5 patients developed ESRA. 3/5 developed ESRA on 2nd or 3rd line E that was not present on AQR to 1st line L or A and 2nd line T. The other 2 developed ESRA on L. 2/5 with ESRA had concomitant CYP19A1 amplification. One patient with ESRA that developed on 3rd line E subsequently responded to MA. No patients with primary resistance to 1st line ET had an ESRM or ESRA.
PIK3CA mutations (PIK3M): 5/20 with AQR had PIK3M (25%). 3/7 had PIK3M at diagnosis and in 3 MAF increased between 1st and 2nd line ET. 2/7 developed PIK3M when resistant to 2nd line ET, 1 of the 2 had ESRA. 2 patients responsive to L had PIK3M at diagnosis and MAF decreased with therapy.
Other Mutations: Unique mutations with limited commonality developed and new clones expanded in the remaining cancers during primary and acquired resistance. Clonality analysis of AQR samples to different ETs showed proliferation of specific clones, characterised by novel sets of mutations, which typically became the dominant clone at the time of resistance to a particular agent.
Summary: 13/20 with acquired resistance had ESRM, ESRA, or PIK3M in resistant tumours: 1 had all 3, 2 ERSM + ESRA, 1 ERSA + PIK3CA, 4 ESRM only, 2 ESRA only and 3 had PIK3M only.
Conclusions:
• Endocrine resistance is complex
• ESRM or ESRA is uncommon at diagnosis and does not explain primary ET resistance
• ESRM (in particular the D538G mutation) occurs in one-third of patients with acquired resistance. 2nd line ET results in clonal selection and expansion of ESRM cells. Assessing recurrences for ESRM by in situ detection has clinical utility
• ESRA is only seen in heavily ET-pre-treated tumours, with its significance being unknown.
Citation Format: Dixon JM, Turnbull AK, Tanioka M, Wheless A, Garrett A, Martinez-Perez C, Parker J, He X, Sims AH, Thomas JS, Carey LA, Perou CM. Causes of endocrine therapy resistance: An in-depth genomic analysis of resistant multidrug ER+ breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-03-01.