Abstract P5-14-12: ESR1-alterations in HR+HER2- breast cancer patients
Authors: Basu Gargi , Udhane Sameer S. , Dombrowski Susan , Hong Lenny , Alyaqoub Fadel , de Moura Michelle Barbi , Chandrasekaran Thiruppavai , Dogruluk Turgut , Driscoll David , Jalkanen Aimee , Noel Pawan , Szelinger Szabolcs , Wang Min , Hall David , Hoag Jess , Lobello Janine , Baehner Frederick , Thakkar Snehal , O’Shaughnessy Joyce 
Published: March 2023

Abstract
Introduction/Background Endocrine therapy remains the fundamental treatment for advanced HR+ breast cancer (BC). For those patients who become refractory to endocrine therapy, resistance may be associated with mutations, amplifications, and fusions in the ESR1-encoded estrogen receptor. Here we examine the frequency of ESR1 alterations and the associated genomic landscape.
Methods HR+/HER2- BC samples were sequenced with the OncomapTM ExTra assay, which uses whole-exome DNA sequencing with germline subtraction to detect somatic single nucleotide substitutions, indels, and copy number alterations (CNAs), and uses RNA sequencing to detect gene fusions. Tumor mutational burden (TMB) and microsatellite instability (MSI) are also reported. For analysis, BC samples were grouped by site: local (primary breast or regional lymph node) versus metastatic. Prior treatment history was unknown. Testing for a possible association between ESR1 and other biomarkers (genes, MSI, and TMB) was done using Fisher’s Exact Test (p≤0.05).
Results A total of 988 HR+HER2- breast cancer patient samples were included in the analysis. Of these, 821 (83.1%) were local samples and the remaining 167 were metastatic samples, with liver (63, 37.7%), bone (20, 12.0%), skin (16, 9.6%) and chest wall (15, 9.0%) being the most common locations. ESR1 alterations were present in 84 tumor samples, 37 local and 47 metastatic, representing 4.5% and 28.1% of samples, respectively. ESR1 alterations included missense mutations (54 samples), fusions (29 samples), and amplifications (8 samples). The most common missense mutations were Y537S (20 samples, 37.0%), D538Q (20 samples, 37.0%), and E380Q (6 samples, 11.1%), which were located in the ligand binding domain and included both clonal and subclonal events. There were 30 ESR1 fusions identified, 17 (2.1%) in local and 13 in metastatic (7.7%) samples. Most fusions (24 samples, 82.8%) involved the same partner, CCDC170, while the other 6 fusions had unique partners. Examination of the 143 other biomarkers altered among ESR1-altered samples revealed 15 genes and MSI-high status that appeared to be over-represented (Table 1). However, none of the associations were statistically significant after correcting for multiple comparisons. Further, there was no evidence that the prevalence of ERBB2, TP53, AKT1 and PIK3CA alterations differed by ESR1 status (Table 1).
Conclusions ESR1 alterations were significantly more common in HR+/HER2- metastatic breast cancer samples compared to local samples. Comprehensive genomic profiling with RNA sequencing identified both common and rare ESR1 fusions, which were most frequent in the metastatic samples. No significant difference in the molecular profile of ESR1 altered vs ESR1 wildtype samples was found in this cohort. Clinical trials with novel selective ER degraders (SERDs) to target these ESR1 alterations are ongoing.
Table 1. Biomarkers that showed the highest association with ESR1 and other notable breast cancer biomarkers.
Citation Format: Gargi Basu, Sameer S. Udhane, Susan Dombrowski, Lenny Hong, Fadel Alyaqoub, Michelle Barbi de Moura, Thiruppavai Chandrasekaran, Turgut Dogruluk, David Driscoll, Aimee Jalkanen, Pawan Noel, Szabolcs Szelinger, Min Wang, David Hall, Jess Hoag, Janine Lobello, Frederick Baehner, Snehal Thakkar, Joyce O’Shaughnessy. ESR1-alterations in HR+HER2- breast cancer patients [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-14-12.